Health Summary Table
FILTERS
Total 2651
Current 2651
Bacteria Synonym Net Effect BAuA Risk Risk Notes Coloniser Symbiosis Pathogenic Notes Source Studies Phylum Class Family Gram OxTol Motil Morph Spore DnaGC Bile
Abiotrophia defectiva Streptococcus defectivus Negative 2 Minor Known Commensal Opportunistic Pathogen human faeces, clinical sources (bacterial endocarditis, blood, wound - CCUG), human saliva and dental plaques RajilicStojanovic2014, Cassir2015, Lagier2016, Byrd2020, De2020, Yang2020, New2022, Hu2019, Zeller2014, Vachida2019, Qin2012 Firmicutes Bacilli Aerococcaceae + FANA Sessile Coccus No spore 46.0-46.6
Absiella argi Eubacterium sp. 1-3 Rare Possible Commensal Non/unknown Pathogen the faeces of an old dog Jeong2021 Firmicutes Erysipelotrichia Erysipelotrichaceae + SANA Sessile Rod No spore 35.8
Absiella innocuum Moderate Possible Mutualist In 94% of Europeans (unseenbio.com). Byrd2020 Firmicutes Erysipelotrichia Erysipelotrichaceae
Absiella tortuosum Eubacterium tortuosum 2 Human and animal pathogen Rare Known Commensal Known Pathogen human faeces, turkey diseases and freshwater Finegold1977, Benno1989, RajilicStojanovic2014, Lagier2016 Firmicutes Erysipelotrichia Erysipelotrichaceae + SANA Sessile Rod No spore 37.9 20(neg)
Acetanaerobacterium elongatum 1 Rare Possible Commensal Non/unknown Pathogen human faeces, and paper mill waste water deGoffau2013, McLaughlin2010, RajilicStojanovic2014, Byrd2020 Firmicutes Clostridia Oscillospiraceae + SANA Swimming Rod No spore 50.5
Acetatifactor muris Rare Possible Commensal Non/unknown Pathogen caecal contents of a mouse Byrd2020 Firmicutes Clostridia Lachnospiraceae + SANA Sessile Rod No spore 48.5
Acetitomaculum ruminis 1 Rare Possible Commensal Non/unknown Pathogen Homoacetogenic. Can consume carbon monoxide. rumen Byrd2020, De2020 Firmicutes Clostridia Lachnospiraceae + SANA vr Rod No spore 32-36
Acetivibrio cellulolyticus 1 Rare Possible Commensal Non/unknown Pathogen a methanogenic enrichment culture from sewage sludge Zupancic2012, Zeller2014, Qin2012 Firmicutes Clostridia Clostridiaceae neg SANA Swimming Rod No spore 38
Acetivibrio clariflavus Clostridium clariflavum Unlikely Transient Non/unknown Pathogen High optimum growth temperature so unlikely to be a gut coloniser. human faeces and anaerobic sludge PerisBondia2011, deGoffau2013, RajilicStojanovic2014, Qin2012 Firmicutes Clostridia Clostridiaceae vr ANA Sessile Rod Endospore 36.9
Acetivibrio ethanolgignens 2 Pathogen for vertebrates; humans are not infected under natural conditions. Minor Possible Commensal Possible Pathogen In 75% of Europeans (unseenbio.com). colon of pigs with dysentry Byrd2020 Firmicutes Clostridia Ruminococcaceae neg SANA Swimming Rod - curved No spore 40 20(neg)
Acetivibrio saccincola Herbivorax saccincola Unlikely Transient Non/unknown Pathogen Thermophilic. Doesn't grow at 37C so unlikely to be a gut coloniser. thermophilic lab-scale biogas fermenter, Germany New2022 Firmicutes Clostridia Clostridiaceae + SANA Sessile Rod Endospore 34.9
Acetivibrio thermocellus Clostridium thermocellum 1 Unlikely Transient Non/unknown Pathogen Cellulolytic. Does not ferment any other sugars. High optimum growth temperature so unlikely to be a gut coloniser. a sewage digestor; has also been detected in human faeces Salonen2014, New2022 Firmicutes Clostridia Oscillospiraceae neg SANA Sessile Rod - curved Endospore 38.1-39.5
Acetoanaerobium sticklandii Clostridium sticklandii Positive 1 Rare Known Commensal Non/unknown Pathogen human faeces, and black mud Benno1986, Benno1986, RajilicStojanovic2014, Lagier2016, New2022, Qin2012 Firmicutes Clostridia Clostridiaceae + SANA Swimming Rod Endospore 31
Acetobacter pasteurianus Acetobacter pasteurianus subsp. pasteurianus 1 Unlikely Transient Non/unknown Pathogen Obligate aerobe; unlikely to be a gut coloniser. fruits, flowers, and vegetables McLaughlin2010, Lagier2016 Proteobacteria Alphaproteobacteria Acetobacteraceae neg SAER Oval-shaped No spore 52-53
Acetobacterium woodii 1 Rare Possible Commensal Non/unknown Pathogen Hydrogen-oxidising, CO2-reducing acetic acid producer. Homoacetogen. Can use CO as an electron donor. marine and freshwater black sediments De2020, New2022 Firmicutes Clostridia Eubacteriaceae + SANA Swimming Oval-shaped No spore 39
Acetomicrobium hydrogeniformans Anaerobaculum hydrogeniformans Unlikely Possible Commensal Non/unknown Pathogen Reduces thiosulfate, sulfur and cysteine to sulfide. High optimum growth temperature so unlikely to be a gut coloniser. oil-contaminated water and human faeces Tyakht2013, Lagier2016, Forster2019 Synergistetes Synergistia Synergistaceae neg SANA Swimming Rod No spore 46.6
Achromobacter denitrificans Alcaligenes denitrificans 2 Unlikely Transient Opportunistic Infection Some strains can utilise acetamide. Borderline cold mesophile, so unlikely to be a gut coloniser. human faeces, soil and clinical specimens (sputum, urine - CCUG) Finegold1977, RajilicStojanovic2014, Lagier2016 Proteobacteria Betaproteobacteria Alcaligenaceae neg SAER Swimming Rod No spore 69.1
Achromobacter insuavis Unlikely Transient Opportunistic Pathogen Obligate aerobe; unlikely to be a gut coloniser. clinical sources (sputum) and water sources (pool) Yang2020 Proteobacteria Betaproteobacteria Alcaligenaceae neg SAER vr Short Rod No spore 68.0
Achromobacter spanius 1 Opportunistic in immunocompromised patients Unlikely Transient Opportunistic Pathogen Obligate aerobe; unlikely to be a gut coloniser. clinical sources (blood) Byrd2020, Yang2020 Proteobacteria Betaproteobacteria Alcaligenaceae neg SAER vr Coccus No spore 64.9
Achromobacter xylosoxidans 2 Rare Known Commensal Opportunistic Pathogen Phototrophic. human faeces, clinical specimens (sputum - CCUG), water and soil RajilicStojanovic2014, Lagier2016, Forster2019, Zeller2014 Proteobacteria Betaproteobacteria Alcaligenaceae neg SAER Swimming Rod No spore 64-70
Acidaminococcus fermentans 2 Human and animal pathogen Widespread Known Commensal Known Pathogen pig gut, human faeces and clinical sources (abdominal and pulmonary abscesses, bacteremia) Moore1974, Finegold1974, Holdeman1976, Finegold1977, Benno1984, Benno1989, MacFarlane2004, Zupancic2012, Nielsen2014, RajilicStojanovic2014, Lagier2016, Forster2019, King2019, Byrd2020, Yang2020, New2022, Dubinkina2017, Hu2019, Jeong2021, Jie2017, Zeller2014, Vachida2019, Minerbi2019 Firmicutes Negativicutes Acidaminococcaceae neg ANA Sessile Diplococci No spore 56
Acidaminococcus intestini Acidaminococcus sp. D21 2 Moderate Known Commensal Rare Opportunist clinical sources, and is a normal commensal of the human gut Nielsen2014, RajilicStojanovic2014, Chung2016, Lagier2016, Rothschild2018, Zou2019, Almeida2019, Chung2019, Forster, King2019, Byrd2020, Yang2020, New2022, Dubinkina2017, Hu2019, Jie2017, Zeller2014, Vachida2019, Wang2020a, Minerbi2019 Firmicutes Negativicutes Acidaminococcaceae neg ANA Sessile Coccus No spore 49.3
Acidaminococcus massiliensis Rare Possible Commensal Non/unknown Pathogen In 8% of Europeans (unseenbio.com). A rare coloniser. human duodenum and human faeces (Bilen2018e) Lagier2016, Byrd2020 Firmicutes Negativicutes Acidaminococcaceae neg ANA Sessile Coccus No spore
Acidaminococcus provencensis Unknown Rare Possible Commensal Non/unknown Pathogen human faeces Firmicutes Negativicutes Acidaminococcaceae neg SANA Coccus 53.2
Acidaminococcus timonensis Rare Possible Commensal Non/unknown Pathogen human faeces (Bilen2018e) Lagier2016, Byrd2020 Firmicutes Negativicutes Acidaminococcaceae neg ANA Sessile Coccus No spore
Acidipropionibacterium acidipropionici Propionibacterium acidipropionici 1 Rare Known Commensal Non/unknown Pathogen human faeces, and dairy fermentation RajilicStojanovic2014, Lagier2016 Actinobacteria Actinomycetia Propionibacteriaceae + ANA Rod No spore 68
Acidipropionibacterium jensenii Propionibacterium jensenii 1 Opportunistic in immunocompromised patients Rare Possible Commensal Opportunistic Infection human faeces, malted barley, and buttermilk Taylor1985, Woodmansey2004, RajilicStojanovic2014, Lagier2016 Actinobacteria Actinomycetia Propionibacteriaceae + ANA Rod No spore 68.5-68.8
Acidisarcina polymorpha Rare Possible Commensal Non/unknown Pathogen acidic soil, Russia New2022 Acidobacteria Acidobacteriia Acidobacteriaceae neg AER Sessile Pleiomorph rod No spore 56.8
Acidovorax facilis Pseudomonas facilis 1 Rare Known Commensal Non/unknown Pathogen human faeces, and lawn soil McLaughlin2010, Walker2011, RajilicStojanovic2014 Proteobacteria Betaproteobacteria Comamonadaceae neg AER Swimming Rod No spore 64–65
Acidovorax sp. strain KKS102 Pseudomonas sp. strain KKS102 Rare Transient Non/unknown Pathogen Biphenyl and polychlorinated biphenyl degrader. human faeces and soil King2019 Proteobacteria Betaproteobacteria Comamonadaceae neg AER Swimming Rod No spore 67
Acidovorax temperans 1 Opportunistic in immunocompromised patients Rare Possible Commensal Rare Opportunist clinical sources (urine) and sludge McLaughlin2010 Proteobacteria Betaproteobacteria Comamonadaceae neg AER Swimming Rod - curved No spore 62-66
Acidovorax wautersii Rare Possible Commensal Rare Opportunist human faeces, clinical sources and the environment Yang2020 Proteobacteria Betaproteobacteria Comamonadaceae neg AER Swimming Rod No spore 67.1
Acinetobacter baumannii Acinetobacter genomospecies 2 2 Unlikely Transient Known Pathogen Obligate aerobe; unlikely to be a gut coloniser. human faeces (Dijkshoorn2005), clinical specimens (blood, urine, sputum - CCUG) and the environment Pandey2012, RajilicStojanovic2014, Lagier2016, Almeida2019, Forster2019, Byrd2020, De2020, New2022 Proteobacteria Gammaproteobacteria Moraxellaceae neg SAER vr Diplococci No spore 40-43
Acinetobacter bereziniae Acinetobacter genomospecies 10 Unlikely Transient Opportunistic Infection Obligate aerobe; unlikely to be a gut coloniser. millk, human faeces (Dijkshoorn2005), clinical specimens (trachea, sputum, uring - CCUG) and the environment Yang2020 Proteobacteria Gammaproteobacteria Moraxellaceae neg SAER vr Coccobacillus No spore
Acinetobacter calcoaceticus Achromobacter anitratus 2 Rare Known Commensal Possible Pathogen human faeces (including ulcerative colitis patients - Alkhalil2017), clinical specimens (wound, urine - CCUG) and soil RajilicStojanovic2014, Lagier2016, De2020 Proteobacteria Gammaproteobacteria Moraxellaceae neg SAER Sessile Diplococci No spore 40-42
Acinetobacter guillouiae Acinetobacter genomospecies 11 Rare Transient Opportunistic Infection Obligate aerobe; has been found in the faeces of non-hospital patients in Leiden (Dijkshoorn2005). human faeces (Dijkshoorn2005), clinical sources (wound, infection, sputum, urine - CCUG) and the environment Byrd2020 Proteobacteria Gammaproteobacteria Moraxellaceae neg SAER Sessile Coccobacillus No spore
Acinetobacter haemolyticus Acinetobacter genomospecies 4 2 Unlikely Transient Opportunistic Infection Obligate aerobe; unlikely to be a gut coloniser. human faeces, clinical specimens (sputum, blood - CCUG) and the environment Wang2005, RajilicStojanovic2014, Lagier2016, New2022, Zeller2014 Proteobacteria Gammaproteobacteria Moraxellaceae neg SAER Sessile Diplococci No spore 40-43
Acinetobacter idrijaensis Rare Resistant to mercury, and probably cobalt, cadmium and zinc. soil Byrd2020 Proteobacteria Gammaproteobacteria Moraxellaceae 36.8
Acinetobacter johnsonii Acinetobacter genomospecies 7 2 Rare Transient Opportunistic Infection Obligate aerobe and grows poorly at 37C, but has been found in the faeces of non-hospitalised patients from Leiden (Dijkshoorn2005). Not detected in Europeans with a healthy microbiome (unseenbio.com). human faeces (Dijkshoorn2005), human duodenum, clinical sources (blood, larynx, sputum - CCUG) and the environment Wang2005, McLaughlin2010, RajilicStojanovic2014, Yang2020, New2022, Zeller2014, Vachida2019, PerezBrocal2015 Proteobacteria Gammaproteobacteria Moraxellaceae neg SAER Sessile Diplococci No spore 44-45
Acinetobacter junii Acinetobacter genomospecies 5 2 Rare Known Commensal Opportunistic Infection In 1% of Europeans (unseenbio.com). Rare coloniser. human faeces (Dijkshoorn2005) and clinical sources (wound, sputum, urine - CCUG) Frank2007, McLaughlin2010, Pandey2012, Tyakht2013, RajilicStojanovic2014, Lagier2016, Forster2019, Yang2020, Hu2019, Zeller2014 Proteobacteria Gammaproteobacteria Moraxellaceae neg SAER Sessile Diplococci No spore 42
Acinetobacter lwoffii Acinetobacter mesopotamicus 2 Unlikely Transient Possible Pathogen Obligate aerobe; unlikely to be a gut coloniser. human faeces (Dijkshoorn2005), clinical sources (blood, wound, abscess - CCUG), animal sources and the environment Wang2005, McLaughlin2010, RajilicStojanovic2014, Lagier2016, Forster2019, Yang2020, Zeller2014, PerezBrocal2015 Proteobacteria Gammaproteobacteria Moraxellaceae neg SAER Sessile Diplococci No spore 46
Acinetobacter parvus 2 Unlikely Transient Opportunistic Infection Obligate aerobe suggests it is unlikely to be a gut coloniser. clinical specimens (eye, ear, skin) Hu2019 Proteobacteria Gammaproteobacteria Moraxellaceae neg SAER Sessile Coccobacillus No spore 41.8
Acinetobacter pittii Acinetobacter genomospecies 3 Unlikely Transient Opportunistic Pathogen Obligate aerobe; unlikely to be a gut coloniser. human faeces, clinical specimens (sputum, urine, wound - CCUG) and the environment Pandey2012, RajilicStojanovic2014, Lagier2016 Proteobacteria Gammaproteobacteria Moraxellaceae neg SAER Sessile Coccobacillus No spore 41-42
Acinetobacter radioresistens Acinetobacter genomospecies 12 1 Rare Possible Commensal Opportunistic Infection soils, cotton clinical sources (blood, infection - CCUG) and human faeces McLaughlin2010, Tyakht2013, RajilicStojanovic2014, Lagier2016 Proteobacteria Gammaproteobacteria Moraxellaceae neg AER Sessile No spore 44.1-44.8
Acinetobacter schindleri 2 Unlikely Transient Opportunistic Pathogen Obligate aerobe; unlikely to be a gut coloniser. human faeces (Bilen2018e) and clinical specimens (urine, infection - CCUG) Lagier2016, PerezBrocal2015 Proteobacteria Gammaproteobacteria Moraxellaceae neg SAER Sessile Coccobacillus No spore
Acinetobacter septicus Unlikely Transient Opportunistic Pathogen Obligate aerobe; unlikely to be a gut coloniser. clinical sources (ulcers, blood) and human faeces RajilicStojanovic2014, Lagier2016 Proteobacteria Gammaproteobacteria Moraxellaceae neg SAER Sessile Coccobacillus No spore
Acinetobacter towneri 1 Unlikely Transient Non/unknown Pathogen Obligate aerobe; unlikely to be a gut coloniser. activated sludge Lagier2016, Byrd2020 Proteobacteria Gammaproteobacteria Moraxellaceae neg SAER Coccobacillus No spore
Acinetobacter ursingii Acinetobacter sp. phenon 1 2 Unlikely Transient Opportunistic Infection Obligate aerobe; unlikely to be a gut coloniser. human faeces (Dijkshoorn2005) and clinical sources (wound, blood, infection - CCUG) Lagier2016 Proteobacteria Gammaproteobacteria Moraxellaceae neg SAER Sessile Coccobacillus No spore
Acinetobacter variabilis Unlikely Transient Opportunistic Infection Obligate aerobe; unlikely to be a gut coloniser. human faeces (CCUG) and clinical sources (blood, urine - CCUG) Lagier2016 Proteobacteria Gammaproteobacteria Moraxellaceae neg SAER Sessile Coccobacillus No spore
Actinobacillus capsulatus 2 Animal pathogen Rare Possible Commensal Possible Pathogen pets and rodent clinical isolates Forster2019 Proteobacteria Gammaproteobacteria Pasteurellaceae neg FANA Sessile Coccus No spore 42.4
Actinobacillus minor 1 Unlikely Non-commensal Opportunistic Pathogen pigs Proteobacteria Gammaproteobacteria Pasteurellaceae neg FANA Sessile Rod No spore 38.2
Actinobacillus pleuropneumoniae Haemophilus pleuropneumoniae 2 Animal pathogen Rare Transient Opportunistic Pathogen human faeces and pneumonic lesions of swine Bik2006, RajilicStojanovic2014, Zeller2014 Proteobacteria Gammaproteobacteria Pasteurellaceae neg FANA Sessile Coccus No spore 43
Actinobacillus succinogenes 1 Rare Possible Commensal Non/unknown Pathogen bovine rumen Tyakht2013 Proteobacteria Gammaproteobacteria Pasteurellaceae neg FANA Sessile Pleiomorph rod No spore 45
Actinobacillus ureae Pasteurella ureae 2 Non Transient Opportunistic Infection Breaks down urea. the human nose. Can cause ozaena and other infections Lagier2016, Zeller2014 Proteobacteria Gammaproteobacteria Pasteurellaceae neg FANA Sessile No spore 41.2-43.7
Actinobaculum massiliense Actinobaculum massiliae 2 Minor Possible Commensal Opportunistic Pathogen Original strain developed resistance to many UTI antibiotics due to misdiagnosis. In 10% of Europeans (unseenbio.com). Minor coloniser. clinical sources (urine) Lagier2016 Actinobacteria Actinomycetia Actinomycetaceae + FANA Sessile Rod No spore 55
Actinomyces bouchesdurhonensis Unlikely Transient Non/unknown Pathogen human stomach and duodenum (Fonkou2018, Bilen2018e), and clinical specimens (stomach wash, tonsil tissue - CCUG) Lagier2016 Actinobacteria Actinomycetia Actinomycetaceae + FANA Sessile Rod No spore 63.3
Actinomyces canis 2 Animal pathogen Non Transient Opportunistic Pathogen human faeces, and dogs McLaughlin2010, RajilicStojanovic2014 Actinobacteria Actinomycetia Actinomycetaceae + FANA Sessile Rod No spore
Actinomyces dentalis 2 Non Transient Opportunistic Infection Produces acetic and lactic acids from glucose fermentation. clinical sources (dental abscess) Lagier2016, Byrd2020 Actinobacteria Actinomycetia Actinomycetaceae + SANA Sessile Filamentous No spore 62
Actinomyces georgiae 1 Non Transient Opportunistic Infection human faeces and human gingival crevices Lagier2012b, RajilicStojanovic2014 Actinobacteria Actinomycetia Actinomycetaceae + FANA Sessile Diplobacilli No spore 65-69
Actinomyces gerencseriae Actinomyces israelii serotype II 2 Unlikely Transient Opportunistic Infection human gingival crevices, abcesses and other clinical specimens Byrd2020 Actinobacteria Actinobacteria Actinomycetaceae + FANA Sessile Filamentous No spore 70-71
Actinomyces graevenitzii 2 Minor Possible Commensal Opportunistic Infection human faeces and human clinical specimens (sputum, abscess - CCUG) RajilicStojanovic2014, Lagier2016, Almeida2019, Byrd2020, De2020, Hu2019, Vachida2019 Actinobacteria Actinomycetia Actinomycetaceae + FANA Sessile Rod No spore
Actinomyces ihuae Actinomyces ihumii Rare Possible Commensal Non/unknown Pathogen stool sample of an HIV-infected man, France Lagier2016 Actinobacteria Actinomycetia Actinomycetaceae + AER Sessile Rod No spore
Actinomyces israelii 2 Non Transient Opportunistic Pathogen clinical sources (tooth infection, abscess, jaw infection - CCUG; appendicitis) and human gastrointestinal tract (Hansen2009) Lagier2016, Byrd2020 Actinobacteria Actinomycetia Actinomycetaceae + ANA Sessile Filamentous No spore
Actinomyces johnsonii Rare Unknown Non/unknown Pathogen healthy gingival crevice Lagier2016, Byrd2020, Vachida2019 Actinobacteria Actinomycetia Actinomycetaceae + FANA Sessile Rod No spore 67
Actinomyces marseillensis Rare Possible Commensal Opportunistic Infection human faeces (Fonkou2018) and sputum Actinobacteria Actinomycetia Actinomycetaceae + AER Sessile Rod No spore 57.1
Actinomyces massiliensis Rare Possible Commensal Possible Pathogen human blood Byrd2020, Vachida2019 Actinobacteria Actinobacteria Actinomycetaceae + ANA Sessile Rod No spore
Actinomyces mediterranea Rare Possible Commensal Non/unknown Pathogen the stomach, duodenum and human faeces (CCUG) Actinobacteria Actinomycetia Actinomycetaceae + Micr Sessile Rod No spore
Actinomyces minihominis Rare Possible Commensal Non/unknown Pathogen human faeces (CCUG) Actinobacteria Actinomycetia Actinomycetaceae + ANA Sessile Rod No spore
Actinomyces naeslundii 2 Human and animal pathogen Minor Known Commensal Opportunistic Pathogen human faeces and clinical sources (plaque, blood, sinus) Finegold1977, Dubourg2013, RajilicStojanovic2014, Cassir2015, Lagier2016, Almeida2019, Forster2019, Byrd2020, Yang2020, New2022, Vachida2019 Actinobacteria Actinomycetia Actinomycetaceae + FANA Sessile Filamentous No spore 66
Actinomyces oris Actinomyces naeslundii genospecies 2 Rare Possible Commensal Opportunistic Infection human faeces and clinical sources (blood, sputum, oral plaque - CCUG) RajilicStojanovic2014, Lagier2016, Byrd2020, De2020, New2022, Vachida2019 Actinobacteria Actinomycetia Actinomycetaceae + FANA Sessile No spore 66
Actinomyces pacaensis Rare Possible Commensal Rare Opportunist sputum, France New2022 Actinobacteria Actinomycetia Actinomycetaceae + ANA Sessile Rod Spore reported
Actinomyces polynesiensis Rare Possible Commensal Non/unknown Pathogen human gut (Cimmino2016) Lagier2016 Actinobacteria Actinomycetia Actinomycetaceae + Micr Swimming Rod No spore 70.8
Actinomyces provencensis Rare Possible Commensal Non/unknown Pathogen human faeces (Ndongo2017) Lagier2016 Actinobacteria Actinomycetia Acidothermaceae + FANA Swimming Rod Exospore
Actinomyces sp. ph3 Actinomyces grossensis Rare Known Commensal Non/unknown Pathogen human faeces Pfleiderer2013, RajilicStojanovic2014, Lagier2016 Actinobacteria Actinomycetia Actinomycetaceae + Sessile No spore 56.0
Actinomyces timonensis Rare Possible Commensal Opportunistic Pathogen a clinical osteo-articular specimen Vachida2019 Actinobacteria Actinomycetia Actinomycetaceae + ANA Sessile Rod No spore
Actinomyces urogenitalis 1 Opportunistic in immunocompromised patients Rare Possible Commensal Opportunistic Infection clinical sources (cervix, vagina, urine, abscess - CCUG) and human faeces Favier2002, RajilicStojanovic2014, Lagier2016, Hu2019, Zeller2014 Actinobacteria Actinomycetia Actinomycetaceae + FANA Sessile Rod No spore 61
Actinomyces viscosus 2 Human and animal pathogen Minor Possible Commensal Opportunistic Pathogen In 17% of Europeans (unseenbio.com). Minor coloniser. human faeces, clinical sources (blood, mouth, lesion - CCUG) and rats RajilicStojanovic2014, Byrd2020, New2022, Zeller2014, Vachida2019 Actinobacteria Actinomycetia Actinomycetaceae + FANA Sessile No spore
Actinosynnema mirum 1 Non Transient Non/unknown Pathogen Aerobic and inability to grow at 37C suggests this not a gut coloniser. river grass blades, USA Zeller2014 Actinobacteria Actinomycetia Pseudonocardiaceae + AER Swimming Filamentous Exospore
Actinotignum schaalii Actinobaculum schaalii 2 Rare Possible Commensal Opportunistic Infection human faeces (26-yr-old healthy woman - CCUG) and clinical sources (blood and urine - CCUG) Actinobacteria Actinomycetia Actinomycetaceae + FANA Sessile Rod No spore 57
Acutalibacter muris Rare Possible Commensal Non/unknown Pathogen mouse caeca Byrd2020, New2022 Firmicutes Clostridia Oscillospiraceae + SANA Rod 54.6
Acutalibacter timonensis Minor Possible Commensal Isolation and characterisation not yet published. In 35% of Europeans (unseenbio.com). Byrd2020 Firmicutes Clostridia Ruminococcaceae
Adhaeribacter aquaticus 1 Unlikely Transient Non/unknown Pathogen Obligate aerobe suggests it is unlikely to be a gut coloniser. a potable water biofilm Bacteroidetes Cytophagia Hymenobacteraceae neg SAER Sessile Rod No spore 40.0
Adlercreutzia caecimuris Enterorhabdus caecimuris Rare Possible Commensal Non/unknown Pathogen caecal suspensions of mice Byrd2020, Vachida2019 Actinobacteria Coriobacteriia Eggerthellaceae + SANA Sessile Rod No spore 64.5 0.5(neg)
Adlercreutzia equolifaciens Positive 1 Moderate Known Commensal Non/unknown Pathogen Produces equol (an isoflavandiol aestrogen) from isoflavones. human faeces (Alkhalil2017), human and rat intestine Zupancic2012, Pfleiderer2013, RajilicStojanovic2014, Lagier2016, Rothschild2018, Forster2019, King2019, Byrd2020, New2022, Chen2020, Dubinkina2017, Hu2019, Jie2017, Vachida2019, Wang2020a Actinobacteria Coriobacteriia Eggerthellaceae + SANA Sessile Coccobacillus No spore 64 20(neg)
Adlercreutzia equolifaciens subsp. celatus Asaccharobacter celatus 1 Rare Possible Commensal Non/unknown Pathogen human faeces , and isolated from the caecal content of a rat RajilicStojanovic2014, Yang2020 Actinobacteria Coriobacteriia Atopobiaceae + SANA Rod No spore 63 20(+)
Adlercreutzia hattorii Rare Possible Commensal Non/unknown Pathogen Doesn't produce equol and is asaccharolytic. human faeces (Sakamoto2021) New2022 Actinobacteria Coriobacteriia Eggerthellaceae + SANA Sessile Rod No spore 63.0 20(w)
Adlercreutzia mucosicola Enterorhabdus mucosicola Rare Possible Commensal Non/unknown Pathogen ileal mucosa of mouse and has been detected in human faeces (Alkhalil2017) Byrd2020 Actinobacteria Coriobacteriia Eggerthellaceae + SANA Sessile Rod No spore 64.2 0.5(neg)
Adlercreutzia rubneri Rare Possible Commensal Non/unknown Pathogen Able to metabolise resveratrol (an antioxidant and antimicrobial). human faeces (Stoll2021a) Actinobacteria Coriobacteriia Eggerthellaceae + SANA Sessile Short Rod No spore 63.3 2(+)
Aeribacillus pallidus Bacillus pallidus Unlikely Transient Non/unknown Pathogen High optimum growth temperature so unlikely to be a gut coloniser. human faeces and heat-treated sewage sludge RajilicStojanovic2014, Lagier2016 Firmicutes Bacilli Bacillaceae + AER Swimming Rod Endospore 39-41
Aerococcus vaginalis Non Unknown Non/unknown Pathogen a cow vagina De2020 Firmicutes Bacilli Aerococcaceae + FANA Sessile Coccus No spore 44.7 2(neg)
Aerococcus viridans Pediococcus urinaeequi 2 Human and animal pathogen Rare Known Commensal Opportunistic Pathogen human faeces, dog faeces, and clinical sources (blood, urine, wound - CCUG) Finegold1977, RajilicStojanovic2014, Lagier2016, Yang2020 Firmicutes Bacilli Aerococcaceae + Micr Sessile Tetrad No spore d
Aeromicrobium massiliense Rare Known Commensal Non/unknown Pathogen human faeces Pfleiderer2013, RajilicStojanovic2014, Lagier2016, Forster2019 Actinobacteria Actinomycetia Nocardioidaceae + AER Swimming Rod No spore 72.49
Aeromicrobium tamlense 1 Rare Possible Commensal Non/unknown Pathogen dried seaweed Lagier2016 Actinobacteria Actinomycetia Nocardioidaceae + AER Sessile Rod No spore 72.7
Aeromonas allosaccharophila 2 Rare Possible Commensal Possible Pathogen human faeces, including diarrheic stools RajilicStojanovic2014, Lagier2016 Proteobacteria Gammaproteobacteria Aeromonadaceae neg FANA Swimming Rod No spore 59.5
Aeromonas bestiarum 1 Human and animal pathogen; opportunistic in immunocompromised patients Rare Possible Commensal Opportunistic Pathogen human faeces (CCUG), animals and the environment RajilicStojanovic2014, Lagier2016 Proteobacteria Gammaproteobacteria Aeromonadaceae neg AER Swimming Rod No spore
Aeromonas caviae Pseudomonas caviae 2 Human and animal pathogen Unlikely Possible Commensal Known Pathogen Pathogenic; unlikely to be a coloniser in a healthy microbiome. human faeces (CCUG), clinical sources (blood, wound - CCUG), sewage, animals and aquatic sources RajilicStojanovic2014, Lagier2016, Yang2020, Zeller2014, Vachida2019 Proteobacteria Gammaproteobacteria Aeromonadaceae neg ANA Swimming Rod No spore 61-63
Aeromonas dhakensis Aeromonas aquariorum 1 Rare Unknown Opportunistic Infection human faeces (diarrhoea - Huys2002) and clinical sources (wound - CCUG) Lagier2016, Vachida2019 Proteobacteria Gammaproteobacteria Aeromonadaceae neg FANA Swimming Rod No spore
Aeromonas encheleia 1 Human and animal pathogen; opportunistic in immunocompromised patients Unlikely Transient Known Pathogen Borderline cold mesophile, with optimum growth temp of 28C. Unlikely gut coloniser. freshwater eels Lagier2016 Proteobacteria Gammaproteobacteria Aeromonadaceae neg FANA Swimming Rod No spore 59.4-60.8
Aeromonas enteropelogenes Aeromonas trota 2 Human and animal pathogen Rare Known Commensal Opportunistic Pathogen human faeces and appendix RajilicStojanovic2014, Lagier2016, Hu2019, Zeller2014, Vachida2019 Proteobacteria Gammaproteobacteria Aeromonadaceae neg AER Swimming Rod No spore
Aeromonas eucrenophila 1 Human and animal pathogen; opportunistic in immunocompromised patients Non Transient Opportunistic Pathogen human faeces (CCUG), fresh uncontaminated brooks and Rivers Lagier2016 Proteobacteria Gammaproteobacteria Aeromonadaceae neg FANA Swimming Rod No spore 59.8-62.6
Aeromonas hydrophila 2 Human and animal pathogen Unlikely Transient Known Pathogen Borderline cold mesophile, with optimum growth temp of 28C. Unlikely gut coloniser. Can reduce Fe(III) with glycerol as a donor. human faeces (CCUG, Pitarangsi1982), clinical sources (wound, blood - CCUG), fresh and marine waters and animals RajilicStojanovic2014, Lagier2016, Zeller2014, Vachida2019 Proteobacteria Gammaproteobacteria Aeromonadaceae neg FANA Swimming Rod No spore 58-62
Aeromonas hydrophila subsp. hydrophila 2 Human and animal pathogen Unlikely Transient Known Pathogen Borderline cold mesophile, with optimum growth temp of 28C. Unlikely gut coloniser. human faeces (CCUG) Proteobacteria Gammaproteobacteria Aeromonadaceae neg FANA Swimming Rod No spore
Aeromonas jandaei 2 Human and animal pathogen Rare Possible Commensal Opportunistic Pathogen human faeces (CCUG), clinical specimens (wound -CCUG) and the environment RajilicStojanovic2014, Lagier2016 Proteobacteria Gammaproteobacteria Aeromonadaceae neg AER Swimming Rod No spore 58.1-61.1
Aeromonas media 1 Rare Unknown Opportunistic Pathogen human faeces, diarrheal disease and aquatic sources RajilicStojanovic2014, Lagier2016 Proteobacteria Gammaproteobacteria Aeromonadaceae neg AER vr Rod No spore 62.3
Aeromonas popoffii 1 Unlikely Transient Non/unknown Pathogen Borderline cold mesophile, with optimum growth temp of 28C. Unlikely gut coloniser. drinking water Lagier2016 Proteobacteria Gammaproteobacteria Aeromonadaceae neg FANA Swimming Rod No spore 57.7-59.6
Aeromonas salmonicida 1 Unlikely Transient Non/unknown Pathogen Could be a mesophilic form of A. salmonicida detected by Lagier(2016). Likely to be sessile. Unlikely gut coloniser. human faeces Lagier2016, Byrd2020, New2022, Zeller2014 Proteobacteria Gammaproteobacteria Aeromonadaceae neg FANA Sessile Rod No spore 57-59
Aeromonas schubertii 2 Non Transient Opportunistic Infection Mannitol-negative fermentation. Unlikely gut coloniser. clinical sources (abscess, blood, wound, drainage) Lagier2016 Proteobacteria Gammaproteobacteria Aeromonadaceae neg FANA Swimming Rod No spore
Aeromonas sobria 2 Human and animal pathogen Rare Possible Commensal Opportunistic Pathogen human faeces (CCUG), clinical sources (blood, wound - CCUG), fish, sewage and water Lagier2016 Proteobacteria Gammaproteobacteria Aeromonadaceae neg FANA Sessile Rod No spore 58-60
Aeromonas taiwanensis Non Transient Opportunistic Infection clinical sources (wound) Lagier2016 Proteobacteria Gammaproteobacteria Aeromonadaceae neg FANA Swimming Rod No spore 62.8
Aeromonas tecta Rare Possible Commensal Non/unknown Pathogen human faeces RajilicStojanovic2014, Lagier2016 Proteobacteria Gammaproteobacteria Aeromonadaceae neg FANA Swimming Rod No spore
Aeromonas trota 2 Rare Possible Commensal Opportunistic Infection human faeces, including pediatric diarrhoea RajilicStojanovic2014 Proteobacteria Gammaproteobacteria Aeromonadaceae neg FANA Swimming Rod No spore
Aeromonas veronii 2 Human and animal pathogen Rare Possible Commensal Known Pathogen human faeces (CCUG), including diarrhoea, animals and aquatic sources RajilicStojanovic2014, Lagier2016, Almeida2019 Proteobacteria Gammaproteobacteria Aeromonadaceae neg AER Swimming Rod No spore 57-58
Aestuariimicrobium kwangyangense 1 Rare Possible Commensal Non/unknown Pathogen oil-contaminated tidal flats in Korea De2020 Actinobacteria Actinomycetia Propionibacteriaceae + AER Sessile Short Rod No spore 68.8-69.2
Afipia birgiae 1 Unlikely Transient Non/unknown Pathogen Can't grow at 35C or above, so unlikely to be a gut coloniser. human faeces and water sources RajilicStojanovic2014 Proteobacteria Alphaproteobacteria Bradyrhizobiaceae neg AER Sessile No spore 59.3
Afipia broomeae 2 Rare Possible Commensal Possible Pathogen human faeces and clinical sources (sputum - CCUG) Yang2020 Proteobacteria Alphaproteobacteria Bradyrhizobiaceae neg FANA Swimming Rod No spore 61.5
Afipia lausannensis Unlikely Transient Opportunistic Pathogen intracellular associations with amoeba isolated from hospital water networks Frank2007, McLaughlin2010 Proteobacteria Alphaproteobacteria Bradyrhizobiaceae neg AER Swimming Rod No spore
Africanella massiliensis Rare Possible Commensal Non/unknown Pathogen human faeces (healthy) Firmicutes Clostridia Lachnospiraceae + ANA Rod
Agathobacter ruminis Rare Possible Commensal Non/unknown Pathogen rumen fluid of sheep Byrd2020 Firmicutes Clostridia Lachnospiraceae + SANA Swimming Rod No spore 41-42
Agathobaculum butyriciproducens Moderate Possible Commensal Non/unknown Pathogen In 99% of Europeans (unseenbio.com). human faeces (Ahn2016) Zou2019, Byrd2020, Minerbi2019 Firmicutes Clostridia Oscillospiraceae + SANA Sessile Rod No spore 52.9
Agathobaculum desmolans Eubacterium desmolans 1 Minor Possible Commensal Non/unknown Pathogen In 39% of Europeans (unseenbio.com). Minor coloniser. human faeces and cat faeces Mangin2004, RajilicStojanovic2014, Byrd2020, Yang2020, Minerbi2019 Firmicutes Clostridia Eubacteriaceae + SANA Swimming Rod No spore 48.5 20(+)
Aggregatibacter actinomycetemcomitans Actinobacillus actinomycetemcomitans 2 Human and animal pathogen Rare Possible Commensal Opportunistic Pathogen dental surfaces of humans and clinical sources (brain abscess, UTI, periodontitis) Forster2019, Byrd2020 Proteobacteria Gammaproteobacteria Pasteurellaceae neg FANA Sessile Short Rod No spore 42.7
Aggregatibacter aphrophilus Haemophilus aphrophilus 2 Minor Possible Commensal Opportunistic Pathogen human faeces, dental and clinical sources (blood, abscess - CCUG) Bik2006, RajilicStojanovic2014, Lagier2016, Byrd2020, Yang2020, New2022, Hu2019, Zeller2014, Vachida2019, Qin2012 Proteobacteria Gammaproteobacteria Pasteurellaceae neg FANA Sessile Rod No spore 42
Aggregatibacter segnis Haemophilus segnis 2 Minor Unknown Opportunistic Infection the appendix (CCUG), pharynx, saliva and dental plaque Lagier2016, Byrd2020, Yang2020, New2022, Dubinkina2017, Hu2019, Jie2017, Zeller2014, Vachida2019, Li2019b, PerezBrocal2015 Proteobacteria Gammaproteobacteria Pasteurellaceae neg FANA Sessile Rod No spore 43-44
Agrilactobacillus composti Lactobacillus composti Positive 1 Unlikely Transient Non/unknown Pathogen compost of distilled shochu residue Firmicutes Bacilli Lactobacillaceae + FANA Sessile Rod No spore 47
Agrobacterium radiobacter Agrobacterium tumefaciens Unlikely Transient Opportunistic Pathogen Borderline cold mesophile, with optimum growth temp of 27C. Unlikely gut coloniser. soil, plants and human faeces Walker2011 Proteobacteria Alphaproteobacteria Rhizobiaceae neg AER Swimming Rod No spore 57-63
Agrobacterium rhizogenes 1 Plant pathogen Unlikely Transient Non/unknown Pathogen Aerobic and optimum growth temp of 25-28C suggests this is unlikely to be a gut coloniser. soil, plant rhizospheres, young gall tissues, and hairy roots of many plant species Byrd2020 Proteobacteria Alphaproteobacteria Rhizobiaceae neg AER Swimming Rod No spore 59-63
Agrobacterium tumefaciens Unlikely Transient Non/unknown Pathogen Borderline cold mesophile, so unlikely to be a gut coloniser. plants and plant diseases RajilicStojanovic2014, Lagier2016, Yang2020 Proteobacteria Alphaproteobacteria Rhizobiaceae neg ANA Swimming Rod No spore 57-63
Agrococcus casei 1 Rare Possible Commensal Non/unknown Pathogen ripening cheese Lagier2016 Actinobacteria Actinomycetia Microbacteriaceae + AER Sessile No spore 65.0
Agrococcus jejuensis 1 Rare Possible Commensal Non/unknown Pathogen human faeces, and dried seaweed RajilicStojanovic2014 Actinobacteria Actinomycetia Microbacteriaceae + AER Sessile Rod No spore 73
Agrococcus jenensis 1 Rare Possible Commensal Non/unknown Pathogen human faeces, soil and land surfaces Hoyles2012, Lagier2016, PerezBrocal2015 Actinobacteria Actinomycetia Microbacteriaceae + Micr Sessile Coccus No spore 74
Agrococcus terreus Unlikely Transient Non/unknown Pathogen Obligate aerobe; unlikely to be a gut coloniser. forest soil and human faeces RajilicStojanovic2014, Lagier2016 Actinobacteria Actinomycetia Microbacteriaceae + SAER Sessile Rod No spore 75.9
Akkermansia glycaniphila Rare Known Commensal Non/unknown Pathogen Can use mucin as a sole C and N source. faeces of reticulated python Byrd2020, De2020, New2022 Verrucomicrobia Verrucomicrobiae Akkermansiaceae neg SANA Sessile Oval-shaped No spore 58.2
Akkermansia muciniphila Positive 1 Widespread Known Mutualist Non/unknown Pathogen This organism might not be picked up in all microbiome surveys as the conventional probes used often don't bind well to its DNA. Found in human breast milk (Jeurink2013). human faeces Walker2011, Zupancic2012, Tyakht2013, Nielsen2014, RajilicStojanovic2014, Lagier2016, Rothschild2018, Zou2019, King2019, Byrd2020, De2020, New2022, Chen2020, Dubinkina2017, Hu2019, Jeong2021, Jie2017, Zeller2014, Wang2018, Vachida2019, Wang2020a, Qin2012, Minerbi2019, Li2019b, Karlsson2013, PerezBrocal2015 Verrucomicrobia Verrucomicrobiae Akkermansiaceae neg SANA Sessile Oval-shaped No spore 55.8
Alcaligenes faecalis Bordetella avium 2 Animal pathogen Rare Possible Commensal Opportunistic Infection human faeces (CCUG), clinical sources (wound, urine - CCUG) and eutrophic water McLaughlin2010, RajilicStojanovic2014, Salonen2014, Lagier2016, Yang2020, Zeller2014 Proteobacteria Betaproteobacteria Alcaligenaceae neg AER Swimming Rod No spore
Alcaligenes faecalis subsp. faecalis Bordetella avium 2 Human and animal pathogen Unlikely Transient Known Pathogen Obligate aerobe; unlikely to be a gut coloniser. human faeces (CCUG), soil, water and clinical sources Proteobacteria Betaproteobacteria Alcaligenaceae neg SAER Swimming Rod No spore 56-59
Aliagarivorans marinus Rare Possible Commensal Non/unknown Pathogen coastal seawater, Taiwan Forster2019 Proteobacteria Gammaproteobacteria Alteromonadaceae neg FANA Swimming Rod No spore 52-53
Aliarcobacter butzleri Campylobacter butzleri Rare Known Commensal Rare Opportunist human faeces (CCUG), clinical sources (diarrhoea), animals and water sources Tyakht2013, RajilicStojanovic2014, Lagier2016, Zeller2014, Vachida2019 Proteobacteria Epsilonproteobacteria Arcobacteraceae neg Micr Swimming Rod - curved No spore 28-31
Aliarcobacter cryaerophilus Campylobacter cryaerophila Rare Possible Commensal Possible Pathogen human faeces and animals RajilicStojanovic2014, Lagier2016, Byrd2020, Yang2020 Proteobacteria Epsilonproteobacteria Arcobacteraceae neg Micr Swimming Rod - curved No spore 31
Aliarcobacter skirrowii Arcobacter skirrowii 1 Human and animal pathogen; opportunistic in immunocompromised patients Rare Possible Commensal Opportunistic Pathogen Carbohydrates are not fermented or oxidised. a lamb with diarrhoea Lagier2016 Proteobacteria Epsilonproteobacteria Arcobacteriaceae neg Micr Swimming Rod - curved No spore 29.0 1(neg)
Alicyclobacillus acidocaldarius Bacillus acidocaldarius 1 Rare Possible Commensal Non/unknown Pathogen acidic thermal terrestrial and aqueous environments, including fruit juices New2022, Zeller2014 Firmicutes Bacilli Alicyclobacillaceae + AER Swimming Rod Endospore 61.2-62.2
Aliiruegeria sabulilitoris Pseudoruegeria sabulilitoris Unlikely Transient Non/unknown Pathogen Mg2+ ions are required for growth. Doesn't grow at 37C, so unlikely gut coloniser. seashore sand, Korea Byrd2020 Proteobacteria Alphaproteobacteria Rhodobacteraceae neg AER Sessile Oval-shaped No spore 64.1
Alistipes communis Bacteroidales bacterium ph8 Rare Known Commensal Non/unknown Pathogen human faeces (obese patient - Sakamoto2020) Lagier2016, New2022, Chen2020, Hu2019, Vachida2019 Bacteroidetes Bacteroidia Rikenellaceae neg SANA Sessile Rod No spore 58.5 20(+)
Alistipes dispar Rare Possible Commensal Non/unknown Pathogen human faeces (Sakamoto2020) New2022 Bacteroidetes Bacteroidia Rikenellaceae neg SANA Sessile Coccobacillus No spore 61.3 20(+)
Alistipes finegoldii Mixed 1 Opportunistic in immunocompromised patients Moderate Known Commensal Opportunistic Infection human faeces and clinical specimens (appendix, abscess, blood - CCUG) Walker2011, Zupancic2012, Nielsen2014, RajilicStojanovic2014, Browne2016, Lagier2016, Rothschild2018, Forster2019, King2019, Byrd2020, De2020, New2022, Chen2020, Hu2019, Vachida2019, Wang2020a, Minerbi2019 Bacteroidetes Bacteroidia Rikenellaceae neg SANA Sessile Rod No spore 56.6 20(+)
Alistipes ihumii Alistipes marseilloanorexicus Moderate Possible Commensal Non/unknown Pathogen In 92% of Europeans (unseenbio.com). human faeces Lagier2016, Byrd2020, Vachida2019, Minerbi2019 Bacteroidetes Bacteroidia Rikenellaceae neg SANA Sessile Rod No spore 57.9
Alistipes indistinctus Moderate Known Commensal Non/unknown Pathogen human faeces Nielsen2014, RajilicStojanovic2014, Lagier2016, Rothschild2018, Zou2019, Forster, Byrd2020, Yang2020, New2022, Chen2020, Dubinkina2017, Hu2019, Jeong2021, Jie2017, Vachida2019, Qin2012, Minerbi2019, Karlsson2013, PerezBrocal2015 Bacteroidetes Bacteroidia Rikenellaceae neg SANA Sessile Coccobacillus No spore 55.2 20(neg)
Alistipes inops Rare Possible Commensal Non/unknown Pathogen human faeces (Shkoporov2015) Forster2019, Yang2020 Bacteroidetes Bacteroidia Rikenellaceae neg SANA Sessile Rod No spore 56.6 20(neg)
Alistipes marseilloanorexicus Rare Possible Commensal Non/unknown Pathogen human faeces Pfleiderer2013, RajilicStojanovic2014 Bacteroidetes Bacteroidia Rikenellaceae neg SANA Sessile No spore
Alistipes massiliensis Rare Possible Commensal Non/unknown Pathogen human faeces Walker2011, Lagier2016, Minerbi2019, PerezBrocal2015 Bacteroidetes Bacteroidia Rikenellaceae neg No spore
Alistipes megaguti Rare Possible Commensal Non/unknown Pathogen human faeces (Bellali2019) New2022 Bacteroidetes Bacteroidia Rikenellaceae neg ANA Sessile Rod No spore 58.6
Alistipes montrealensis Unknown Rare Possible Commensal Non/unknown Pathogen human faeces (colitis/cancer patient) Bacteroidetes Bacteroidia Rikenellaceae neg SANA Sessile Rod No spore 57.2 R
Alistipes obesi Moderate Possible Commensal Non/unknown Pathogen In 97% of Europeans (unseenbio.com). human faeces (obese patient) RajilicStojanovic2014, Byrd2020, Jeong2021, Urban2020, Minerbi2019 Bacteroidetes Bacteroidia Rikenellaceae neg SANA Swimming Rod No spore 58.6
Alistipes onderdonkii 1 Opportunistic in immunocompromised patients Moderate Possible Commensal Opportunistic Infection human faeces and clinical sources (blood, abdominal abscess - CCUG) Frank2007, Pfleiderer2013, RajilicStojanovic2014, Lagier2016, Rothschild2018, Zou2019, Forster, Byrd2020, Yang2020, New2022, Chen2020, Dubinkina2017, Hu2019, Jeong2021, Jie2017, Vachida2019, Urban2020, Minerbi2019 Bacteroidetes Bacteroidia Rikenellaceae neg SANA Sessile Rod No spore 58 20(+)
Alistipes onderdonkii subsp. vulgaris Rare Possible Commensal Opportunistic Infection human faeces and clinical sources (abdominal abscess) Bacteroidetes Bacteroidia Rikenellaceae neg SANA Sessile Rod No spore 58 20(+)
Alistipes provencensis Rare Possible Commensal Non/unknown Pathogen human faeces (Bilen2018e) Lagier2016 Bacteroidetes Bacteroidia Rikenellaceae neg ANA Sessile Coccobacillus No spore 58.3
Alistipes putredinis Bacteroides putredinis 2 Human and animal pathogen Widespread Known Commensal Opportunistic Pathogen human faeces and clinical sources (appendicitis, abscess, blood) Finegold1974, Finegold1977, Benno1989, Mangin2004, Walker2011, Zupancic2012, Tyakht2013, Nielsen2014, RajilicStojanovic2014, Lagier2016, Rothschild2018, Forster2019, Byrd2020, Yang2020, Chen2020, Dubinkina2017, Hu2019, Jeong2021, Jie2017, Zeller2014, Wang2018, Vachida2019, Wang2020a, Urban2020, Minerbi2019, Karlsson2013 Bacteroidetes Bacteroidia Rikenellaceae neg SANA Sessile Rod No spore 53.3 20(neg)
Alistipes senegalensis Moderate Known Commensal Non/unknown Pathogen In 97% of Europeans (unseenbio.com). human faeces RajilicStojanovic2014, Lagier2016, Rothschild2018, Forster2019, Byrd2020, Chen2020, Hu2019, Vachida2019, Minerbi2019 Bacteroidetes Bacteroidia Rikenellaceae neg SANA Sessile Rod No spore
Alistipes shahii Positive 1 Opportunistic in immunocompromised patients Widespread Known Commensal Rare Opportunist human faeces and clinical specimens (appendix, urine) Tyakht2013, RajilicStojanovic2014, Lagier2016, Rothschild2018, Zou2019, Chung2019, Forster, King2019, Byrd2020, Yang2020, New2022, Chen2020, Dubinkina2017, Hu2019, Jeong2021, Jie2017, Zeller2014, Wang2018, Vachida2019, Wang2020a, Urban2020, Minerbi2019, Karlsson2013 Bacteroidetes Bacteroidia Rikenellaceae neg SANA Sessile Rod No spore 57.6 20(+)
Alistipes timonensis Moderate Known Commensal Non/unknown Pathogen In 89% of Europeans (unseenbio.com). human faeces RajilicStojanovic2014, Lagier2016, Forster2019, Byrd2020, Minerbi2019 Bacteroidetes Bacteroidia Rikenellaceae neg SANA Sessile Rod No spore 58.82 20(+)
Alkalibacillus halophilus Unlikely Transient Non/unknown Pathogen Requires high salt (min 5%) and can grow in 30% salt, so unlikely gut coloniser. hypersaline soil in China Lagier2016 Firmicutes Bacilli Bacillaceae + Swimming Rod Endospore 39
Alkalihalobacillus alcalophilus Bacillus alcalophilus 1 Unlikely Transient Non/unknown Pathogen No growth at pH7 so unlikely to be a gut coloniser. human faeces (Attie2014) and lake sediment Lagier2016 Firmicutes Bacilli Bacillaceae + AER Swimming Rod Endospore 36.2–38.4
Alkalihalobacillus gibsonii Bacillus gibsonii 1 Rare Possible Commensal Non/unknown Pathogen Tolerates up to 9% salt. soil Lagier2016 Firmicutes Bacilli Bacillaceae + AER Short Rod Endospore 41.1
Alkalihalobacillus halodurans Bacillus halodurans 1 Rare Possible Commensal Non/unknown Pathogen human faeces and soil Tyakht2013, RajilicStojanovic2014, Lagier2016 Firmicutes Bacilli Bacillaceae + AER Swimming Rod Endospore 43.2
Alkalihalobacillus oshimensis Bacillus oshimensis 1 Unlikely Transient Non/unknown Pathogen Assumed to utilise glucose. Requires sodium for growth. High salt required for optimum growth, so unlikely gut coloniser. soil from Japan Lagier2016 Firmicutes Bacilli Bacillaceae + AER Sessile Rod Endospore 40.8
Alkaliphilus metalliredigens Rare Possible Commensal Non/unknown Pathogen Can grow in the presence of 10mM sodium borate. Yeast can be used as an electron donor and Fe(III), Co(III) or Cr(VI) as electron acceptors. borate-enriched leachate ponds, USA New2022 Firmicutes Clostridia Clostridiaceae + SANA Swimming Rod Endospore
Alkaliphilus oremlandii Non Transient Non/unknown Pathogen Able to reduce As(V) and thiosulfate (electron acceptors). No growth at or below pH 7.5 suggests it is not a gut coloniser polluted river sediments, USA Firmicutes Clostridia Clostridiaceae + SANA Swimming Rod Endospore 36.1
Alkaliphilus transvaalensis 1 Non Transient Non/unknown Pathogen Requires high pH (minimum 8.5) suggest it is not a gut coloniser an ultra-deep gold mine under extreme alkaline conditions PerezBrocal2015 Firmicutes Clostridia Clostridiaceae + SANA Swimming Rod - curved Endospore 36.4
Alkanindiges illinoisensis 1 Non Transient Rare Opportunist Only hydrocarbons and Tween surfactants support good growth. Able to degrade squalene. crude oil-contaminated soil Lagier2016 Proteobacteria Gammaproteobacteria Moraxellaceae vr AER Sessile Coccus No spore
Allisonella histaminiformans 1 Opportunistic in immunocompromised patients Minor Possible Commensal Opportunistic Pathogen human faeces, and cow rumen McLaughlin2010, RajilicStojanovic2014, Lagier2016, Zou2019, Byrd2020, De2020, Minerbi2019 Firmicutes Negativicutes Veillonellaceae neg FANA Sessile Oval-shaped No spore 46.8
Allobaculum fili Unknown Rare Possible Commensal Possible Pathogen human faeces (UC patient) Firmicutes Erysipelotrichales Erysipelotrichaceae + SANA Sessile Rod 50.5
Allobaculum mucilyticum Unknown Rare Possible Commensal Possible Pathogen Mucin-degrading bacterium human faeces (UC patient) Firmicutes Erysipelotrichales Erysipelotrichaceae + SANA Sessile Rod 48.6
Alloprevotella rava Prevotella sp. oral taxon 302 Rare Possible Commensal Non/unknown Pathogen Probably an oral commensal that passes through the GI tract. oral cavity Byrd2020, De2020, Vachida2019 Bacteroidetes Bacteroidia Prevotellaceae neg SANA Sessile Rod No spore 47 20(neg)
Alloprevotella tannerae Prevotella tannerae 2 Minor Possible Commensal Opportunistic Pathogen human faeces and gingival crevices MacFarlane2004, Woodmansey2004, Walker2011, RajilicStojanovic2014, Salonen2014, Lagier2016, Byrd2020, De2020, Zeller2014, Vachida2019, Li2019b Bacteroidetes Bacteroidia Prevotellaceae neg ANA Sessile Rod No spore 46.6
Alloscardovia omnicolens Bifidobacterium urinalis 2 Minor Possible Commensal Opportunistic Infection In 32% of Europeans (unseenbio.com). Minor coloniser. human faeces and clinical sources (blood, urine, cervix - CCUG) Lagier2016, Almeida2019, Forster2019, Byrd2020, Hu2019, Vachida2019 Actinobacteria Actinomycetia Bifidobacteriaceae + FANA Sessile Rod No spore 47-48
Alteracholeplasma palmae Acholeplasma palmae 1 Rare Possible Commensal Non/unknown Pathogen Cholesterol or serum is not required for growth. plant surfaces Byrd2020, New2022 Tenericutes Mollicutes Acholeplasmataceae unk FANA Sessile Coccus No spore 30.0
Alterileibacterium massiliense Ileibacterium massiliense Rare Possible Commensal Non/unknown Pathogen human faeces (Crohn's) Firmicutes Clostridia Eubacteriales Family XIII. Incertae Sedis neg SANA Sessile Rod No spore 35.9
Amaricoccus kaplicensis 1 Unlikely Transient Non/unknown Pathogen Borderline cold mesophile, so unlikely to be a gut coloniser. human faeces RajilicStojanovic2014 Proteobacteria Alphaproteobacteria Rhodobacteraceae neg AER Sessile Coccus No spore 56
Amedibacillus dolichus Eubacterium dolichum 1 Minor Possible Commensal Non/unknown Pathogen human faeces (Ikeyama2020) Woodmansey2004, Yang2020, Dubinkina2017, Hu2019, Jeong2021, Zeller2014, Vachida2019, Wang2020a, PerezBrocal2015 Firmicutes Erysipelotrichia Erysipelotrichales + SANA Sessile Rod No spore 38.1 20(+)
Amedibacterium intestinale Rare Possible Commensal Non/unknown Pathogen human faeces (Ikeyama2020) New2022 Firmicutes Erysipelotrichia Erysipelotrichaceae + SANA Sessile Rod No spore 33.9 20(+)
Aminipila butyrica Rare Possible Commensal Non/unknown Pathogen Doesn't utilise carbohydrates. a methanogenic reactor treating cattle waste, Japan New2022 Firmicutes Clostridia Eubacteriales Family XIII. Incertae Sedis + SANA Swimming Rod No spore 44.7
Aminipila terrae Rare Possible Commensal Non/unknown Pathogen Fermentation products from glucose are glycolic and glyceric acids. the Geum river sediment, Korea New2022 Firmicutes Clostridia Eubacteriales Family XIII. Incertae Sedis + SANA Rod 37.0
Aminomonas paucivorans 1 Rare Possible Commensal Non/unknown Pathogen Asaccharolytic but yeast extract is required for growth. a dairy wastewater treatment plant, Colombia New2022, Zeller2014 Synergistetes Synergistia Synergistaceae neg SANA Sessile Rod - curved No spore 43
Ammonifex degensii 1 Non Transient Non/unknown Pathogen Cannot grow when temperatures drop below 57C, so likely not a gut coloniser. a solfataric spring, Indonesia New2022 Firmicutes Clostridia Thermoanaerobacteraceae neg SANA Swimming Rod No spore 54
Amycolatopsis alba 1 Rare Possible Commensal Non/unknown Pathogen Produces a new glycopeptide antibiotic related to vancomycin. soil Byrd2020 Actinobacteria Actinobacteria Pseudonocardiaceae + AER Sessile Filamentous Exospore
Amycolatopsis mediterranei 1 Rare Possible Commensal Non/unknown Pathogen soil Zeller2014 Actinobacteria Actinomycetia Pseudonocardiaceae + AER Sessile Filamentous Exospore 67-69
Amycolatopsis thailandensis Rare Possible Commensal Non/unknown Pathogen soil, Thailand Byrd2020 Actinobacteria Actinobacteria Pseudonocardiaceae + AER Sessile Filamentous Exospore 67
Amycolatopsis vancoresmycina 1 Unlikely Transient Non/unknown Pathogen The metabolites Vancoresmycin and Homorifamycin are produced. soil, India Byrd2020 Actinobacteria Actinobacteria Pseudonocardiaceae + AER Sessile Filamentous
Anaerobiospirillum succiniciproducens 2 human and animal pathogen Rare Possible Commensal Rare Opportunist human faeces, clinical sources (blood - CCUG) and animals Zupancic2012, RajilicStojanovic2014, Lagier2016, Byrd2020 Proteobacteria Gammaproteobacteria Succinivibrionaceae neg SANA Swimming Spirochete No spore 44
Anaerobiospirillum thomasii 2 Human and animal pathogen Rare Possible Commensal Opportunistic Pathogen human faeces (CCUG, diarrhoea) and animals RajilicStojanovic2014, Lagier2016 Proteobacteria Gammaproteobacteria Succinivibrionaceae neg SANA Swimming Spirochete No spore 39-42
Anaerobutyricum hallii Eubacterium hallii Positive 1 Widespread Known Commensal Non/unknown Pathogen human faeces Moore1974, Holdeman1976, Finegold1977, Walker2011, deGoffau2013, Tyakht2013, Nielsen2014, RajilicStojanovic2014, Salonen2014, Browne2016, Lagier2016, Rothschild2018, Zou2019, Byrd2020, Yang2020, New2022, Chen2020, Dubinkina2017, Hu2019, Jeong2021, Jie2017, Zeller2014, Wang2018, Vachida2019, Wang2020a, Qin2012, Karlsson2013 Firmicutes Clostridia Eubacteriaceae + SANA Sessile Rod Endospore 38
Anaerobutyricum soehngenii Rare Possible Commensal Non/unknown Pathogen human faeces (infant - Shetty2018) Firmicutes Clostridia Lachnospiraceae + SANA Sessile Rod 38.6
Anaerococcus hydrogenalis Peptostreptococcus hydrogenalis 1 Opportunistic in immunocompromised patients Rare Possible Commensal Opportunistic Pathogen human faeces and clinical sources (vaginal discharges, ovarian abscesses and atherosclerotic plaques) Tyakht2013, RajilicStojanovic2014, Lagier2016, Forster2019, Zeller2014 Firmicutes Tissierellia Peptoniphilaceae + SANA Sessile Diplococci No spore 31
Anaerococcus jeddahensis Rare Known Commensal Non/unknown Pathogen human faeces (Dione2018) Lagier2016 Firmicutes Tissierellia Peptoniphilaceae + SANA Sessile Coccus No spore 29.8
Anaerococcus lactolyticus Peptostreptococcus lactolyticus 1 Opportunistic in immunocompromised patients Rare Possible Commensal Opportunistic Pathogen vaginal discharges and ovarian abscesses Zeller2014, Vachida2019 Firmicutes Tissierellia Peptoniphilaceae + SANA Sessile Coccus No spore 30-34
Anaerococcus marasmi Rare Known Commensal Possible Pathogen human faeces (child with marasmus - Tall2020) Firmicutes Tissierellia Peptoniphilaceae + SANA Sessile Coccus No spore 35.4
Anaerococcus mediterraneensis Rare Possible Commensal Possible Pathogen a woman with bacterial vaginosis New2022 Firmicutes Tissierellia Peptoniphilaceae + ANA Rod
Anaerococcus murdochii Rare Transient Opportunistic Pathogen human faeces (probably transient) and clinical sources (ulcer) Lagier2016, Yang2020 Firmicutes Tissierellia Peptoniphilaceae + SANA Sessile Coccus No spore
Anaerococcus obesiensis Rare Known Commensal Non/unknown Pathogen human faeces RajilicStojanovic2014, Lagier2016, Byrd2020, New2022, Vachida2019 Firmicutes Tissierellia Peptoniphilaceae + SANA Sessile Coccus No spore
Anaerococcus octavius Peptostreptococcus octavius 1 Opportunistic in immunocompromised patients Rare Possible Commensal Opportunistic Infection human faeces and clinical specimens (nasal, vagina, blood, skin) Dubourg2013, Aujoulat2014, RajilicStojanovic2014, Lagier2016, De2020, Yang2020 Firmicutes Tissierellia Peptoniphilaceae + SANA Sessile Streptococci No spore 26-31
Anaerococcus prevotii Peptostreptococcus prevotii 2 Minor Possible Commensal Opportunistic Pathogen human faeces, vagina and clinical sources (abscesses) Finegold1974, Finegold1977, Benno1989, MacFarlane2004, RajilicStojanovic2014, Lagier2016, Almeida2019, Forster2019, King2019, De2020, Yang2020, New2022, Zeller2014 Firmicutes Tissierellia Peptoniphilaceae + SANA Sessile Diplococci No spore 29-33
Anaerococcus provencensis Anaerococcus provenciensis Rare Possible Commensal Non/unknown Pathogen human faeces (Lagier2016) Lagier2016 Firmicutes Tissierellia Peptoniphilaceae + SANA Sessile Coccus No spore
Anaerococcus rubeinfantis Rare Possible Commensal Possible Pathogen human faeces (infant suffering from kwashiorkor - Alou2016) Lagier2016 Firmicutes Tissierellia Peptoniphilaceae + SANA Sessile Coccus No spore 29.5
Anaerococcus senegalensis Rare Known Commensal Non/unknown Pathogen human faeces and vagina RajilicStojanovic2014, Lagier2016, Forster2019 Firmicutes Tissierellia Peptoniphilaceae + SANA Sessile Diplococci No spore 28.6
Anaerococcus tetradius Peptostreptococcus tetradius 1 Opportunistic in immunocompromised patients Rare Possible Commensal Opportunistic Pathogen vaginal discharges and ovarian abscesses Vachida2019 Firmicutes Tissierellia Peptoniphilaceae + SANA Sessile Tetrad No spore 30-32
Anaerococcus vaginalis Peptostreptococcus vaginalis 2 Minor Possible Commensal Opportunistic Pathogen human faeces, vaginal discharges and ovarian abscesses Mangin2004, RajilicStojanovic2014, Lagier2016, Byrd2020, Yang2020, New2022, Dubinkina2017, Hu2019, Jie2017, Zeller2014, Vachida2019 Firmicutes Tissierellia Peptoniphilaceae + SANA Sessile Streptococci No spore 30-34
Anaerocolumna aminovalerica Clostridium aminovalericum 1 Rare Known Commensal Non/unknown Pathogen human faeces, calf rumen, sewage sludge, urine and animal faeces Finegold1974, Finegold1977, Benno1989, RajilicStojanovic2014, Lagier2016, Byrd2020 Firmicutes Clostridia Clostridiaceae + SANA Swimming Rod Endospore 33 20(neg)
Anaerocolumna cellulosilytica Rare Possible Commensal Non/unknown Pathogen Slightly alkaliphilic. a methanogenic reactor New2022 Firmicutes Clostridia Clostridiaceae + SANA Swimming Rod Endospore 38.1
Anaerocolumna chitinilytica Rare Possible Commensal Non/unknown Pathogen soil, Japan New2022 Firmicutes Clostridia Clostridiaceae + SANA Swimming Short Rod Endospore 38.3
Anaerocolumna sedimenticola Rare Possible Commensal Non/unknown Pathogen the sediment of the Geum River, Korea New2022 Firmicutes Clostridia Clostridiaceae + SANA Swimming Rod - curved Endospore 36.7
Anaerocolumna xylanovorans Clostridium xylanovorans 1 Rare Possible Commensal Non/unknown Pathogen deGoffau2013 Firmicutes Clostridia Clostridiaceae + SANA Swimming Rod Endospore 40
Anaerofilum pentosovorans 1 Rare Transient Non/unknown Pathogen human faeces, and a bioreactor RajilicStojanovic2014 Firmicutes Clostridia Oscillospiraceae + SANA Sessile Rod No spore 55
Anaerofustis stercorihominis 1 Minor Possible Commensal Non/unknown Pathogen human faeces (CCUG) Zupancic2012, Tyakht2013, RajilicStojanovic2014, Lagier2016, Zou2019, Forster2019, Byrd2020, Yang2020, Hu2019, Zeller2014, Vachida2019, Qin2012 Firmicutes Clostridia Eubacteriaceae + SANA Rod No spore 70 20(+)
Anaeroglobus geminatus 1 Opportunistic in immunocompromised patients Minor Known Commensal Opportunistic Pathogen In 18% of Europeans (unseenbio.com). Minor coloniser. gastrointestinal tract (Carlier2002), a wound (CCUG) and mouth Lagier2016, Chung2019, Byrd2020, Jeong2021, Vachida2019 Firmicutes Negativicutes Veillonellaceae neg SANA Sessile Coccus No spore 51.8
Anaeromassilibacillus senegalensis Rare Possible Commensal Non/unknown Pathogen human faeces (child with kwashiorkor) Lagier2016, Byrd2020 Firmicutes Clostridia Oscillospiraceae neg ANA Swimming Rod Endospore
Anaerorhabdus furcosa Bacteroides furcosus 2 Rare Known Commensal Opportunistic Pathogen human faeces Moore1974, Benno1989, RajilicStojanovic2014, Lagier2016, Byrd2020 Firmicutes Erysipelotrichia Erysipelotrichaceae neg SANA Sessile Rod No spore 34
Anaerosalibacter bizertensis Rare Possible Commensal Non/unknown Pathogen discarded motor oil and has been detected in human faeces (Bilen2018e) Lagier2016 Firmicutes Tissierellia Tissierellaceae + SANA Swimming Rod Endospore 31.1
Anaerosalibacter massiliensis Rare Possible Commensal Non/unknown Pathogen human faeces (Dione2016) Lagier2016 Firmicutes Tissierellia Tissierellaceae + SANA Swimming Rod Endospore 29.7
Anaerosphaera massiliensis Rare Known Commensal Non/unknown Pathogen human faeces (Takakura2019a) Firmicutes Tissierellia Peptoniphilaceae + SANA Coccus 28.1
Anaerospora hongkongensis Rare Possible Commensal Opportunistic Pathogen Relatively inert biochemically. clinical sources (bacteremia) Lagier2016 Firmicutes Negativicutes Sporomusaceae neg SANA Swimming Rod - curved Endospore 46.8
Anaerostipes butyraticus Rare Possible Commensal Non/unknown Pathogen human faeces RajilicStojanovic2014 Firmicutes Clostridia Lachnospiraceae + SANA Sessile Rod Endospore 44
Anaerostipes caccae 1 Moderate Known Commensal Possible Pathogen human faeces, and clinical sources (blood - CCUG) Tyakht2013, Nielsen2014, RajilicStojanovic2014, Salonen2014, Lagier2016, Zou2019, Forster2019, Byrd2020, Yang2020, New2022, Dubinkina2017, Hu2019, Zeller2014, Vachida2019, Wang2020a, Qin2012, Minerbi2019 Firmicutes Clostridia Lachnospiraceae + SANA Sessile Rod No spore 46
Anaerostipes coli Rare Possible Commensal Non/unknown Pathogen human faeces RajilicStojanovic2014, Lagier2016 Firmicutes Clostridia Lachnospiraceae + SANA Sessile Rod No spore
Anaerostipes hadrus Eubacterium hadrum Positive 1 Moderate Known Commensal Non/unknown Pathogen human faeces Frank2007, Nielsen2014, RajilicStojanovic2014, Browne2016, Chung2016, Lagier2016, Rothschild2018, Zou2019, Forster2019, King2019, Byrd2020, Yang2020, New2022, Chen2020, Dubinkina2017, Hu2019, Jeong2021, Jie2017, Vachida2019, Wang2020a, Minerbi2019 Firmicutes Clostridia Lachnospiraceae + SANA Sessile Rod No spore 32-33 20(+)
Anaerostipes hominis Rare Possible Commensal Non/unknown Pathogen From a patient with Crohn's disease. Produces butyrate, propionate, oxaloacetate and fumarate from fermentation. human faeces (Lee2021) Firmicutes Clostridia Lachnospiraceae vr SANA Rod Endospore 43.5 +
Anaerostipes rhamnosivorans Rare Possible Commensal Non/unknown Pathogen human gastrointestinal tract (Bui2014) Lagier2016, Yang2020, New2022 Firmicutes Clostridia Lachnospiraceae vr SANA Sessile Rod - curved Endospore 44.5
Anaerostipes rhamnosus Rare Possible Commensal Non/unknown Pathogen human faeces RajilicStojanovic2014 Firmicutes Clostridia Lachnospiraceae + SANA Sessile Rod No spore
Anaerotignum faecicola Rare Possible Commensal Non/unknown Pathogen human faeces (Choi2019) Firmicutes Clostridia Clostridiaceae + SANA Sessile Rod No spore 47.3
Anaerotignum lactatifermentans Clostridium lactatifermentans 1 Moderate Possible Commensal Non/unknown Pathogen In 95% of Europeans (unseenbio.com). human faeces, and caeca of a chicken McLaughlin2010, Walker2011, RajilicStojanovic2014, Lagier2016, Byrd2020, Yang2020, Jeong2021, Minerbi2019 Firmicutes Clostridia Lachnospiraceae neg SANA Sessile Rod No spore 44.6
Anaerotignum neopropionicum Clostridium neopropionicum 1 Rare Possible Commensal Non/unknown Pathogen anoxic digester sludge Byrd2020 Firmicutes Clostridia Lachnospiraceae neg SANA Swimming Rod Endospore 34.5
Anaerotignum propionicum Clostridium propionicum 1 Rare Possible Commensal Non/unknown Pathogen black mud. KS24 - a closely related bacterium (S16 94%) - was detected in human faeces (probably transient) Lagier2016, New2022 Firmicutes Clostridia Lachnospiraceae + SANA Swimming Rod Endospore 36
Anaerotruncus colihominis 1 Moderate Known Commensal Opportunistic Pathogen human faeces and clinical sources (blood, abdominal fluid - CCUG) Walker2011, Zupancic2012, Tyakht2013, RajilicStojanovic2014, Salonen2014, Browne2016, Lagier2016, Rothschild2018, Zou2019, Forster2019, Byrd2020, Yang2020, Chen2020, Dubinkina2017, Hu2019, Jie2017, Zeller2014, Wang2018, Vachida2019, Urban2020, Qin2012, Minerbi2019 Firmicutes Clostridia Oscillospiraceae + SANA Sessile Rod Endospore 54
Anaerotruncus massiliensis Anaerotruncus massiliense Rare Possible Commensal Non/unknown Pathogen Succinate-producer. human faeces (obese patient - Togo2019) Lagier2016, Byrd2020 Firmicutes Clostridia Oscillospiraceae neg ANA Sessile Rod
Anaerotruncus rubiinfantis Moderate Possible Commensal Non/unknown Pathogen In 75% of Europeans (unseenbio.com). human faeces (girl with kwashiorkor - Bilen2018e) Lagier2016, Byrd2020, Minerbi2019 Firmicutes Clostridia Oscillospiraceae + ANA Rod
Anaerovorax odorimutans 1 Rare Transient Non/unknown Pathogen anoxic brackish water sediment; has been detected in human faeces Salonen2014 Firmicutes Clostridia Eubacteriales Family XIII. Incertae Sedis vr SANA Rod - curved No spore 29.6
Ancylobacter polymorphus 1 Rare Possible Commensal Non/unknown Pathogen river mud and human faeces RajilicStojanovic2014, Lagier2016 Proteobacteria Alphaproteobacteria Xanthobacteraceae neg AER Sessile Rod - curved No spore 65.5
Aneurinibacillus aneurinilyticus Bacillus aneurinilyticus 1 Rare Known Commensal Non/unknown Pathogen human faeces RajilicStojanovic2014, Lagier2016, Forster2019 Firmicutes Bacilli Paenibacillaceae + SAER Swimming Rod Endospore 42.9
Aneurinibacillus migulanus Bacillus migulanus 1 Rare Known Commensal Non/unknown Pathogen human faeces and garden soil RajilicStojanovic2014, Lagier2016 Firmicutes Bacilli Paenibacillaceae + SAER Swimming Rod Endospore 42.5
Angelakisella massiliensis Rare Possible Commensal Non/unknown Pathogen the ileum of an elderly woman Byrd2020, De2020 Firmicutes Clostridia Oscillospiraceae neg ANA Swimming Rod No spore
Anoxybacillus flavithermus Bacillus flavothermus 1 Non Transient Non/unknown Pathogen Weak growth at 37 degrees so unlikely to be a gut coloniser. a New Zealand hotsprings Lagier2016, Zeller2014 Firmicutes Bacilli Bacillaceae + FANA Swimming Rod Endospore 41.6
Anoxybacillus gonensis 1 Unlikely Transient Non/unknown Pathogen Weak growth at 37 degrees so unlikely to be a gut coloniser. Gonen hot springs, Turkey New2022 Firmicutes Bacilli Bacillaceae + FANA Swimming Rod Endospore 57
Anoxynatronum sibiricum 1 Rare Possible Commensal Non/unknown Pathogen human faeces, and saline carbonate lakes PerisBondia2011, RajilicStojanovic2014 Firmicutes Clostridia Clostridiaceae + ANA Swimming Rod - curved No spore 48.1-48.4
Anseongella ginsenosidimutans Unlikely Transient Non/unknown Pathogen Obligate aerobe; unlikely to be a gut coloniser. Pocheon city, Republic of Korea New2022 Bacteroidetes Sphingobacteriia Sphingobacteriaceae neg SAER Sessile Rod No spore 51.9
Aquabacterium citratiphilum 1 Rare Possible Commensal Non/unknown Pathogen drinking water and human faeces Aujoulat2014, Yang2020 Proteobacteria Betaproteobacteria Comamonadaceae neg Micr Swimming Rod No spore 66
Aquabacterium commune 1 Rare Possible Commensal Non/unknown Pathogen drinking water and human faeces Aujoulat2014, RajilicStojanovic2014 Proteobacteria Betaproteobacteria Comamonadaceae neg Micr Swimming Rod No spore 66
Aquabacterium parvum 1 Rare Possible Commensal Non/unknown Pathogen drinking water and human faeces Yang2020 Proteobacteria Betaproteobacteria Comamonadaceae neg Micr Swimming Rod No spore 65
Aquamicrobium lusatiense Defluvibacter lusatiae 1 Unlikely Transient Non/unknown Pathogen Mesophilic and strictly aerobic. Can degrade 2,4-dichlorophenol and 4-chlorophenol; unlikely to be a gut coloniser. activated sludge Lagier2016 Proteobacteria Alphaproteobacteria Phyllobacteriaceae neg SAER Swimming Rod No spore 61.4
Aquincola tertiaricarbonis 1 Non Transient Non/unknown Pathogen Degrades t-butanol, a breakdown product of MTBE. Obligate aerobe, so likely a gut non-coloniser. MTBE-contaminated water and human gastrointestinal tract (Wang2020) Yang2020 Proteobacteria Betaproteobacteria Burkholderiales genera incertae sedis neg SAER Pili Coccobacillus No spore 69-70.5
Arabia massiliensis Rare Possible Commensal Non/unknown Pathogen human faeces (Bilen2018e) Lagier2016, Byrd2020, New2022 Actinobacteria Coriobacteriia Eggerthellaceae neg SANA Swimming Rod No spore
Arachnia propionica Propionibacterium propionicum 2 Rare Possible Commensal Opportunistic Infection human faeces and clinical specimens (abscess, lachrymal duct, IUD device - CCUG) RajilicStojanovic2014, Lagier2016, New2022, Vachida2019 Actinobacteria Actinomycetia Propionibacteriaceae + ANA Rod No spore
Arcanobacterium haemolyticum Corynebacterium haemolyticum 2 Human and animal pathogen Rare Possible Commensal Opportunistic Pathogen human faeces and clinical sources (throat, blood, wound, abscess - CCUG) RajilicStojanovic2014, Lagier2016 Actinobacteria Actinomycetia Actinomycetaceae + FANA Sessile Rod No spore 50-52
Arthrobacter agilis Micrococcus agilis 1 Non Transient Non/unknown Pathogen Skin commensal but can't grow at 37C. Gut transient. soil, water and human skin Lagier2016 Actinobacteria Actinomycetia Micrococcaceae + AER Swimming Coccus No spore 67-69
Arthrobacter castelli 1 Rare Possible Commensal Non/unknown Pathogen human faeces Dubourg2013, Pfleiderer2013, RajilicStojanovic2014, Lagier2016 Actinobacteria Actinomycetia Micrococcaceae + AER Sessile Coccobacillus No spore 68.1
Arthrobacter citreus 1 Unlikely Transient Non/unknown Pathogen Obligate aerobe; unlikely to be a gut coloniser. chicken faeces New2022 Actinobacteria Actinomycetia Micrococcaceae vr SAER vr Rod No spore
Arthrobacter gandavensis 2 Animal pathogen Unlikely Transient Opportunistic Pathogen Obligate aerobe; unlikely to be a gut coloniser. cattle infections Lagier2016 Actinobacteria Actinomycetia Micrococcaceae + SAER Swimming Coccobacillus No spore 65
Arthrobacter globiformis 1 Unlikely Possible Commensal Non/unknown Pathogen Nonpathogenic and has been used in foods and bioremediation. Generally requires biotin for growth. soil Byrd2020, Yang2020 Actinobacteria Actinomycetia Micrococcaceae + FANA Sessile Rod-coccus cycle No spore 62.0-65.5
Arthrobacter koreensis 1 Unlikely Transient Non/unknown Pathogen Obligate aerobe; unlikely to be a gut coloniser. soil from Korea Lagier2016 Actinobacteria Actinomycetia Micrococcaceae + SAER Swimming Coccus No spore 63
Arthrobacter luteolus 2 Unlikely Transient Opportunistic Infection Strict aerobe, so unlikely to be a gut coloniser. an infected surgical wound Lagier2016 Actinobacteria Actinomycetia Micrococcaceae + SAER Swimming No spore
Arthrobacter parietis 1 Non Transient Non/unknown Pathogen Doesn't grow well at 37C, so probably a gut transient organism. a Roman tomb painting Lagier2016 Actinobacteria Actinomycetia Micrococcaceae + AER Sessile No spore 63.8
Arthrobacter pigmenti 1 Non Transient Non/unknown Pathogen Doesn't grow well at 37C, so probably a gut non-coloniser. a Roman tomb painting Lagier2016 Actinobacteria Actinomycetia Micrococcaceae + AER Sessile No spore 61.2
Arthrobacter russicus 1 Unlikely Transient Non/unknown Pathogen Can't grow at 37C, so unlikely to be a gut coloniser. human faeces and space station air samples Yang2020 Actinobacteria Actinomycetia Micrococcaceae + AER Sessile Rod No spore 65.5
Asaccharospora irregularis Clostridium irregulare Rare Known Commensal Opportunistic Pathogen human faeces, lesions, soil and horses Finegold1974, PerisBondia2011, RajilicStojanovic2014, Lagier2016, Byrd2020 Firmicutes Clostridia Clostridiaceae + ANA Swimming Rod Endospore 20(neg)
Asticcacaulis biprosthecium 1 Unlikely Transient Non/unknown Pathogen Obligate aerobe; unlikely to be a gut coloniser. pond water Frank2007 Proteobacteria Alphaproteobacteria Caulobacteraceae neg SAER Swimming Rod No spore 61
Asticcacaulis excentricus 1 Unlikely Transient Non/unknown Pathogen a freshwater pond, USA New2022 Proteobacteria Alphaproteobacteria Caulobacteraceae neg AER Swimming Rod No spore 55-60
Atlantibacter hermannii Escherichia hermannii 2 Rare Possible Commensal Rare Opportunist human faeces (CCUG), clinical sources (urine, infection - CCUG) and wastewater treatment Pfleiderer2013, RajilicStojanovic2014, Lagier2016, Byrd2020, Dubinkina2017, Vachida2019 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Swimming Rod No spore 53-58
Atopobium minutum Lactobacillus minutus 2 Minor Transient Opportunistic Pathogen human faeces and clinical sources (blood, abscess - CCUG) Moore1974, Finegold1974, Finegold1977, RajilicStojanovic2014, Lagier2016, Byrd2020, Vachida2019 Actinobacteria Coriobacteriia Atopobiaceae + SANA Sessile Rod No spore 44 neg
Atopostipes suicloacalis Atopostipes suicloacale 1 Unlikely Transient Non/unknown Pathogen No growth at 33C, so not likely to be a gut coloniser. pig manure slurry Cassir2015 Firmicutes Bacilli Carnobacteriaceae + FANA Sessile Short Rod No spore 43.9
Aureimonas altamirensis Aurantimonas altamirensis 1 Unlikely Transient Rare Opportunist Borderline cold mesophile, with optimum growth temp of 28C. Unlikely gut coloniser. human faeces and clinical sources (blood, infection, vagina - CCUG) McLaughlin2010, RajilicStojanovic2014 Proteobacteria Alphaproteobacteria Aurantimonadaceae neg SAER Sessile Rod No spore 71.8
Aureimonas ureilytica Aurantimonas ureilytica 1 Unlikely Transient Non/unknown Pathogen Obligate aerobe; unlikely to be a gut coloniser. human faeces and air samples Yang2020 Proteobacteria Alphaproteobacteria Aurantimonadaceae neg SAER Swimming Rod No spore 67
Averyella dalhousiensis Rare Possible Commensal Rare Opportunist human faeces (Alkhalil2017), and wounds RajilicStojanovic2014, Lagier2016 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Swimming Rod No spore
Azoarcus pumilus Rare Possible Commensal Non/unknown Pathogen seawater in Sanya, China New2022 Proteobacteria Betaproteobacteria Rhodocyclaceae neg FANA Swimming Rod No spore 66.5
Azospirillum lipoferum 1 Rare Possible Commensal Non/unknown Pathogen roots of cereal crops New2022, Zeller2014 Proteobacteria Alphaproteobacteria Azospirillaceae neg FANA Swimming Pleiomorph rod No spore 69-70 1(+)
Azotobacter vinelandii 1 Non Transient Non/unknown Pathogen Obligate aerobe and low optimum temperature suggest it is not a gut coloniser. soil Zeller2014 Proteobacteria Gammaproteobacteria Pseudomonadaceae neg SAER Oval-shaped No spore
Bacilliculturomica massiliensis Rare Possible Commensal Non/unknown Pathogen human faeces (Traore2017a) Firmicutes Clostridia Eubacteriales Family XIII. Incertae Sedis + SANA Sessile Rod No spore
Bacillus altitudinis 1 Rare Possible Commensal Non/unknown Pathogen human faeces, and high altitudes RajilicStojanovic2014, Lagier2016, Yang2020 Firmicutes Bacilli Bacillaceae + AER Swimming Rod 43
Bacillus amyloliquefaciens Positive 1 Rare Known Commensal Non/unknown Pathogen human faeces, soil and industrial fermentation RajilicStojanovic2014, Lagier2016 Firmicutes Bacilli Bacillaceae + SAER Swimming Rod Endospore 44.6
Bacillus andreraoultii Rare Possible Commensal Non/unknown Pathogen the faeces of a boy with kwashiorkor Lagier2016 Firmicutes Bacilli Bacillaceae + FANA Swimming Rod Endospore 35.4
Bacillus aneurinolyticus Aneurinibacillus aneurinilyticus 1 Rare Possible Commensal Non/unknown Pathogen Obligate aerobe, but produces spores. human faeces (Aoyama1952) Firmicutes Bacilli Bacillaceae + SAER Swimming Rod Endospore 41.1-43.4
Bacillus anthracis 3 Zoonotic pathogen Non Transient Dangerous Pathogen Causative agent of the disease anthrax. blood, carcasses, soil and animal products Zou2019 Firmicutes Bacilli Bacillaceae + FANA Sessile Short Rod Endospore 32.2-33.9
Bacillus atrophaeus Positive 1 Opportunistic in immunocompromised patients Rare Known Commensal Opportunistic Infection human faeces and soil RajilicStojanovic2014, Lagier2016 Firmicutes Bacilli Bacillaceae + AER Swimming Rod Endospore
Bacillus badius DSM 23T Bacillus badius Positive 1 Rare Known Commensal Non/unknown Pathogen human faeces, food, marine sources, and dust Pfleiderer2013, RajilicStojanovic2014, Lagier2016 Firmicutes Bacilli Bacillaceae + AER Swimming Rod Endospore 43.9
Bacillus badius DSM 5610 Bacillus badius Positive 1 Rare Known Commensal Non/unknown Pathogen human faeces, food, marine sources, and dust Pfleiderer2013, RajilicStojanovic2014, Lagier2016 Firmicutes Bacilli Bacillaceae + AER Swimming Rod Endospore 43.6
Bacillus baekryungensis Bacillus genomospecies SW-93 Non Unknown Non/unknown Pathogen Requires sodium and can withstand 20% salt concentration. seawater from Korea Lagier2016 Firmicutes Bacilli Bacillaceae + AER Swimming Rod Endospore 41.0
Bacillus benzoevorans Positive 1 Rare Known Commensal Non/unknown Pathogen human faeces, clinical sources (blood - CCUG) and soil RajilicStojanovic2014, Lagier2016 Firmicutes Bacilli Bacillaceae + FANA Swimming Rod Endospore 41.3
Bacillus caccae Rare Possible Commensal Non/unknown Pathogen human faeces (Pham2017, Lo2021) Firmicutes Bacilli Bacillaceae + AER Rod
Bacillus cereus Negative 2 Toxin produced Minor Known Commensal Known Pathogen human faeces, clinical sources (blood, wound - CCUG), food and environment Pfleiderer2013, Aujoulat2014, RajilicStojanovic2014, Lagier2016, Zou2019, Byrd2020, Yang2020, New2022, Zeller2014 Firmicutes Bacilli Bacillaceae + FANA Swimming Rod Endospore 35
Bacillus circulans 1 Opportunistic in immunocompromised patients Rare Known Commensal Opportunistic Infection human faeces, clinical sources (blood, pleura - CCUG), soil, sewage, food and infant bile Taylor1985, Pfleiderer2013, RajilicStojanovic2014, Lagier2016, Byrd2020 Firmicutes Bacilli Bacillaceae + FANA Swimming Rod Endospore 37-41
Bacillus clausii Positive 1 Rare Known Commensal Non/unknown Pathogen May be able to persist in the gut, albeit in low numbers, by residing in niches close to epithelial cells (Ilinskaya2017). human faeces, and is used as a probiotic. Also from soil and clay Hoyles2012, Dubourg2013, Pfleiderer2013, RajilicStojanovic2014, Lagier2016, Zeller2014 Firmicutes Bacilli Bacillaceae + AER Rod Endospore 42.8-45.5
Bacillus cytotoxicus Negative Rare Possible Commensal Known Pathogen diarrhoea as a result of food poisoning (Guinebretiere2013) King2019, Zeller2014 Firmicutes Bacilli Bacillaceae + FANA Swimming Rod Endospore 35.8
Bacillus dakarensis Rare Possible Commensal Non/unknown Pathogen human faeces (CCUG, Sarr2020) Firmicutes Bacilli Bacillaceae + AER Swimming Rod Endospore 38.6
Bacillus endophyticus Positive 1 Unlikely Transient Non/unknown Pathogen Borderline cold mesophile, with optimum growth temp of 28C. Unlikely gut coloniser. plants and human faeces RajilicStojanovic2014, Lagier2016 Firmicutes Bacilli Bacillaceae + SAER Sessile Rod Endospore
Bacillus firmus Positive 1 Rare Known Commensal Non/unknown Pathogen human faeces, clinical sources (blood - CCUG), soil and the environment RajilicStojanovic2014, Lagier2016 Firmicutes Bacilli Bacillaceae + FANA Swimming Rod Endospore 40.7-41.4
Bacillus fordii Positive 1 Rare Known Commensal Non/unknown Pathogen dairy and human faeces Hoyles2012, RajilicStojanovic2014, Lagier2016 Firmicutes Bacilli Bacillaceae neg SAER Swimming Rod Endospore 41.9
Bacillus halotolerans Brevibacterium halotolerans 1 Rare Possible Commensal Non/unknown Pathogen human faeces and river sediment RajilicStojanovic2014, Lagier2016 Firmicutes Bacilli Bacillaceae + AER Swimming Rod Endospore 41.0
Bacillus idriensis Rare Possible Commensal Opportunistic Pathogen human faeces, and clinical sources (sepsis) RajilicStojanovic2014, Lagier2016 Firmicutes Bacilli Bacillaceae + AER Rod Endospore 41.2
Bacillus infantis Rare Known Commensal Opportunistic Pathogen human faeces and clinical sources (sepsis) RajilicStojanovic2014, Lagier2016, Byrd2020, Yang2020 Firmicutes Bacilli Bacillaceae + AER Rod Endospore 40.8
Bacillus kwashiorkori Rare Possible Commensal Non/unknown Pathogen the faeces of a child with acute malnutrition Firmicutes Bacilli Bacillaceae + FANA Swimming Rod Endospore 35.2
Bacillus licheniformis Positive 1 Opportunistic in immunocompromised patients Minor Known Commensal Opportunistic Pathogen May be able to persist in the gut, albeit in low numbers, by residing in niches close to epithelial cells (Ilinskaya2017). Probiotic. human faeces, clinical sources (blood - CCUG), soil and other environments Frank2007, Hoyles2012, Pfleiderer2013, RajilicStojanovic2014, Lagier2016, Zou2019, Forster2019, Byrd2020, Zeller2014, Vachida2019 Firmicutes Bacilli Bacillaceae + FANA Swimming Rod Endospore 44.7-46.4
Bacillus marasmi Rare Possible Commensal Non/unknown Pathogen human faeces (child with marasmus - Pham2017a) Firmicutes Bacilli Bacillaceae + AER Rod Endospore 38.2
Bacillus massilioanorexius Bacillus marseilloanorexicus Rare Known Commensal Non/unknown Pathogen human faeces RajilicStojanovic2014, Lagier2016, Forster2019 Firmicutes Bacilli Bacillaceae + AER Swimming Rod No spore 34.1
Bacillus massiliogabonensis Unlikely Transient Non/unknown Pathogen Obligate aerobe; unlikely to be a gut coloniser. human faeces (CCUG, Sarr2020) Lagier2016 Firmicutes Bacilli Bacillaceae neg SAER Swimming Rod Endospore 37.9
Bacillus massilionigeriensis Rare Possible Commensal Non/unknown Pathogen faeces of a healthy child from Niger Lagier2016 Firmicutes Bacilli Bacillaceae + AER Swimming Fusiform No spore 36.7
Bacillus mediterraneensis Bacillus massilionigeriensis Rare Known Commensal Non/unknown Pathogen May be able to persist in the gut, albeit in low numbers, by residing in niches close to epithelial cells (Ilinskaya2017). the faeces (Cadoret2017) of a healthy child, Senegal Lagier2016 Firmicutes Bacilli Bacillaceae + AER Swimming Rod Endospore 42.3
Bacillus methanolicus 1 Non Transient Non/unknown Pathogen Obligate aerobe and high salt required for optimum growth, so likely a gut non-coloniser. soil, wastewater treatment systems and hotsprings King2019 Firmicutes Bacilli Bacillaceae + SAER Sessile Rod Endospore 48-50
Bacillus mojavensis Positive 1 Rare Known Commensal Non/unknown Pathogen desert soils and human faeces RajilicStojanovic2014, Lagier2016 Firmicutes Bacilli Bacillaceae + AER Swimming Rod Endospore 43
Bacillus mycoides Bacillus weihenstephanensis Positive 1 Rare Known Commensal Opportunistic Pathogen human faeces and soil RajilicStojanovic2014, Lagier2016, Zeller2014 Firmicutes Bacilli Bacillaceae + FANA Sessile Rod 34.8-35.6
Bacillus niameyensis Rare Possible Commensal Non/unknown Pathogen human faeces (Alou2015a) Lagier2016 Firmicutes Bacilli Bacillaceae + FANA Swimming Rod Endospore 37.40
Bacillus pakistanensis Rare Possible Commensal Non/unknown Pathogen salt mines in Pakistan Lagier2016 Firmicutes Bacilli Bacillaceae + AER Sessile Rod Endospore 39.1
Bacillus phocaeensis Rare Known Commensal Non/unknown Pathogen the faeces (CCUG) of a child with kwashiorkor, Senegal. Lagier2016 Firmicutes Bacilli Bacillaceae + FANA Swimming Fusiform Endospore 38.3
Bacillus pseudofirmus Positive 1 Rare Known Commensal Non/unknown Pathogen soil, animal and human faeces RajilicStojanovic2014, Lagier2016 Firmicutes Bacilli Bacillaceae + AER Rod Endospore 39.0-40.8
Bacillus pseudomycoides 1 Unlikely Transient Non/unknown Pathogen Borderline cold mesophile, with optimum growth temp of 28C. Unlikely gut coloniser. soil Lagier2016, Zou2019 Firmicutes Bacilli Bacillaceae + FANA Sessile Rod Endospore 34-36
Bacillus pumilus 1 Opportunistic in immunocompromised patients Rare Known Commensal Opportunistic Pathogen May be able to persist in the gut, albeit in low numbers, by residing in niches close to epithelial cells (Ilinskaya2017). human faeces, food, clinical sources (blood, wound - CCUG) and other environments Hoyles2012, Pfleiderer2013, RajilicStojanovic2014, Lagier2016, Zeller2014 Firmicutes Bacilli Bacillaceae + AER Swimming Rod Endospore 40.7-41.9
Bacillus rubiinfantis Rare Possible Commensal Non/unknown Pathogen human faeces (Alou2015) Lagier2016 Firmicutes Bacilli Bacillaceae + FANA Swimming Rod Endospore 40.0
Bacillus sinesaloumensis Unlikely Transient Non/unknown Pathogen High salt required for optimum growth, so unlikely gut coloniser. human faeces (CCUG, Sarr2020) Firmicutes Bacilli Bacillaceae + AER Swimming Pleiomorph rod Endospore 37.9
Bacillus siralis Positive 1 Rare Known Commensal Rare Opportunist silage, clinical sources (blood - CCUG) and human faeces RajilicStojanovic2014, Lagier2016 Firmicutes Bacilli Bacillaceae + SANA Rod Endospore
Bacillus smithii 1 Rare Possible Commensal Non/unknown Pathogen food and human faeces Lagier2016, Forster2019 Firmicutes Bacilli Bacillaceae + FANA Swimming Rod Endospore 38.7-39.7
Bacillus sonorensis Positive 1 Rare Known Commensal Non/unknown Pathogen human faeces and soil Hoyles2012, Pfleiderer2013, RajilicStojanovic2014, Lagier2016, Zou2019 Firmicutes Bacilli Bacillaceae + FANA Swimming Rod Endospore 46
Bacillus subtilis Positive 1 Opportunistic in immunocompromised patients Minor Known Commensal Rare Opportunist May be able to persist in the gut, albeit in low numbers, by residing in niches close to epithelial cells (Ilinskaya2017). human faeces (CCUG) and clinical sources (blood, wound - CCUG) Benno1984, Benno1986, Benno1989, Pfleiderer2013, RajilicStojanovic2014, Lagier2016, Forster2019, Byrd2020, Zeller2014, Vachida2019 Firmicutes Bacilli Bacillaceae + AER Swimming Rod Endospore 42.9-43.1
Bacillus testis Rare Possible Commensal Non/unknown Pathogen the faeces of a healthy boy from Senegal Lagier2016 Firmicutes Bacilli Bacillaceae + FANA Swimming Rod Unknown 42.8
Bacillus thuringiensis Positive 1 Opportunistic in immunocompromised patients, invertebrate pathogen Rare Known Commensal Opportunistic Infection May be able to persist in the gut, albeit in low numbers, by residing in niches close to epithelial cells (Ilinskaya2017). human faeces and soil. Is an invertebrate pathogen RajilicStojanovic2014, Cassir2015, Lagier2016, Forster2019, Byrd2020, Hu2019 Firmicutes Bacilli Bacillaceae + FANA Swimming Rod Endospore 33.8-34.3
Bacillus timonensis Positive Rare Known Commensal Non/unknown Pathogen human faeces RajilicStojanovic2014, Lagier2016, Forster2019, Byrd2020 Firmicutes Bacilli Bacillaceae neg AER Swimming Rod Endospore 37.3
Bacillus tuaregi Rare Known Commensal Non/unknown Pathogen the faeces (Cadoret2017) of a healthy child, Nigeria Firmicutes Bacilli Bacillaceae + AER Swimming Fusiform No spore 39.4
Bacillus vallismortis Positive 1 Rare Known Commensal Rare Opportunist desert soils, clinical sources (blood - CCUG) and human faeces Pfleiderer2013, RajilicStojanovic2014, Lagier2016 Firmicutes Bacilli Bacillaceae + AER Swimming Rod Endospore 43
Bacillus velezensis Variant polyfermenticus Bacillus polyfermenticus Rare Known Commensal Non/unknown Pathogen human faeces and river mouth Pfleiderer2013, RajilicStojanovic2014, Lagier2016, New2022 Firmicutes Bacilli Bacillaceae + AER Swimming Rod Endospore 46.4
Bacillus wiedmannii Rare Possible Commensal Possible Pathogen Psychrotolerant and cytotoxic. raw milk Zou2019 Firmicutes Bacilli Bacillaceae + FANA Swimming Rod Endospore 35.3
Bacteroides acidifaciens 1 Moderate Possible Commensal Non/unknown Pathogen In 100% of Europeans (unseenbio.com). mouse caeca and human faeces (Bilen2018e) Forster2019, De2020, Urban2020, Minerbi2019, Li2019b Bacteroidetes Bacteroidia Bacteroidaceae neg SANA Sessile Rod No spore 39.4-42.2 20(+)
Bacteroides bouchesdurhonensis Bacteroides bouchedurhonense Moderate Possible Commensal Non/unknown Pathogen In 96% of Europeans (unseenbio.com). Reported attributes are confusing and have been added to a limited extent. human faeces (healthy individual - Ndongo2017c) Lagier2016, Byrd2020 Bacteroidetes Bacteroidia Bacteroidaceae neg ANA Sessile Rod No spore 39.8
Bacteroides caccae 2 Widespread Known Commensal Opportunistic Pathogen human faeces (CCUG), vagina and infection Benno1989, Favier2002, MacFarlane2004, Woodmansey2004, McLaughlin2010, Walker2011, Pfleiderer2013, Tyakht2013, Nielsen2014, RajilicStojanovic2014, Browne2016, Chung2016, Lagier2016, Rothschild2018, Zou2019, Almeida2019, Chung2019, Forster2019, King2019, Byrd2020, Yang2020, New2022, Chen2020, Dubinkina2017, Hu2019, Jeong2021, Jie2017, Zeller2014, Wang2018, Vachida2019, Wang2020a, Urban2020, Minerbi2019, Moore1995, Li2019b, LeChatelier2013, Karlsson2013, PerezBrocal2015 Bacteroidetes Bacteroidia Bacteroidaceae neg ANA Sessile Rod No spore 40-42 20(+)
Bacteroides caecimuris Rare Possible Commensal Non/unknown Pathogen mouse intestine and detected in human faeces (Alkhalil2017) King2019, Byrd2020, New2022, Urban2020 Bacteroidetes Bacteroidia Bacteroidaceae neg ANA Sessile Rod No spore 42.6
Bacteroides cellulosilyticus Mixed 1 Moderate Known Commensal Rare Opportunist A common gut microbe and one that digests cellulose. human faeces (CCUG) and clinical sources (blood - CCUG) Pfleiderer2013, Tyakht2013, Nielsen2014, RajilicStojanovic2014, Lagier2016, Rothschild2018, Zou2019, Forster2019, King2019, Byrd2020, Yang2020, New2022, Chen2020, Dubinkina2017, Hu2019, Jeong2021, Jie2017, Vachida2019, Wang2020a, Urban2020, Minerbi2019, Karlsson2013 Bacteroidetes Bacteroidia Bacteroidaceae neg SANA Sessile Rod No spore 41.1
Bacteroides clarus Moderate Known Commensal Non/unknown Pathogen human faeces (CCUG, Alkhalil2017) Tyakht2013, Nielsen2014, RajilicStojanovic2014, Lagier2016, Rothschild2018, Zou2019, Forster2019, Byrd2020, Yang2020, Chen2020, Dubinkina2017, Hu2019, Jie2017, Zeller2014, Wang2018, Vachida2019, Wang2020a, Urban2020, Minerbi2019, Karlsson2013 Bacteroidetes Bacteroidia Bacteroidaceae neg SANA Sessile Rod No spore 45.3
Bacteroides congonensis Moderate Transient Non/unknown Pathogen High salt required for optimum growth. In 99% of Europeans (unseenbio.com). human faeces (CCUG) Lagier2016, Byrd2020, Urban2020 Bacteroidetes Bacteroidia Bacteroidaceae neg ANA Swimming Coccobacillus No spore 43.0
Bacteroides coprosuis 1 Rare Possible Commensal Non/unknown Pathogen pig faeces Byrd2020, New2022, Zeller2014 Bacteroidetes Bacteroidia Bacteroidaceae neg ANA Sessile Rod No spore 35.0-36.4
Bacteroides cutis Moderate Possible Commensal Rare Opportunist In 76% of Europeans (unseenbio.com). neck abcess Byrd2020 Bacteroidetes Bacteroidia Bacteroidaceae neg SANA Swimming Rod No spore
Bacteroides eggerthii 2 Widespread Known Commensal Opportunistic Pathogen human faeces Benno1984, Benno1986, Benno1989, Woodmansey2004, Zupancic2012, Tyakht2013, Nielsen2014, RajilicStojanovic2014, Chung2016, Lagier2016, Rothschild2018, Zou2019, Almeida2019, Forster2019, Byrd2020, New2022, Chen2020, Dubinkina2017, Hu2019, Jie2017, Zeller2014, Wang2018, Vachida2019, Wang2020a, Urban2020, Minerbi2019, Li2019b, Karlsson2013, PerezBrocal2015 Bacteroidetes Bacteroidia Bacteroidaceae neg SANA Sessile Rod No spore 46 +
Bacteroides faecalis Rare Possible Commensal Non/unknown Pathogen human faeces (Yu2019) Bacteroidetes Bacteroidia Bacteroidaceae neg SANA Sessile Coccobacillus No spore 39.5
Bacteroides faecichinchillae Rare Possible Commensal Non/unknown Pathogen human faeces and chinchilla faeces Byrd2020, Yang2020, Urban2020 Bacteroidetes Bacteroidia Bacteroidaceae neg SANA Sessile Rod No spore 41 +
Bacteroides faecis Moderate Known Commensal Non/unknown Pathogen In 100% of Europeans (unseenbio.com). human faeces Nielsen2014, RajilicStojanovic2014, Lagier2016, Rothschild2018, Zou2019, Forster2019, Byrd2020, Yang2020, Chen2020, Hu2019, Vachida2019, Urban2020, Minerbi2019 Bacteroidetes Bacteroidia Bacteroidaceae neg ANA Sessile Rod No spore 42.7 neg
Bacteroides finegoldii 1 Widespread Known Commensal Non/unknown Pathogen human faeces McLaughlin2010, Zupancic2012, Tyakht2013, Nielsen2014, RajilicStojanovic2014, Browne2016, Lagier2016, Rothschild2018, Forster2019, Byrd2020, Yang2020, Chen2020, Dubinkina2017, Hu2019, Jeong2021, Jie2017, Zeller2014, Wang2018, Vachida2019, Wang2020a, Urban2020, Minerbi2019, LeChatelier2013, Karlsson2013 Bacteroidetes Bacteroidia Bacteroidaceae neg SANA Sessile Rod No spore 42.4-43.0 +
Bacteroides fluxus Moderate Possible Commensal Non/unknown Pathogen In 95% of Europeans (unseenbio.com). human faeces Tyakht2013, RajilicStojanovic2014, Lagier2016, Forster2019, Byrd2020, Dubinkina2017, Hu2019, Jie2017, Zeller2014, Vachida2019, Urban2020 Bacteroidetes Bacteroidia Bacteroidaceae neg SANA Sessile Rod No spore 45.2
Bacteroides fragilis 2 Human and animal pathogen Widespread Known Commensal Opportunistic Pathogen human faeces (Alkhalil2017) and clinical sources (blood - CCUG) Finegold1974, Holdeman1976, Finegold1977, Benno1984, Benno1986, Benno1989, Mangin2004, MacFarlane2004, Woodmansey2004, Wang2005, McLaughlin2010, Walker2011, Zupancic2012, deGoffau2013, Pfleiderer2013, Tyakht2013, Nielsen2014, RajilicStojanovic2014, Salonen2014, Lagier2016, Rothschild2018, Zou2019, Almeida2019, Chung2019, Forster2019, King2019, Byrd2020, De2020, Yang2020, New2022, Chen2020, Dubinkina2017, Hu2019, Jeong2021, Jie2017, Zeller2014, Wang2018, Vachida2019, Wang2020a, Urban2020, Qin2012, Minerbi2019, Moore1995, Li2019b, LeChatelier2013, Karlsson2013, PerezBrocal2015 Bacteroidetes Bacteroidia Bacteroidaceae neg SANA Sessile Rod No spore 43.1 20(+)
Bacteroides galacturonicus 1 Opportunistic in immunocompromised patients Rare Known Commensal Opportunistic Infection human faeces Walker2011, RajilicStojanovic2014, Lagier2016, Yang2020 Bacteroidetes Bacteroidia Bacteroidaceae neg SANA Sessile Rod No spore 36 20(+)
Bacteroides gallinarum Moderate Possible Commensal Non/unknown Pathogen In 88% of Europeans (unseenbio.com). the caecum of chickens Forster2019, Byrd2020, Urban2020, Minerbi2019 Bacteroidetes Bacteroidia Bacteroidaceae neg SANA Sessile Rod No spore 47.0 +
Bacteroides graminisolvens Rare Known Commensal Non/unknown Pathogen human faeces, and methanogenic reactor treating cattle waste RajilicStojanovic2014, Cassir2015, Lagier2016, Byrd2020, Urban2020 Bacteroidetes Bacteroidia Bacteroidaceae neg SANA Sessile Rod No spore 41.5
Bacteroides helcogenes 2 Animal pathogen Rare Known Commensal Opportunistic Pathogen human faeces and pig faeces Zupancic2012, King2019, Byrd2020, New2022, Zeller2014, Urban2020 Bacteroidetes Bacteroidia Bacteroidaceae neg SANA Sessile Rod No spore 44.72 neg
Bacteroides heparinolyticus Prevotella heparinolyticus 2 Human and animal pathogen Rare Possible Commensal Non/unknown Pathogen Produces heparinase. patients with periodontitis Byrd2020, New2022 Bacteroidetes Bacteroidia Bacteroidaceae neg ANA Sessile Rod No spore 47-49 20(neg)
Bacteroides ihuae Rare Known Commensal Non/unknown Pathogen human faeces (Andrieu2018) and human sputum Byrd2020, Urban2020 Bacteroidetes Bacteroidia Bacteroidaceae neg ANA Swimming Rod No spore 39.71
Bacteroides ilei Minor Possible Commensal Non/unknown Pathogen In 68% of Europeans (unseenbio.com). human ileum and colon (Andrieu2018) Byrd2020 Bacteroidetes Bacteroidia Bacteroidaceae neg ANA Sessile Fusobacterium No spore 45.02
Bacteroides intestinalis 1 Widespread Known Commensal Rare Opportunist human faeces and clinical sources (blood - CCUG) Zupancic2012, Tyakht2013, Nielsen2014, RajilicStojanovic2014, Salonen2014, Cassir2015, Lagier2016, Rothschild2018, Zou2019, Forster2019, Byrd2020, Yang2020, New2022, Chen2020, Dubinkina2017, Hu2019, Jeong2021, Zeller2014, Wang2018, Vachida2019, Urban2020, Minerbi2019, Karlsson2013 Bacteroidetes Bacteroidia Bacteroidaceae neg SANA Sessile Rod No spore 44 +
Bacteroides luhongzhouii Rare Possible Commensal Non/unknown Pathogen fresh faeces from healthy humans (Ge2021) Bacteroidetes Bacteroidia Bacteroidaceae neg SANA Sessile Rod No spore 41.5
Bacteroides luti Rare Possible Commensal Non/unknown Pathogen methanogenic sludge Byrd2020, Urban2020 Bacteroidetes Bacteroidia Bacteroidaceae neg SANA Sessile Rod No spore 44.4 S
Bacteroides mediterraneensis Moderate Known Commensal Non/unknown Pathogen In 87% of Europeans (unseenbio.com). human faeces (Andrieu2018) Lagier2016, Byrd2020 Bacteroidetes Bacteroidia bacteroidaceae neg ANA Swimming Rod No spore 47.5
Bacteroides ndongoniae Minor Possible Commensal Non/unknown Pathogen In 39% of Europeans (unseenbio.com). Minor coloniser. human right colon (Andrieu2018); a 76-year-old woman with oesophagitis Byrd2020 Bacteroidetes Bacteroidia bacteroidaceae neg ANA Sessile Rod No spore 47.7
Bacteroides neonati Minor Possible Commensal Non/unknown Pathogen In 63% of Europeans (unseenbio.com). Minor coloniser. human faeces (neonate stool - Cassir2014) Cassir2015, Lagier2016, Byrd2020, Urban2020 Bacteroidetes Bacteroidia Bacteroidaceae neg SANA Sessile Rod No spore 43.5
Bacteroides nordii 2 Moderate Known Commensal Rare Opportunist human faeces, clinical sources (peritoneal fluid - CCUG) and human gut Pfleiderer2013, RajilicStojanovic2014, Cassir2015, Lagier2016, Rothschild2018, Zou2019, Forster2019, Byrd2020, Yang2020, Chen2020, Hu2019, Vachida2019, Urban2020, Minerbi2019, PerezBrocal2015 Bacteroidetes Bacteroidia Bacteroidaceae neg SANA Sessile Rod No spore 41.4 20(+)
Bacteroides oleiciplenus Moderate Possible Commensal Non/unknown Pathogen In 97% of Europeans (unseenbio.com). human faeces (CCUG) RajilicStojanovic2014, Lagier2016, Zou2019, Forster2019, Byrd2020, Dubinkina2017, Hu2019, Vachida2019, Urban2020 Bacteroidetes Bacteroidia Bacteroidaceae neg SANA Sessile Rod No spore 43.6
Bacteroides ovatus 2 Widespread Known Commensal Rare Opportunist Shows growth in methanol-containing media up to 12.5% (Caldwell1989). human faeces and clinical sources (blood, infection - CCUG) Finegold1974, Holdeman1976, Finegold1977, Benno1984, Benno1986, Benno1989, Mangin2004, MacFarlane2004, Woodmansey2004, McLaughlin2010, Walker2011, Zupancic2012, deGoffau2013, Pfleiderer2013, Tyakht2013, Nielsen2014, RajilicStojanovic2014, Salonen2014, Browne2016, Chung2016, Lagier2016, Rothschild2018, Zou2019, Almeida2019, Chung2019, Forster2019, King2019, Byrd2020, Yang2020, New2022, Chen2020, Dubinkina2017, Hu2019, Jeong2021, Jie2017, Zeller2014, Wang2018, Vachida2019, Wang2020a, Urban2020, Minerbi2019, Moore1995, Li2019b, LeChatelier2013, Karlsson2013, PerezBrocal2015 Bacteroidetes Bacteroidia Bacteroidaceae neg ANA Sessile Rod No spore 41.9 20(+)
Bacteroides pectinophilus 1 Opportunistic in immunocompromised patients Moderate Known Commensal Opportunistic Infection human faeces Zupancic2012, Tyakht2013, Nielsen2014, RajilicStojanovic2014, Lagier2016, Rothschild2018, Byrd2020, De2020, Yang2020, Dubinkina2017, Jie2017, Zeller2014, Vachida2019, Urban2020, Qin2012, Minerbi2019, LeChatelier2013, Karlsson2013 Bacteroidetes Bacteroidia Bacteroidaceae neg SANA Sessile Rod No spore 45 20(+)
Bacteroides propionicifaciens 1 Rare Possible Commensal Non/unknown Pathogen a methanogenic reactor De2020 Bacteroidetes Bacteroidia bacteroidaceae neg SANA Sessile Rod No spore 38.0 0.1(neg)
Bacteroides pyogenes Bacteroides tectum 2 Animal pathogen Minor Possible Commensal Rare Opportunist In 58% of Europeans (unseenbio.com). A minor coloniser. human faeces, clinical sources (blood - CCUG), and pig faeces MacFarlane2004, Woodmansey2004, RajilicStojanovic2014, Lagier2016, Byrd2020, Urban2020 Bacteroidetes Bacteroidia Bacteroidaceae neg SANA Sessile Rod No spore 46.1-47.6 neg
Bacteroides reticulotermitis Rare Possible Commensal Non/unknown Pathogen the gut of the subterranean termite Reticulitermes speratus Byrd2020, Urban2020 Bacteroidetes Bacteroidia Bacteroidaceae neg SANA Sessile Rod No spore 44.9 S(20)
Bacteroides salyersiae 2 Moderate Known Commensal Opportunistic Pathogen human faeces and appendix Zupancic2012, RajilicStojanovic2014, Browne2016, Lagier2016, Rothschild2018, Zou2019, Forster2019, Byrd2020, Yang2020, Chen2020, Hu2019, Jeong2021, Vachida2019, Urban2020, Minerbi2019 Bacteroidetes Bacteroidia Bacteroidaceae neg SANA Sessile Rod No spore 42.0 20(+)
Bacteroides sp. Strain D8 Rare Possible Commensal Non/unknown Pathogen human faeces (Gerard2007) Bacteroidetes Bacteroidia Bacteroidaceae neg SANA Rod No spore 40
Bacteroides stercorirosoris Moderate Possible Commensal Non/unknown Pathogen In 98% of Europeans (unseenbio.com). human faeces and chinchilla faeces Byrd2020, Yang2020, Urban2020, Minerbi2019 Bacteroidetes Bacteroidia Bacteroidaceae neg SANA Sessile Rod No spore 45.7 +
Bacteroides stercoris 1 Opportunistic in immunocompromised patients Widespread Known Commensal Rare Opportunist human faeces (Song2010Bergeys) and clinical sources (blood - CCUG) Benno1989, Mangin2004, MacFarlane2004, McLaughlin2010, Zupancic2012, Tyakht2013, Nielsen2014, RajilicStojanovic2014, Salonen2014, Chung2016, Lagier2016, Rothschild2018, Zou2019, Almeida2019, Chung2019, Forster2019, Byrd2020, Yang2020, Chen2020, Dubinkina2017, Hu2019, Jeong2021, Jie2017, Zeller2014, Wang2018, Vachida2019, Wang2020a, Urban2020, Minerbi2019, Moore1995, Karlsson2013 Bacteroidetes Bacteroidia Bacteroidaceae neg ANA Sessile Rod No spore 43-47 20(+)
Bacteroides thetaiotaomicron Positive 2 Widespread Known Commensal Opportunistic Infection Produces external peptic lyases (PL1, PL9, etc.) human faeces and clinical sources (blood - CCUG) Finegold1974, Holdeman1976, Finegold1977, Benno1984, Benno1986, Benno1989, Mangin2004, MacFarlane2004, Woodmansey2004, Wang2005, Frank2007, McLaughlin2010, Walker2011, deGoffau2013, Pfleiderer2013, Tyakht2013, Nielsen2014, RajilicStojanovic2014, Cassir2015, Browne2016, Chung2016, Lagier2016, Rothschild2018, Zou2019, Almeida2019, Forster2019, King2019, Byrd2020, Yang2020, New2022, Chen2020, Dubinkina2017, Hu2019, Jeong2021, Jie2017, Zeller2014, Wang2018, Vachida2019, Wang2020a, Urban2020, Minerbi2019, Moore1995, LeChatelier2013 Bacteroidetes Bacteroidia Bacteroidaceae neg SANA Sessile Rod No spore 42 20(+)
Bacteroides timonensis Rare Possible Commensal Non/unknown Pathogen human faeces Pfleiderer2013, RajilicStojanovic2014, Lagier2016, Byrd2020, Urban2020 Bacteroidetes Bacteroidia Bacteroidaceae neg SANA Sessile Rod No spore 43.3
Bacteroides togonis Minor Possible Commensal Non/unknown Pathogen In 68% of Europeans (unseenbio.com). Minor coloniser. human gut (Andrieu2018) Byrd2020 Bacteroidetes Bacteroidia Bacteroidaceae neg SANA Sessile Rod No spore 48.26
Bacteroides uniformis Positive 2 Widespread Known Commensal Rare Opportunist human faeces and clinical sources (blood, wound - CCUG) Benno1984, Benno1986, Benno1989, Mangin2004, MacFarlane2004, Woodmansey2004, Wang2005, McLaughlin2010, PerisBondia2011, Walker2011, Zupancic2012, Pfleiderer2013, Tyakht2013, Nielsen2014, RajilicStojanovic2014, Salonen2014, Browne2016, Chung2016, Lagier2016, Rothschild2018, Zou2019, Almeida2019, Chung2019, Forster2019, Byrd2020, Yang2020, New2022, Chen2020, Dubinkina2017, Hu2019, Jeong2021, Jie2017, Zeller2014, Wang2018, Vachida2019, Wang2020a, Urban2020, Minerbi2019, Moore1995, Li2019b, LeChatelier2013, Karlsson2013, PerezBrocal2015 Bacteroidetes Bacteroidia Bacteroidaceae neg ANA Sessile Rod No spore 46.1-47.8
Bacteroides xylanisolvens Bacteroides sp 2 1 16 Positive Widespread Known Commensal Non/unknown Pathogen human faeces McLaughlin2010, Walker2011, Tyakht2013, RajilicStojanovic2014, Browne2016, Lagier2016, Rothschild2018, Zou2019, Almeida2019, Chung2019, Forster2019, King2019, Byrd2020, Yang2020, New2022, Chen2020, Dubinkina2017, Hu2019, Jie2017, Zeller2014, Wang2018, Vachida2019, Wang2020a, Urban2020, LeChatelier2013 Bacteroidetes Bacteroidia Bacteroidaceae neg SANA Sessile Rod No spore 42.8
Bacteroides zhangwenhongi Rare Possible Commensal Non/unknown Pathogen fresh faeces from healthy humans (Ge2021) Bacteroidetes Bacteroidia Bacteroidaceae neg SANA Sessile Rod No spore 42.6
Bacteroides zoogleoformans Prevotella zoogleoformans Rare Possible Commensal Rare Opportunist Haemin is required for growth. patients with periodontitis Byrd2020, New2022 Bacteroidetes Bacteroidia Bacteroidaceae neg SANA Sessile Rod No spore 47 20(neg)
Bariatricus massiliensis Minor Possible Commensal Non/unknown Pathogen In 41% of Europeans (unseenbio.com). Minor coloniser. human faeces (Bessis2016) Lagier2016, Byrd2020 Firmicutes Clostridia Lachnospiraceae + SANA Rod
Barnesiella intestinihominis Moderate Known Commensal Non/unknown Pathogen human faeces (Alkhalil2017) McLaughlin2010, Pfleiderer2013, RajilicStojanovic2014, Chung2016, Lagier2016, Rothschild2018, Zou2019, Chung2019, Forster2019, Byrd2020, Yang2020, Chen2020, Dubinkina2017, Hu2019, Vachida2019, Minerbi2019 Bacteroidetes Bacteroidia Barnesiellaceae neg SANA Sessile Rod No spore 45.5
Barnesiella viscericola Rare Known Commensal Non/unknown Pathogen caeca of chickens and human faeces King2019, Byrd2020, New2022, PerezBrocal2015 Bacteroidetes Bacteroidia Barnesiellaceae neg SANA Sessile Rod No spore 52.0 20(neg)
Bartonella vinsonii Rochalimaea vinsonii 2 Opportunistic in immunocompromised patients Non Transient Possible Pathogen voles and dogs Lagier2016 Proteobacteria Alphaproteobacteria Bartonellaceae neg AER Sessile Rod No spore 38.5-41
Bavariicoccus seileri Rare Possible Commensal Non/unknown Pathogen surface of cheese Forster2019, Byrd2020, De2020 Firmicutes Bacilli Enterococcaceae + ANA Sessile Coccus No spore 38-39
Bdellovibrio bacteriovorus Positive Moderate Possible Mutualist Non/unknown Pathogen Pathogen of Gram negative bacteria. Proposed as a probiotic. Detected in the mucosa of most healthy patients, with the highest bacterial count in the duodenum where oxygen is higher than the bowel. UC patients showed an almost complete absence of this bacterium. freshwater, terrestrial, sewage, soil and the gut Bdellovibrionota Bdellovibrionia Pseudobdellovibrionaceae neg AER Swimming Vibrio No spore 50.4
Beduinella massiliensis Rare Possible Commensal Non/unknown Pathogen human faeces (healthy) Firmicutes Clostridia Beduinellaceae neg SANA Sessile Rod No spore
Beduini massiliensis Rare Possible Commensal Non/unknown Pathogen human faeces (Mourembou2015) Lagier2016 Firmicutes Clostridia Clostridiaceae neg SANA Swimming Rod Endospore 35.9
Beduinibacterium massiliense Rare Possible Commensal Non/unknown Pathogen human faeces (Bilen2018e) Firmicutes Clostridia Christensenellaceae + SANA Swimming Coccobacillus No spore
Belnapia soli Rare Possible Commensal Non/unknown Pathogen soil sample and human faeces Yang2020 Proteobacteria Alphaproteobacteria Acetobacteraceae neg AER Sessile Coccus No spore 72.1
Berryella intestinalis Rare Possible Commensal Non/unknown Pathogen Doesn't utilise carbohydrates. the ileal content of a pig, USA New2022 Actinobacteria Coriobacteriia Eggerthellaceae + Short Rod No spore 63.6
Bhargavaea beijingensis Bacillus beijingensis Rare Known Commensal Non/unknown Pathogen human faeces RajilicStojanovic2014, Lagier2016 Firmicutes Bacilli Planococcaceae + SAER Sessile Coccobacillus No spore 53.1
Bhargavaea cecembensis Non Transient Non/unknown Pathogen deep sea sediment Lagier2016 Firmicutes Bacilli Planococcaceae + AER Sessile Rod No spore 59.5
Bifidobacterium adolescentis Positive 1 Opportunistic in immunocompromised patients Widespread Known Commensal Opportunistic Infection Produces GABA (Sahab2020). Found in human breast milk (Jeurink2013). human faeces Moore1974, Finegold1974, Holdeman1976, Finegold1977, Benno1984, Benno1986, Benno1989, MacFarlane2004, Woodmansey2004, deGoffau2013, Tyakht2013, Nielsen2014, RajilicStojanovic2014, Browne2016, Lagier2016, Rothschild2018, Zou2019, Almeida2019, Forster2019, King2019, Byrd2020, New2022, Chen2020, Dubinkina2017, Hu2019, Jeong2021, Jie2017, Zeller2014, Wang2018, Vachida2019, Wang2020a, Minerbi2019, Moore1995, Li2019b, Karlsson2013 Actinobacteria Actinomycetia Bifidobacteriaceae + ANA Sessile Rod No spore 61.2
Bifidobacterium aerophilum Rare Possible Commensal Non/unknown Pathogen the faeces of a cotton-top tamarin De2020 Actinobacteria Actinomycetia Bifidobacteriaceae + FANA Sessile Rod No spore 63.3
Bifidobacterium angulatum 1 Moderate Known Commensal Non/unknown Pathogen human faeces MacFarlane2004, Woodmansey2004, Tyakht2013, RajilicStojanovic2014, Lagier2016, Rothschild2018, Forster2019, Byrd2020, De2020, New2022, Dubinkina2017, Jie2017, Zeller2014, Vachida2019, Moore1995 Actinobacteria Actinomycetia Bifidobacteriaceae + SANA Sessile Rod No spore 59.0
Bifidobacterium animalis Bifidobacterium lactis Positive 1 Moderate Known Commensal Rare Opportunist Found in human breast milk (Jeurink2013). human faeces, clinical sources (blood - CCUG), faeces of chickens, rats, and rabbits, and sewage Pfleiderer2013, Tyakht2013, Nielsen2014, RajilicStojanovic2014, Lagier2016, Rothschild2018, Zou2019, Almeida2019, Forster2019, Byrd2020, De2020, New2022, Chen2020, Hu2019, Zeller2014, Vachida2019, Wang2020a, Minerbi2019, Karlsson2013 Actinobacteria Actinomycetia Bifidobacteriaceae + ANA Sessile Rod No spore 60
Bifidobacterium animalis subsp. lactis Bifidobacterium lactis 1 Rare Known Commensal Non/unknown Pathogen Tolerates up to 10% oxygen. fermented milk, animal faeces, sewage and human faeces Lagier2016, King2019, Dubinkina2017, Jie2017, Wang2018, LeChatelier2013 Actinobacteria Actinomycetia Bifidobacteriaceae + ANA Sessile Pleiomorph rod No spore 61.0
Bifidobacterium asteroides 1 Rare Possible Commensal Non/unknown Pathogen CO2 required for growth. honeybee gut New2022 Actinobacteria Actinomycetia Bifidobacteriaceae + FANA Sessile Rod - curved No spore 59
Bifidobacterium avesanii Rare Possible Commensal Non/unknown Pathogen the faeces of a cotton-top tamarin De2020 Actinobacteria Actinomycetia Bifidobacteriaceae + FANA Sessile Rod No spore 63.1
Bifidobacterium biavatii Rare Possible Commensal Non/unknown Pathogen the faeces of a red-handed tamarin Byrd2020, De2020 Actinobacteria Actinomycetia Bifidobacteriaceae + FANA Sessile Rod No spore 63.1
Bifidobacterium bifidum Positive 1 Widespread Known Commensal Non/unknown Pathogen B. bifidum produces an alpha-L-fucosidase that attacks HMOs and allows further hydrolysis of the oligosaccharide. Found in human breast milk (Jeurink2013). human faeces (Sanz2007, Nouioui2018) Moore1974, Finegold1974, Benno1984, Benno1986, Benno1989, MacFarlane2004, Woodmansey2004, Pandey2012, Tyakht2013, Nielsen2014, RajilicStojanovic2014, Browne2016, Lagier2016, Rothschild2018, Zou2019, Almeida2019, Forster2019, King2019, Byrd2020, De2020, New2022, Chen2020, Dubinkina2017, Hu2019, Jie2017, Zeller2014, Wang2018, Vachida2019, Wang2020a, Minerbi2019, Karlsson2013 Actinobacteria Actinomycetia Bifidobacteriaceae + ANA Sessile Rod No spore 62.7
Bifidobacterium boum 1 Rare Known Commensal Non/unknown Pathogen human faeces Woodmansey2004, RajilicStojanovic2014, Lagier2016, Byrd2020 Actinobacteria Actinomycetia Bifidobacteriaceae + ANA Sessile Rod No spore 60.0
Bifidobacterium breve Positive 1 Opportunistic in immunocompromised patients Widespread Known Commensal Rare Opportunist Found in human breast milk (Jeurink2013). human faeces and clinical sources (blood, infection - CCUG) Finegold1974, Benno1984, Favier2002, MacFarlane2004, Woodmansey2004, Pandey2012, Tyakht2013, Aujoulat2014, Nielsen2014, RajilicStojanovic2014, Cassir2015, Lagier2016, Almeida2019, Forster2019, King2019, Byrd2020, New2022, Dubinkina2017, Hu2019, Jie2017, Zeller2014, Vachida2019, Wang2020a Actinobacteria Actinomycetia Bifidobacteriaceae + ANA Sessile Rod No spore
Bifidobacterium callitrichidarum Rare Possible Commensal Non/unknown Pathogen the faeces of an emperor tamarin Byrd2020 Actinobacteria Actinobacteria Bifidobacteriaceae + Micr Sessile Pleiomorph rod No spore 60.9
Bifidobacterium catenulatum 1 Moderate Known Commensal Non/unknown Pathogen human faeces Woodmansey2004, Tyakht2013, RajilicStojanovic2014, Lagier2016, Rothschild2018, Chung2019, Forster2019, Byrd2020, New2022, Chen2020, Dubinkina2017, Hu2019, Jie2017, Zeller2014, Wang2018, Vachida2019, Karlsson2013 Actinobacteria Actinomycetia Bifidobacteriaceae + ANA Sessile Rod No spore 54.7
Bifidobacterium catenulatum subsp. kashiwanohense Bifidobacterium kashiwanohense Positive Rare Known Commensal Non/unknown Pathogen human faeces RajilicStojanovic2014, Lagier2016, King2019 Actinobacteria Actinomycetia Bifidobacteriaceae + SANA Sessile Rod No spore 56-59
Bifidobacterium choerinum 1 Rare Possible Commensal Non/unknown Pathogen Doesn't require CO2 for growth. in the faeces of piglets and sewage Byrd2020, New2022 Actinobacteria Actinomycetia Bifidobacteriaceae + ANA Sessile Short Rod No spore 66.3
Bifidobacterium coryneforme 1 Rare Possible Commensal Non/unknown Pathogen human faeces Woodmansey2004, RajilicStojanovic2014, Lagier2016 Actinobacteria Actinomycetia Bifidobacteriaceae + ANA Sessile Club rod No spore
Bifidobacterium cuniculi 1 Rare Possible Commensal Non/unknown Pathogen rabbit faeces Byrd2020 Actinobacteria Actinobacteria Bifidobacteriaceae + SANA Sessile Pleiomorph rod No spore 64.1
Bifidobacterium dentium 2 Moderate Known Commensal Opportunistic Infection Found in human breast milk (Jeurink2013). dental caries, human faeces (Sanz2007) and clinical sources (blood - CCUG) Mangin2004, MacFarlane2004, Woodmansey2004, Tyakht2013, RajilicStojanovic2014, Lagier2016, Almeida2019, Forster2019, King2019, Byrd2020, New2022, Chen2020, Dubinkina2017, Hu2019, Jie2017, Zeller2014, Wang2018, Vachida2019, Wang2020a, Karlsson2013 Actinobacteria Actinomycetia Bifidobacteriaceae + ANA Sessile Rod No spore 61.2
Bifidobacterium eulemuris Rare Possible Commensal Non/unknown Pathogen a black lemur faeces, Italy Byrd2020, New2022 Actinobacteria Actinomycetia Bifidobacteriaceae + Micr Sessile Rod No spore 62.3
Bifidobacterium faecale Rare Possible Commensal Non/unknown Pathogen human faeces (Choi2014) Zou2019, Yang2020 Actinobacteria Actinomycetia Bifidobacteriaceae + SANA Sessile Rod No spore 58.6
Bifidobacterium gallicum 1 Rare Known Commensal Non/unknown Pathogen human faeces Tyakht2013, RajilicStojanovic2014, Lagier2016, Forster2019, Byrd2020, Zeller2014 Actinobacteria Actinomycetia Bifidobacteriaceae + ANA Sessile Rod No spore 61
Bifidobacterium imperatoris Rare Possible Commensal Non/unknown Pathogen Byrd2020, New2022 Actinobacteria Actinomycetia Bifidobacteriaceae + FANA Sessile Rod No spore 56.1
Bifidobacterium indicum 1 Rare Possible Commensal Non/unknown Pathogen the intestine of Apis cerana subsp. indica from Malaysia. Lagier2016 Actinobacteria Actinomycetia Bifidobacteriaceae + ANA Sessile Coccobacillus No spore 60
Bifidobacterium lemurum Rare Possible Commensal Non/unknown Pathogen the faeces of a ring-tail lemur Byrd2020, New2022 Actinobacteria Actinomycetia Bifidobacteriaceae + Micr Sessile Rod - curved No spore 57.2
Bifidobacterium longum subsp. infantis Bifidobacterium infantis 1 Moderate Known Commensal Non/unknown Pathogen In 83% of Europeans (unseenbio.com). human faeces (Sanz2007) Moore1974, Finegold1974, Holdeman1976, Finegold1977, Mangin2004, Woodmansey2004, Pandey2012, Tyakht2013, Lagier2016, King2019, Byrd2020, Dubinkina2017, Jie2017, Wang2018 Actinobacteria Actinomycetia Bifidobacteriaceae + ANA Sessile Rod No spore 60.5
Bifidobacterium longum subsp. longum Bifidobacterium longum 1 Widespread Known Commensal Rare Opportunist Found in human breast milk (Jeurink2013). human faeces and clinical sources (blood - CCUG) Moore1974, Finegold1974, Holdeman1976, Finegold1977, Benno1984, Benno1986, Benno1989, MacFarlane2004, Woodmansey2004, Tyakht2013, Aujoulat2014, Nielsen2014, RajilicStojanovic2014, Cassir2015, Lagier2016, Rothschild2018, Zou2019, Almeida2019, Forster2019, King2019, Byrd2020, De2020, Yang2020, New2022, Chen2020, Dubinkina2017, Hu2019, Jeong2021, Jie2017, Zeller2014, Vachida2019, Wang2020a, Urban2020, Minerbi2019, Moore1995, Li2019b, LeChatelier2013, Karlsson2013, PerezBrocal2015 Actinobacteria Actinomycetia Bifidobacteriaceae + ANA Sessile Rod No spore 61
Bifidobacterium longum subsp. suis Bifidobacterium suis 1 Rare Possible Commensal Non/unknown Pathogen Riboflavin required for growth. the faeces of piglets Woodmansey2004 Actinobacteria Actinomycetia Bifidobacteriaceae + ANA Sessile Rod - curved No spore 62
Bifidobacterium merycicum 1 Rare Possible Commensal Non/unknown Pathogen rumen Byrd2020 Actinobacteria Actinobacteria Bifidobacteriaceae + SANA Sessile Pleiomorph rod No spore 59
Bifidobacterium minimum 1 Rare Possible Commensal Non/unknown Pathogen sewage Byrd2020 Actinobacteria Actinobacteria Bifidobacteriaceae + ANA Sessile Pleiomorph rod No spore
Bifidobacterium mongoliense Unlikely Transient Non/unknown Pathogen Known to temporarily colonise the human gut through the ingestion of parmesan cheese. Unlikely long-term gut coloniser. human faeces, and fermented mare's milk RajilicStojanovic2014, Byrd2020 Actinobacteria Actinomycetia Bifidobacteriaceae + FANA Sessile Rod No spore 61.1-61.9
Bifidobacterium moukalabense Rare Possible Mutualist Non/unknown Pathogen faeces of wild west lowland gorilla Byrd2020 Actinobacteria Actinobacteria Bifidobacteriaceae + SANA Sessile Rod No spore 60.1
Bifidobacterium myosotis Rare Possible Commensal Non/unknown Pathogen faeces of the common marmoset Byrd2020 Actinobacteria Actinobacteria Bifidobacteriaceae + ANA Sessile Pleiomorph rod No spore 65.1
Bifidobacterium pseudocatenulatum Positive 1 Widespread Known Commensal Non/unknown Pathogen Found in human breast milk (Jeurink2013). human faeces (Sanz2007) Favier2002, MacFarlane2004, Woodmansey2004, deGoffau2013, Tyakht2013, Nielsen2014, RajilicStojanovic2014, Browne2016, Chung2016, Lagier2016, Rothschild2018, Zou2019, Forster2019, Byrd2020, Byrd2020, Yang2020, New2022, Chen2020, Dubinkina2017, Hu2019, Jeong2021, Jie2017, Vachida2019, Wang2020a, Minerbi2019, Karlsson2013 Actinobacteria Actinomycetia Bifidobacteriaceae + ANA Sessile Rod No spore 57.5
Bifidobacterium pseudolongum 1 Minor Known Commensal Non/unknown Pathogen human faeces Moore1974, RajilicStojanovic2014, Lagier2016, Zou2019, Byrd2020, New2022, Vachida2019, Li2019b Actinobacteria Actinomycetia Bifidobacteriaceae + ANA Sessile Rod No spore
Bifidobacterium pseudolongum subsp. globosum Bifidobacterium globosum 1 Rare Possible Commensal Non/unknown Pathogen human faeces and animal faeces Moore1974, Lagier2016 Actinobacteria Actinomycetia Bifidobacteriaceae + ANA Sessile Coccobacillus No spore 64.5
Bifidobacterium pullorum subsp. gallinarum Bifidobacterium gallinarum 1 Rare Possible Commensal Non/unknown Pathogen caeca of chickens. Also from human faeces (Alkhalil2017) Byrd2020, De2020, New2022 Actinobacteria Actinomycetia Bifidobacteriaceae + SANA Sessile Rod - curved No spore 65.7
Bifidobacterium pullorum subsp. saeculare Bifidobacterium saeculare 1 Rare Possible Commensal Non/unknown Pathogen the faeces of a rabbit Lagier2016, De2020 Actinobacteria Actinomycetia Bifidobacteriaceae + ANA Sessile Rod - curved No spore 63
Bifidobacterium ramosum Rare Possible Commensal Non/unknown Pathogen the faeces of a cotton-top tamarin De2020 Actinobacteria Actinomycetia Bifidobacteriaceae + FANA Sessile Rod No spore 63.0
Bifidobacterium reuteri Rare Possible Commensal Non/unknown Pathogen faeces of a common marmoset Byrd2020 Actinobacteria Actinobacteria Bifidobacteriaceae + FANA Sessile Pleiomorph rod No spore 61.3
Bifidobacterium ruminantium 1 Minor Possible Commensal Non/unknown Pathogen In 70% of Europeans (unseenbio.com). Minor coloniser. human faeces, and rumen of cattle RajilicStojanovic2014, Byrd2020 Actinobacteria Actinomycetia Bifidobacteriaceae + ANA Sessile Rod No spore 57
Bifidobacterium saguini Rare Possible Commensal Non/unknown Pathogen the faeces of a red-handed tamarin, South Africa Byrd2020, New2022 Actinobacteria Actinomycetia Bifidobacteriaceae + FANA Sessile Pleiomorph rod No spore 57.3
Bifidobacterium scardovii 1 Opportunistic in immunocompromised patients Minor Known Commensal Opportunistic Infection In 27% of Europeans (unseenbio.com). Minor coloniser. clinical sources (blood, urine - CCUG) and human faeces RajilicStojanovic2014, Lagier2016, Byrd2020, New2022 Actinobacteria Actinomycetia Bifidobacteriaceae + ANA Sessile Rod No spore 60.1
Bifidobacterium stellenboschense Rare Possible Commensal Non/unknown Pathogen the faeces of a red-handed tamarin, South Africa Byrd2020 Actinobacteria Actinobacteria Bifidobacteriaceae + FANA Sessile Pleiomorph rod No spore 66.3
Bifidobacterium subtile 1 Rare Possible Commensal Non/unknown Pathogen Non-proteolytic. sewage and caries lesions Byrd2020, New2022 Actinobacteria Actinomycetia Bifidobacteriaceae + ANA Sessile Rod No spore 61.5
Bifidobacterium thermacidophilum 1 Rare Known Commensal Non/unknown Pathogen human faeces, and an anaerobic digester Finegold1974, RajilicStojanovic2014, Lagier2016, Byrd2020 Actinobacteria Actinomycetia Bifidobacteriaceae + ANA Sessile Rod No spore 55.4-58.3
Bifidobacterium thermophilum Positive 1 Rare Possible Commensal Non/unknown Pathogen human faeces RajilicStojanovic2014, Lagier2016, King2019, New2022 Actinobacteria Actinomycetia Bifidobacteriaceae + Micr Sessile Rod No spore 59.7
Bifissio spartinae Rare Possible Commensal Non/unknown Pathogen human faeces McLaughlin2010, Walker2011, RajilicStojanovic2014 Bacteroidetes Bacteroidetes incertae sedis neg No spore
Bilophila wadsworthia Negative 2 Human and animal pathogen Widespread Known Commensal Opportunistic Pathogen human faeces and clinical sources (blood - CCUG) McLaughlin2010, Walker2011, Zupancic2012, Pfleiderer2013, Tyakht2013, Nielsen2014, RajilicStojanovic2014, Lagier2016, Rothschild2018, Zou2019, Chung2019, Forster2019, Byrd2020, Yang2020, Chen2020, Dubinkina2017, Hu2019, Jeong2021, Jie2017, Zeller2014, Wang2018, Vachida2019, Wang2020a, Urban2020, Minerbi2019 Desulfobacterota Deltaproteobacteria Desulfovibrionaceae neg SANA Sessile No spore 39-40 20(+)
Bittarella massiliensis Moderate Possible Commensal Non/unknown Pathogen In 90% of Europeans (unseenbio.com). human faeces (Bilen2018e) Lagier2016, Byrd2020 Firmicutes Clostridia Oscillospiraceae neg ANA Sessile Rod
Blastococcus massiliensis Rare Possible Commensal Non/unknown Pathogen human faeces Pfleiderer2013, RajilicStojanovic2014, Lagier2016 Actinobacteria Actinomycetia Geodermatophilaceae + Micr Sessile Rod No spore
Blastomonas natatoria Blastobacter natatorius 1 Unlikely Possible Commensal Non/unknown Pathogen human faeces, and freshwater Dubourg2013, RajilicStojanovic2014 Proteobacteria Alphaproteobacteria Sphingomonadaceae neg AER Swimming Club rod No spore 65
Blautia brookingsii Rare Possible Commensal Non/unknown Pathogen human faeces (Ghimire2020) Firmicutes Clostridia Lachnospiraceae + SANA Sessile Coccobacillus No spore 44.1
Blautia caecimuris Rare Possible Commensal Non/unknown Pathogen mouse faeces Jeong2021 Firmicutes Clostridia Lachnospiraceae + SANA Sessile Oval-shaped Unknown 43.0
Blautia coccoides Clostridium coccoides 1 Minor Possible Commensal Non/unknown Pathogen Homoacetogen. human faeces (Alkhalil2017) and caecum of mice Benno1984, Benno1986, McLaughlin2010, Pfleiderer2013, RajilicStojanovic2014, Lagier2016, Byrd2020, Yang2020 Firmicutes Clostridia Lachnospiraceae + SANA Sessile Oval-shaped Endospore 43-45 20(w)
Blautia faecicola Rare Possible Commensal Non/unknown Pathogen human faeces (Kim2020) Firmicutes Clostridia Lachnospiraceae + SANA Sessile Oval-shaped No spore 44.7
Blautia faecis Rare Known Commensal Non/unknown Pathogen human faeces RajilicStojanovic2014, Lagier2016, Zou2019, Forster2019, Minerbi2019 Firmicutes Clostridia Lachnospiraceae + SANA Swimming Coccobacillus No spore 41.6
Blautia glucerasea Rare Possible Commensal Non/unknown Pathogen Ferments pectin and fructo-oligosaccharides human faeces, and dog faeces RajilicStojanovic2014, Minerbi2019 Firmicutes Clostridia Lachnospiraceae + SANA Swimming Rod Endospore 40.7
Blautia hansenii Ruminococcus hansenii 1 Moderate Known Commensal Non/unknown Pathogen human faeces Moore1974, Finegold1977, Walker2011, Tyakht2013, Nielsen2014, RajilicStojanovic2014, Lagier2016, Zou2019, Forster2019, King2019, Byrd2020, Yang2020, New2022, Dubinkina2017, Hu2019, Jeong2021, Jie2017, Zeller2014, Vachida2019, Wang2020a, Qin2012, LeChatelier2013 Firmicutes Clostridia Lachnospiraceae + SANA Sessile Oval-shaped No spore 44-45
Blautia hominis Rare Possible Commensal Non/unknown Pathogen human faeces (Shin2018) Byrd2020 Firmicutes Clostridia Lachnospiraceae + SANA Sessile Oval-shaped Endospore 46.3 20(+)
Blautia hydrogenotrophica Ruminococcus hydrogenotrophicus Positive 1 Moderate Known Commensal Non/unknown Pathogen Homoacetogen. human faeces Pfleiderer2013, Tyakht2013, Nielsen2014, RajilicStojanovic2014, Browne2016, Lagier2016, Rothschild2018, Forster2019, Byrd2020, De2020, Chen2020, Dubinkina2017, Hu2019, Jie2017, Zeller2014, Vachida2019, Wang2020a, Qin2012, Minerbi2019, LeChatelier2013, Karlsson2013 Firmicutes Clostridia Lachnospiraceae + SANA Sessile Coccobacillus No spore 45.2
Blautia intestinalis Rare Possible Commensal Non/unknown Pathogen from a stool specimen from an autistic child Firmicutes Clostridia Lachnospiraceae + SANA Sessile Oval-shaped No spore 42.4
Blautia liquoris Rare Possible Commensal Non/unknown Pathogen a mud fermentation cellar, China New2022 Firmicutes Clostridia Lachnospiraceae + SANA Sessile Coccus No spore
Blautia luti Ruminococcus luti 1 Minor Known Commensal Non/unknown Pathogen human faeces (CCUG) RajilicStojanovic2014, Cassir2015, Lagier2016, Zou2019, Forster2019, Yang2020, Minerbi2019 Firmicutes Clostridia Lachnospiraceae + SANA Sessile Oval-shaped No spore 43.3
Blautia marasmi Rare Possible Commensal Non/unknown Pathogen human faeces (CCUG) Firmicutes Clostridia Lachnospiraceae + SANA Coccus
Blautia massiliensis Moderate Known Commensal Non/unknown Pathogen In 100% of Europeans (unseenbio.com). human faeces RajilicStojanovic2014, Lagier2016, Byrd2020, De2020, Minerbi2019 Firmicutes Clostridia Lachnospiraceae neg SANA Sessile Coccobacillus No spore 44.0
Blautia obeum Ruminococcus obeum Positive 1 Widespread Known Commensal Non/unknown Pathogen human faeces Mangin2004, Woodmansey2004, Walker2011, Zupancic2012, Tyakht2013, Nielsen2014, RajilicStojanovic2014, Salonen2014, Browne2016, Lagier2016, Rothschild2018, Zou2019, Forster2019, King2019, Byrd2020, Yang2020, Chen2020, Dubinkina2017, Hu2019, Jeong2021, Jie2017, Zeller2014, Wang2018, Vachida2019, Wang2020a, Urban2020, Minerbi2019, Moore1995, LeChatelier2013, Karlsson2013, PerezBrocal2015 Firmicutes Clostridia Lachnospiraceae + SANA Sessile Oval-shaped Endospore 40-41 vr
Blautia phocaeensis Rare Possible Commensal Non/unknown Pathogen human faeces (Bilen2018e) Lagier2016 Firmicutes Clostridia Lachnospiraceae + SANA Swimming Coccus Endospore
Blautia producta Ruminococcus productus Positive 1 Widespread Known Commensal Non/unknown Pathogen aka peptostreptococcus productus. Can reduce carbon monoxide. Homoacetogens. human faeces and septicemia Moore1974, Finegold1974, Holdeman1976, Finegold1977, Benno1984, Benno1986, Benno1989, Woodmansey2004, Walker2011, Zupancic2012, RajilicStojanovic2014, Lagier2016, Forster2019, Byrd2020, New2022, Dubinkina2017, Hu2019, Jie2017, Vachida2019, Wang2020a, Moore1995, Li2019b, PerezBrocal2015 Firmicutes Clostridia Lachnospiraceae + SANA Sessile Oval-shaped No spore 43-45
Blautia provencensis Rare Possible Commensal Non/unknown Pathogen human faeces (Pham2017) Firmicutes Clostridia Lachnospiraceae + SANA Coccus
Blautia pseudococcoides Blautia coccoides strain YL58 Rare Possible Commensal Non/unknown Pathogen mice Wang2020a Firmicutes Clostridia Lachnospiraceae + SANA Sessile Oval-shaped Endospore 43-45
Blautia schinkii Ruminococcus schinkii 1 Rare Unknown Non/unknown Pathogen Walker2011 found a related species in human faeces, but is likely an uncharacterised species. Homoacetogen. rumen. Presence in the human gut is not clear Byrd2020 Firmicutes Clostridia Lachnospiraceae + SANA Sessile Coccobacillus No spore 46–47
Blautia stercoris Minor Known Commensal Non/unknown Pathogen human faeces (Alkhalil2017) RajilicStojanovic2014, Lagier2016, Zou2019, De2020, Yang2020, Jeong2021, Minerbi2019 Firmicutes Clostridia Lachnospiraceae + SANA Sessile Coccus No spore 35.6
Blautia wexlerae Moderate Known Commensal Non/unknown Pathogen In 100% of Europeans (unseenbio.com). human faeces Dubourg2013, Nielsen2014, RajilicStojanovic2014, Cassir2015, Browne2016, Lagier2016, Zou2019, Almeida2019, Forster2019, Byrd2020, Yang2020, Dubinkina2017, Minerbi2019 Firmicutes Clostridia Lachnospiraceae + SANA Coccobacillus No spore
Bordetella bronchiseptica 2 Human and animal pathogen Non Transient Known Pathogen Few isolates from humans; likely a gut non-coloniser the respiratory systems of animals and humans Lagier2016, Zeller2014 Proteobacteria Betaproteobacteria Alcaligenaceae neg SAER Swimming Coccobacillus No spore 67-69
Bordetella hinzii 2 Human and animal pathogen Unlikely Transient Known Pathogen Obligate aerobe; unlikely to be a gut coloniser. human faeces, chicken sources, and clinical sources Walker2011, RajilicStojanovic2014 Proteobacteria Betaproteobacteria Alcaligenaceae neg SAER Swimming Rod No spore 65-67
Bordetella trematum 2 Non Non-commensal Known Pathogen clinical sources (ear infections, blood, wounds) Pandey2012, Lagier2016 Proteobacteria Betaproteobacteria Alcaligenaceae neg AER Swimming Coccobacillus No spore 65
Bosea massiliensis 1 Rare Possible Commensal Non/unknown Pathogen hospital water supply and human faeces Yang2020 Proteobacteria Alphaproteobacteria Boseaceae neg AER Swimming Rod No spore 66.7-67.9
Brachybacterium conglomeratum 1 Rare Possible Commensal Non/unknown Pathogen corn steep liquour PerezBrocal2015 Actinobacteria Actinomycetia Dermabacteraceae + FANA Sessile Coccus No spore 70.2-71.6
Brachybacterium faecium 1 Unlikely Transient Non/unknown Pathogen Aerobic and optimum growth temperature of 20-30C suggests this is an unlikely gut coloniser. poultry deep litter Zeller2014 Actinobacteria Actinomycetia Dermabacteraceae + AER Sessile Coccus No spore 68-71.5
Brachybacterium ginsengisoli Unlikely Transient Non/unknown Pathogen Borderline cold mesophile, so unlikely to be a gut coloniser. human faeces and soil in Korea Yang2020 Actinobacteria Actinomycetia Dermabacteraceae + AER Sessile Oval-shaped 71
Brachybacterium massiliense Rare Possible Commensal Non/unknown Pathogen human faeces (Mekhalif2019) Lagier2016 Actinobacteria Actinomycetia Dermabacteraceae + AER Sessile Coccus No spore 70.7
Brachybacterium muris 1 Rare Possible Commensal Non/unknown Pathogen lab mice Hu2019 Actinobacteria Actinomycetia Dermabacteraceae + Micr Sessile Oval-shaped No spore
Brachybacterium paraconglomeratum 1 Rare Possible Commensal Non/unknown Pathogen human faeces RajilicStojanovic2014, Lagier2016, Yang2020 Actinobacteria Actinomycetia Dermabacteraceae + FANA Sessile Oval-shaped No spore 68.6
Brachymonas chironomi Unlikely Transient Non/unknown Pathogen Obligate aerobe; unlikely to be a gut coloniser. midge egg, Israel Forster2019 Proteobacteria Betaproteobacteria Comamonadaceae neg SAER Sessile Pleiomorph rod No spore 60.0
Brachyspira aalborgi Negative 2 Human and animal pathogen Rare Possible Commensal Opportunistic Pathogen human faeces, and human colon RajilicStojanovic2014, Lagier2016 Spirochaetes Spirochaetia Brachyspiraceae neg ANA Swimming Spirochete No spore 27.1
Brachyspira hyodysenteriae Treponema hyodysenteriae 2 Opportunistic in immunocompromised patients Rare Possible Commensal Non/unknown Pathogen Cholesterol is required and is reduced to cholestanol. the faeces of pigs and other mammals Cassir2015, Byrd2020, New2022, Zeller2014 Spirochaetes Spirochaetia Brachyspiraceae neg Micr Swimming Helical No spore 25-26
Brachyspira pilosicoli Serpulina pilosicoli 2 Human and animal pathogen Unlikely Possible Commensal Opportunistic Pathogen Pathogenic; unlikely to be a coloniser in a healthy microbiome. human faeces, and pig intestine RajilicStojanovic2014, Lagier2016, Byrd2020, New2022, Zeller2014, Vachida2019 Spirochaetes Spirochaetia Brachyspiraceae neg FANA Swimming Spirochete No spore 24.6
Bradyrhizobium denitrificans Blastobacter denitrificans 1 Rare Possible Commensal Opportunistic Pathogen human faeces, plant endosymbiotic, and clinical sources Bik2006, RajilicStojanovic2014 Proteobacteria Alphaproteobacteria Bradyrhizobiaceae neg AER Swimming Rod No spore
Bradyrhizobium elkanii 1 Rare Possible Commensal Non/unknown Pathogen human faeces, and plant endosymbiotic origin McLaughlin2010, Walker2011, RajilicStojanovic2014 Proteobacteria Alphaproteobacteria Bradyrhizobiaceae neg AER Swimming Rod No spore
Bradyrhizobium ganzhouense Unlikely Transient Non/unknown Pathogen Reported to not 'grow' on glucose, but apparently utilises it as a sole carbon source. Borderline cold mesophile, with optimum growth temp of 28C. Unlikely gut coloniser. the nodules of an Acacia sp Yang2020 Proteobacteria Alphaproteobacteria Bradyrhizobiaceae neg AER Sessile Rod No spore 64.6
Bradyrhizobium icense Unlikely Transient Non/unknown Pathogen Can't grow at 37C, so unlikely to be a gut coloniser. human faeces and root nodules Yang2020 Proteobacteria Alphaproteobacteria Bradyrhizobiaceae neg AER Swimming Rod No spore 61.9
Bradyrhizobium japonicum Rhizobium japonicum 1 Rare Possible Commensal Non/unknown Pathogen human faeces, and plant endosymbiotic origin RajilicStojanovic2014, Zeller2014 Proteobacteria Alphaproteobacteria Bradyrhizobiaceae neg AER Swimming Rod No spore 61-65
Bradyrhizobium neotropicale Rare Possible Commensal Non/unknown Pathogen human faeces and root nodules Yang2020 Proteobacteria Alphaproteobacteria Bradyrhizobiaceae neg AER Swimming Rod No spore 63.9
Brassicibacter mesophilus Rare Possible Commensal Non/unknown Pathogen wasterwater Lagier2016 Firmicutes Clostridia Thermohalobacteraceae neg SANA Swimming Rod No spore 28.2
Brenneria populi Li et al. 2015 Rare Possible Commensal Non/unknown Pathogen tree cankers De2020 Proteobacteria Gammaproteobacteria Pectobacteriaceae neg FANA Swimming Rod No spore 54.9-55.7
Brevibacillus agri Bacillus agri 1 Opportunistic in immunocompromised patients Unlikely Transient Opportunistic Pathogen Borderline cold mesophile, with optimum growth temp of 28C. Unlikely gut coloniser. human faeces (Hoyles2012), soil, water and clinical specimens Hoyles2012, Dubourg2013, Pfleiderer2013, RajilicStojanovic2014, Lagier2016 Firmicutes Bacilli Paenibacillaceae + FANA Swimming Rod Endospore 53
Brevibacillus borstelensis Bacillus borstelensis 1 Rare Known Commensal Possible Pathogen human faeces, soil and clinical sources (blood - CCUG) Pfleiderer2013, RajilicStojanovic2014, Lagier2016 Firmicutes Bacilli Paenibacillaceae + SAER Swimming Rod Endospore 50-52
Brevibacillus brevis Bacillus brevis Positive 1 Opportunistic in immunocompromised patients Rare Known Commensal Opportunistic Infection human faeces, soil and dust Taylor1985, RajilicStojanovic2014, Lagier2016 Firmicutes Bacilli Paenibacillaceae vr SAER Swimming Rod Endospore 47-51.9
Brevibacillus centrosporus Bacillus centrosporus 1 Opportunistic in immunocompromised patients Unlikely Transient Opportunistic Infection Borderline cold mesophile, with optimum growth temp of 28C. Unlikely gut coloniser. human faeces (child - Logan2011bBergey), clinical sources (respiratory lavage, blood), spinach and seagrass Firmicutes Bacilli Paenibacillaceae + SAER Swimming Rod Endospore 49-51
Brevibacillus choshinensis Bacillus choshinensis 1 Rare Possible Commensal Non/unknown Pathogen soils from Japan Lagier2016, New2022 Firmicutes Bacilli Paenibacillaceae + AER Swimming Rod Endospore 48.2-50.5
Brevibacillus formosus Bacillus formosus 1 Unlikely Transient Non/unknown Pathogen Obligate aerobe; unlikely to be a gut coloniser. soil, pig faeces compost and chicken faeces Lagier2016 Firmicutes Bacilli Paenibacillaceae + SAER Swimming Rod Endospore 46.8-47.2
Brevibacillus laterosporus Bacillus laterosporus 1 Opportunistic in immunocompromised patients Rare Possible Commensal Opportunistic Infection soil, tap water, insects, food and clinical sources (eye infection) Lagier2016 Firmicutes Bacilli Paenibacillaceae vr FANA Swimming Rod Endospore 40
Brevibacillus massiliensis Rare Known Commensal Non/unknown Pathogen human faeces RajilicStojanovic2014, Lagier2016 Firmicutes Bacilli Paenibacillaceae + SAER Swimming Rod Endospore 53.1
Brevibacillus parabrevis Bacillus parabrevis 1 Opportunistic in immunocompromised patients Unlikely Transient Opportunistic Infection Obligate aerobe; unlikely to be a gut coloniser. clinical sources and cheese Lagier2016 Firmicutes Bacilli Paenibacillaceae vr SAER Swimming Rod Endospore 51-52
Brevibacillus thermoruber Bacillus thermoruber 1 Non Transient Opportunistic Infection Obligate aerobe and high salt required for optimum growth, so likely a gut non-coloniser. compost, human faeces (CCUG) and clinical specimens (blood - CCUG) Firmicutes Bacilli Paenibacillaceae + SAER Swimming Rod Endospore 57
Brevibacterium aurantiacum 1 Unlikely Transient Non/unknown Pathogen Optimum growth temperature is 24-26C, so unlikely to be a gut coloniser. cheese Byrd2020 Actinobacteria Actinobacteria Brevibacteriaceae + AER Sessile Coccus No spore 60.1-64.3
Brevibacterium casei 1 Opportunistic in immunocompromised patients Rare Possible Commensal Rare Opportunist cheese, milk, clinical sources (blood, wound - CCUG) and human faeces RajilicStojanovic2014, Lagier2016 Actinobacteria Actinomycetia Brevibacteriaceae + AER Sessile Pleiomorphic No spore 66.2-67.2
Brevibacterium celere 1 Rare Possible Commensal Non/unknown Pathogen decaying brown algae Lagier2016 Actinobacteria Actinomycetia Brevibacteriaceae + AER Sessile Coryneform No spore 61.4
Brevibacterium epidermidis 1 Opportunistic in immunocompromised patients Rare Possible Commensal Rare Opportunist human skin and human faeces RajilicStojanovic2014, Lagier2016 Actinobacteria Actinomycetia Brevibacteriaceae + AER Sessile Pleiomorphic No spore 63.4
Brevibacterium ihuae Rare Possible Commensal Non/unknown Pathogen human faeces (healthy) Actinobacteria Actinomycetia Brevibacteriaceae + FANA Swimming Rod No spore
Brevibacterium iodinum 1 Unlikely Transient Non/unknown Pathogen Borderline cold mesophile, so unlikely to be a gut coloniser. cheese and human faeces RajilicStojanovic2014, Lagier2016 Actinobacteria Actinomycetia Brevibacteriaceae vr AER Sessile Pleiomorphic No spore 63
Brevibacterium linens 1 Unlikely Transient Non/unknown Pathogen Optimum growth temp is low (20-25C), so unlikely to be a gut coloniser. human faeces RajilicStojanovic2014, Lagier2016, Zeller2014 Actinobacteria Actinomycetia Brevibacteriaceae + AER Sessile Pleiomorphic No spore 60-64
Brevibacterium luteolum Brevibacterium lutescens 1 Opportunistic in immunocompromised patients Rare Unknown Rare Opportunist Produces methanethiol. human and environmental samples Lagier2016, De2020 Actinobacteria Actinomycetia Brevibacteriaceae + AER Sessile Diphtheroidal No spore 68.8
Brevibacterium mcbrellneri 2 Unlikely Transient Opportunistic Pathogen Obligate aerobe suggests it is unlikely to be a gut coloniser. genital hair Zeller2014 Actinobacteria Actinomycetia Brevibacteriaceae + SAER Sessile Rod-coccus cycle No spore 63
Brevibacterium otitidis 1 Opportunistic in immunocompromised patients Non Transient Rare Opportunist clinical sources (ear infection, cyst) Lagier2016 Actinobacteria Actinomycetia Brevibacteriaceae + FANA Sessile Diphtheroidal No spore
Brevibacterium paucivorans 2 Rare Possible Commensal Rare Opportunist human sources Lagier2016 Actinobacteria Actinomycetia Brevibacteriaceae + FANA Sessile Diphtheroidal No spore 55.8
Brevibacterium pityocampae Rare Possible Commensal Non/unknown Pathogen human faeces and caterpillars RajilicStojanovic2014, Lagier2016 Actinobacteria Actinomycetia Brevibacteriaceae + AER Sessile Rod No spore 69.8
Brevibacterium ravenspurgense Brevibacterium massiliense Rare Possible Commensal Opportunistic Pathogen clinical sources (blood, wound, vagina - CCUG) and human faeces Dubourg2013, RajilicStojanovic2014, Lagier2016 Actinobacteria Actinomycetia Brevibacteriaceae + AER Sessile Rod No spore
Brevibacterium samyangense 1 Rare Possible Commensal Non/unknown Pathogen human faeces and beach sand sediment Yang2020 Actinobacteria Actinomycetia Brevibacteriaceae + AER Swimming Coccus No spore 70.7
Brevibacterium sanguinis 2 Rare Possible Commensal Rare Opportunist clinical sources (blood, aspirate) Yang2020 Actinobacteria Actinomycetia Brevibacteriaceae + AER Sessile Coryneform No spore 69.9
Brevibacterium senegalense Positive Rare Known Commensal Non/unknown Pathogen human faeces RajilicStojanovic2014, Lagier2016, Forster2019 Actinobacteria Actinomycetia Brevibacteriaceae + AER Sessile Rod No spore 70.0
Brevundimonas aurantiaca Caulobacter henricii subsp. aurantiacus 1 Rare Possible Commensal Non/unknown Pathogen human faeces Yang2020 Proteobacteria Alphaproteobacteria Caulobacteraceae neg AER Vibrio No spore 67
Brevundimonas bacteroides Caulobacter bacteroides 1 Rare Possible Commensal Non/unknown Pathogen human faeces Bik2006, RajilicStojanovic2014 Proteobacteria Alphaproteobacteria Caulobacteraceae neg AER Swimming Rod No spore 66
Brevundimonas bullata Mycoplana bullata 1 Rare Possible Commensal Non/unknown Pathogen human faeces and soil Yang2020 Proteobacteria Alphaproteobacteria Caulobacteraceae neg AER Swimming Rod No spore 66-68
Brevundimonas diminuta Pseudomonas diminuta 2 Rare Known Commensal Opportunistic Pathogen human faeces and clinical sources (blood, wound, urine - CCUG) Walker2011, RajilicStojanovic2014, Lagier2016, Yang2020, Zeller2014, PerezBrocal2015 Proteobacteria Alphaproteobacteria Caulobacteraceae neg AER Swimming Rod No spore 66-68
Brevundimonas intermedia Caulobacter intermedius 1 Rare Possible Commensal Non/unknown Pathogen Grows a stalk (prostheca). Requires biotin. pond water McLaughlin2010 Proteobacteria Alphaproteobacteria Caulobacteraceae neg AER Swimming Vibrio No spore 66
Brevundimonas nasdae 1 Rare Possible Commensal Non/unknown Pathogen human faeces McLaughlin2010, Walker2011 Proteobacteria Alphaproteobacteria Caulobacteraceae neg AER Swimming Rod No spore 66.5
Brevundimonas terrae 1 Rare Possible Commensal Non/unknown Pathogen human faeces, and alkaline soil RajilicStojanovic2014 Proteobacteria Alphaproteobacteria Caulobacteraceae neg AER Swimming Rod No spore 61.8
Brevundimonas vesicularis Pseudomonas vesicularis 1 Opportunistic in immunocompromised patients Rare Known Commensal Opportunistic Pathogen clinical sources (wounds, vagina, pleural liquid - CCUG) and human faeces Bik2006, McLaughlin2010, RajilicStojanovic2014 Proteobacteria Alphaproteobacteria Caulobacteraceae neg AER Swimming Rod No spore 65-66
Brochothrix thermosphacta Microbacterium thermosphactum 1 Unlikely Transient Non/unknown Pathogen Grows poorly at 37C, so unlikely a gut coloniser. human faeces Walker2011, RajilicStojanovic2014, Yang2020 Firmicutes Bacilli Listeriaceae + FANA Sessile Rod No spore 38
Brucella anthropi Ochrobactrum anthropi 2 Human and animal pathogen Unlikely Transient Opportunistic Pathogen Obligate aerobe; unlikely to be a gut coloniser. clinical sources (infection, blood, cerebrospinal fluid - CCUG) and human faeces (CCUG - as Ochrobactrum anthropi) Zeller2014 Proteobacteria Alphaproteobacteria Brucellaceae neg SAER Swimming Rod No spore 56-59
Brucella cytisi Ochrobactrum cytisi 1 Rare Possible Commensal Non/unknown Pathogen root nodules Yang2020 Proteobacteria Alphaproteobacteria Brucellaceae neg AER Swimming Rod No spore 56.4
Brucella melitensis Negative 3 Zoonotic pathogen Non Non-commensal Dangerous Pathogen humans and animals Lagier2016 Proteobacteria Alphaproteobacteria Brucellaceae neg AER Sessile Oval-shaped No spore 58
Brucella tritici Ochrobactrum tritici 1 Unlikely Transient Non/unknown Pathogen Obligate aerobe; unlikely to be a gut coloniser. wheat rhizosphere Lagier2016 Proteobacteria Alphaproteobacteria Brucellaceae neg SAER Swimming No spore 59
Buchnera aphidicola 1 Non Non-colonising Non/unknown Pathogen endosymbionts of aphids De2020, New2022 Proteobacteria Gammaproteobacteria Erwiniaceae neg Sessile Coccus No spore 30
Bulleidia extructa 2 Rare Transient Opportunistic Pathogen human faeces, and oral cavity RajilicStojanovic2014, De2020, Dubinkina2017, Zeller2014, Vachida2019 Firmicutes Erysipelotrichia Erysipelotrichaceae + SANA Sessile Rod No spore 38 neg
Burkholderia arboris 2 Rare Possible Commensal Opportunistic Pathogen clinical sources (cystic fibrosis patients) and the environment Yang2020 Proteobacteria Betaproteobacteria Burkholderiaceae neg AER Swimming Rod No spore 67
Burkholderia cepacia Pseudomonas cepacia 2 Human, animal and plant pathogen Rare Possible Commensal Opportunistic Pathogen human faeces, clinical sources (sputum, blood, urine - CCUG), and plant pathogen RajilicStojanovic2014, Lagier2016, Byrd2020 Proteobacteria Betaproteobacteria Burkholderiaceae neg AER Swimming Rod No spore 66.6
Burkholderia gladioli 2 Plant pathogen Unlikely Transient Opportunistic Pathogen cystic fibrosis patients New2022, Zeller2014 Proteobacteria Betaproteobacteria Burkholderiaceae neg FANA Swimming Rod No spore 67.9
Burkholderia mallei 3 Can be passed from animals to humans Unlikely Unknown Dangerous Pathogen Cause of glanders disease in horses and has a high mortality rate in humans if not treated. horses (parasite) Proteobacteria Betaproteobacteria Burkholderiaceae neg AER Sessile Rod No spore 69
Burkholderia multivorans Burkholderia sp. VTT E-072683 2 Rare Unknown Opportunistic Pathogen cystic fibrosis patients, a brain abscess and a flower vase Zeller2014 Proteobacteria Betaproteobacteria Burkholderiaceae neg AER Swimming Rod No spore 68-69
Burkholderia pseudomallei 3 Pathogen of humans and vertebrates Unlikely Unknown Opportunistic Pathogen soil and pathogen (malioidosis) Zeller2014 Proteobacteria Betaproteobacteria Burkholderiaceae neg AER Swimming Rod No spore 69.5
Burkholderia pyrrocinia 1 Unlikely Transient Non/unknown Pathogen Strains produce the antibiotic pyrrolnitrin. soil, Japan Frank2007 Proteobacteria Betaproteobacteria Burkholderiaceae neg FANA Swimming Rod No spore 65
Burkholderia vietnamiensis 2 Rare Unknown Opportunistic Infection rice roots, cystic fibrosis patients and soil Zeller2014 Proteobacteria Betaproteobacteria Burkholderiaceae neg AER Swimming Rod No spore 67.9
Buttiauxella agrestis 1 Rare Possible Commensal Non/unknown Pathogen snails and slugs, soil and drinking water Lagier2016 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg ANA Swimming Rod No spore
Butyribacter intestini Rare Possible Commensal Non/unknown Pathogen human faeces Firmicutes Clostridia Lachnospiraceae + SANA Sessile Rod No spore 36.8
Butyricicoccus faecihominis Rare Possible Commensal Non/unknown Pathogen human faeces (Takada2016) Zou2019, De2020, Minerbi2019 Firmicutes Clostridia Clostridiaceae + SANA Sessile Coccus No spore 55.6
Butyricicoccus porcorum Rare Possible Mutualist Non/unknown Pathogen swine intestinal tract Byrd2020 Firmicutes Clostridia Clostridiaceae + SANA Sessile Coccus 54
Butyricicoccus pullicaecorum Positive Minor Possible Commensal Non/unknown Pathogen In 65% of Europeans (unseenbio.com). human faeces, and caeca of a chicken RajilicStojanovic2014, Cassir2015, Lagier2016, Forster2019, Byrd2020, Hu2019, Vachida2019, PerezBrocal2015 Firmicutes Clostridia Clostridiaceae + ANA Sessile Coccus 54.5
Butyricimonas faecalis Rare Possible Commensal Non/unknown Pathogen human faeces (Roy2019) New2022, Wang2020a Bacteroidetes Bacteroidia Odoribacteraceae neg SANA Sessile Rod No spore 44.2 0-3.75(+)
Butyricimonas faecihominis Rare Possible Commensal Non/unknown Pathogen human faeces (Alkhalil2017, CCUG) and blood Lagier2016, Yang2020 Bacteroidetes Bacteroidia Odoribacteraceae neg SANA Sessile Rod No spore 45.2 0-4.5(+)
Butyricimonas paravirosa Rare Possible Commensal Non/unknown Pathogen human faeces (Alkhalil2017, CCUG) Lagier2016, Yang2020, Minerbi2019 Bacteroidetes Bacteroidia Odoribacteraceae neg SANA Sessile Rod No spore 44.9 0-4.5(+)
Butyricimonas phoceensis Rare Possible Commensal Non/unknown Pathogen human faeces (Togo2016) Lagier2016 Bacteroidetes Bacteroidia Odoribacteraceae neg ANA Swimming Rod No spore 42.5
Butyricimonas synergistica Minor Possible Commensal Non/unknown Pathogen In 54% of Europeans (unseenbio.com). A minor coloniser. human faeces, and rat faeces RajilicStojanovic2014, Byrd2020, Hu2019, Jie2017, Vachida2019 Bacteroidetes Bacteroidia Odoribacteraceae neg SANA Sessile Rod No spore 44.8 0-3.5(+)
Butyricimonas virosa Moderate Known Commensal Opportunistic Infection In 81% of Europeans (unseenbio.com). rat faeces and human faeces (Alkhalil2017) Pfleiderer2013, RajilicStojanovic2014, Lagier2016, Zou2019, Forster2019, Byrd2020, Yang2020, New2022, Minerbi2019 Bacteroidetes Bacteroidia Odoribacteraceae neg ANA Sessile Rod No spore 42.3 0-3.5(+)
Butyrivibrio crossotus 1 Widespread Known Commensal Non/unknown Pathogen human faeces Walker2011, Tyakht2013, Nielsen2014, RajilicStojanovic2014, Salonen2014, Lagier2016, Rothschild2018, Forster2019, Byrd2020, De2020, Yang2020, Chen2020, Dubinkina2017, Hu2019, Jie2017, Zeller2014, Wang2018, Vachida2019, Qin2012, Minerbi2019, Moore1995, LeChatelier2013, Karlsson2013 Firmicutes Clostridia Lachnospiraceae neg SANA Swimming Rod - curved No spore 36−37 vr
Butyrivibrio fibrisolvens 1 Minor Possible Commensal Non/unknown Pathogen human faeces, and rumen Tyakht2013, RajilicStojanovic2014, Lagier2016, Byrd2020, New2022, Zeller2014, Qin2012 Firmicutes Clostridia Lachnospiraceae neg SANA Swimming Rod - curved No spore 41–42
Butyrivibrio hungatei 1 Unlikely Transient Non/unknown Pathogen rumen Byrd2020, New2022 Firmicutes Clostridia Lachnospiraceae neg SANA Swimming Rod No spore 41.6
Butyrivibrio proteoclasticus Clostridium proteoclasticum 1 Rare Transient Non/unknown Pathogen rumen Byrd2020, New2022, Zeller2014, Qin2012 Firmicutes Clostridia Lachnospiraceae + SANA Sessile Rod No spore 28 S
Caballeronia novacaledonica Burkholderia novacaledonica Rare Possible Commensal Non/unknown Pathogen Able to utilise telurite. plant roots, New Caledonia Byrd2020 Proteobacteria Betaproteobacteria Burkholderiaceae neg FANA Rod No spore
Caecibacter massiliensis Rare Isolation and characterisation not yet published. Byrd2020 Firmicutes Negativicutes Veillonellaceae
Caldibacillus thermoamylovorans Bacillus thermoamylovorans Positive 1 Unlikely Possible Commensal Non/unknown Pathogen High optimum growth temperature so unlikely to be a gut coloniser. human faeces and palm wine Hoyles2012, RajilicStojanovic2014, Lagier2016, Byrd2020, PerezBrocal2015 Firmicutes Bacilli Bacillaceae + FANA Swimming Rod No spore 38.8
Caldicellulosiruptor diazotrophicus Non Transient Non/unknown Pathogen Optimum growth temperature is 70C, so likely not a gut coloniser. Nakabusa hot springs, Japan New2022 Firmicutes Clostridia Thermoanaerobacterales Family III. Incertae Sedis + Short Rod No spore 34.8
Caldicoprobacter faecalis Acetomicrobium faecalis Unlikely Transient Non/unknown Pathogen The minimum temperature for growth is 55C, so unlikely to be a gut coloniser. sewage sludge Forster2019 Firmicutes Clostridia Caldicoprobacteraceae neg SANA Swimming Rod - curved No spore 45
Caloranaerobacter azorensis 1 Non Transient Non/unknown Pathogen No growth at 37C, so unlikely to be a gut coloniser. a deep-sea hydrothermal vent New2022 Firmicutes Clostridia Thermohalobacteraceae neg ANA Swimming Rod No spore 27
Campylobacter avium Non Unknown Possible Pathogen the caecal contents of chickens and turkeys De2020 Proteobacteria Epsilonproteobacteria Campylobacteraceae neg Micr Swimming Rod No spore 35 1(d)
Campylobacter coli Negative 2 Zoonotic pathogen Unlikely Possible Commensal Known Pathogen Pathogenic; unlikely to be a coloniser in a healthy microbiome. human faeces and clinical sources (blood - CCUG) Tyakht2013, RajilicStojanovic2014, Lagier2016, King2019, New2022, Zeller2014, LeChatelier2013 Proteobacteria Epsilonproteobacteria Campylobacteraceae neg Micr Swimming Corkscrew No spore 31–35 2(d)
Campylobacter concisus Negative 2 Minor Known Commensal Opportunistic Pathogen human faeces, and oral cavity Bik2006, Walker2011, RajilicStojanovic2014, Lagier2016, Forster2019, Byrd2020, De2020, Yang2020, New2022, Hu2019, Zeller2014, Vachida2019 Proteobacteria Epsilonproteobacteria Campylobacteraceae neg Micr Swimming Rod - curved No spore 37–41 2(d)
Campylobacter curvus Wolinella curva 2 Rare Possible Commensal Opportunistic Pathogen clinical sources and human faeces RajilicStojanovic2014, Lagier2016, Almeida2019, Zeller2014, Vachida2019 Proteobacteria Epsilonproteobacteria Campylobacteraceae neg Micr Swimming Helical No spore 43–47
Campylobacter faecalis Rare Possible Commensal Non/unknown Pathogen human faeces RajilicStojanovic2014, De2020 Proteobacteria Epsilonproteobacteria Campylobacteraceae neg Micr Swimming No spore
Campylobacter fetus subsp. fetus 2 Zoonotic pathogen Rare Possible Commensal Possible Pathogen human faeces, clinical sources (blood - CCUG), and human gut RajilicStojanovic2014, Lagier2016, New2022 Proteobacteria Epsilonproteobacteria Campylobacteraceae neg Micr Swimming Rod - curved No spore 33-36
Campylobacter gracilis Bacteroides gracilis 2 Minor Possible Commensal Possible Pathogen clinical sources (dental disease - CCUG) and human faeces RajilicStojanovic2014, Lagier2016, Yang2020, New2022, Hu2019, Zeller2014, Vachida2019 Proteobacteria Epsilonproteobacteria Campylobacteraceae neg Micr Sessile Rod No spore 44–46
Campylobacter hominis 1 Minor Possible Commensal Non/unknown Pathogen human faeces RajilicStojanovic2014, Lagier2016, King2019, Byrd2020, Yang2020, New2022, Dubinkina2017, Hu2019, Zeller2014, Vachida2019 Proteobacteria Epsilonproteobacteria Campylobacteraceae neg SANA Sessile Rod No spore 32–33 2(d)
Campylobacter hyointestinalis subsp. hyointestinalis 2 Zoonotic pathogen Unlikely Transient Possible Pathogen human faeces, human gut, and animal intestines RajilicStojanovic2014, Lagier2016 Proteobacteria Epsilonproteobacteria Campylobacteraceae neg Micr Swimming Rod - curved No spore 33-36 1.5(+)
Campylobacter jejuni subsp. doylei 2 Rare Possible Commensal Possible Pathogen clinical sources and human faeces (young girl with diarrhoea - CCUG) Proteobacteria Epsilonproteobacteria Campylobacteraceae neg Micr Swimming Rod - curved No spore 29
Campylobacter jejuni subsp. jejuni Campylobacter jejuni 2 Zoonotic pathogen Unlikely Possible Commensal Known Pathogen Pathogenic; unlikely to be a coloniser in a healthy microbiome. human faeces and clinical sources (blood - CCUG) RajilicStojanovic2014, Lagier2016, Almeida2019, Forster2019, King2019, Yang2020, New2022, Zeller2014 Proteobacteria Epsilonproteobacteria Campylobacteraceae neg Micr Swimming Vibrio No spore 30-33
Campylobacter lanienae 1 Opportunistic in immunocompromised patients Rare Possible Commensal Possible Pathogen human faeces (VanDamme2005Bergey) Proteobacteria Epsilonproteobacteria Campylobacteraceae neg Micr Swimming Rod No spore 36
Campylobacter lari subsp. concheus 2 Rare Possible Commensal Opportunistic Pathogen human faeces (diarrhoea - CCUG), an infection and shellfish Proteobacteria Epsilonproteobacteria Campylobacteraceae neg Micr Swimming Rod - curved No spore 31-33
Campylobacter lari subsp. lari Campylobacter lari 2 Zoonotic pathogen Rare Possible Commensal Opportunistic Pathogen human faeces RajilicStojanovic2014, Lagier2016, Byrd2020, New2022 Proteobacteria Epsilonproteobacteria Campylobacteraceae neg Micr Swimming Rod - curved No spore
Campylobacter mucosalis 2 Opportunistic in immunocompromised patients Rare Possible Commensal Non/unknown Pathogen pig faeces. Has also been detected in human faeces (Bilen2018e) Lagier2016 Proteobacteria Epsilonproteobacteria Campylobacteraceae neg Micr Swimming Rod - curved No spore 36-38
Campylobacter peloridis Rare Possible Commensal Possible Pathogen human faeces (CCUG), clinical specimens and shellfish Lagier2016 Proteobacteria Epsilonproteobacteria Campylobacteraceae neg Micr Swimming Rod - curved No spore
Campylobacter rectus Wolinella recta 2 Zoonotic pathogen Rare Transient Opportunistic Pathogen human faeces, and dental diseases RajilicStojanovic2014, Lagier2016, Byrd2020, New2022, Zeller2014 Proteobacteria Epsilonproteobacteria Campylobacteraceae neg ANA Swimming Rod No spore 42-46
Campylobacter showae 1 Opportunistic in immunocompromised patients Rare Possible Commensal Opportunistic Infection human faeces, and human dental plaque Bik2006, RajilicStojanovic2014, Lagier2016, Yang2020, Zeller2014, Vachida2019 Proteobacteria Epsilonproteobacteria Campylobacteraceae neg Micr Swimming Rod No spore 44-46
Campylobacter sputorum 2 Non Transient Opportunistic Pathogen human mouth and human faeces Lagier2016 Proteobacteria Epsilonproteobacteria Campylobacteraceae neg Micr Swimming Rod - curved No spore 30-33
Campylobacter troglodytis Rare Possible Commensal Possible Pathogen chimpanzee stools. Also detected in human faeces (Bilen2018e) Proteobacteria Epsilonproteobacteria Campylobacteraceae neg Swimming Rod - curved No spore 34-38 2(neg)
Campylobacter upsaliensis 2 Zoonotic pathogen Rare Possible Commensal Rare Opportunist human faeces, clinical sources (blood - CCUG) and animals Tyakht2013, RajilicStojanovic2014, Lagier2016, Forster2019, Vachida2019 Proteobacteria Epsilonproteobacteria Campylobacteraceae neg Micr Swimming Rod - curved No spore 32-36 2(+)
Campylobacter ureolyticus Bacteroides ureolyticus 2 Human and animal pathogen Minor Possible Commensal Known Pathogen clinical sources (blood, vagina, placenta - CCUG) and human faeces Benno1986, Benno1989, RajilicStojanovic2014, Lagier2016, Byrd2020, Yang2020, New2022, Vachida2019, PerezBrocal2015 Proteobacteria Epsilonproteobacteria Campylobacteraceae neg ANA Sessile Rod No spore 28-30 1.5(neg)
Candidatus Babela massiliensis Unlikely Transient Non/unknown Pathogen intracellular commensal of amoeba, which is associated with clinical sources (eye infection) De2020 Candidatus Dependentiae Candidatus Babeliae Candidatus Babeliaceae neg Sessile Coccus No spore
Candidatus Dorea massiliensis Dorea massiliensis Rare Possible Commensal Non/unknown Pathogen human faeces Pfleiderer2013, RajilicStojanovic2014, Lagier2016, Minerbi2019 Firmicutes Clostridia Lachnospiraceae + FANA Sessile Rod No spore
Candidatus Stoquefichus massiliensis Stoquefichus massiliensis Rare Possible Commensal Non/unknown Pathogen human faeces Pfleiderer2013, RajilicStojanovic2014, Lagier2016, Byrd2020 Firmicutes Erysipelotrichia Erysipelotrichaceae + ANA Sessile Rod No spore
Capnocytophaga canimorsus 2 Pathogen of humans and vertebrates Unlikely Transient Known Pathogen Mortality rate about 75% for patients with underlying disease. a dog bite infection and septicemia New2022 Bacteroidetes Flavobacteriia Flavobacteriaceae neg Micr Gliding Rod No spore 36
Capnocytophaga gingivalis 2 Non Unknown Possible Pathogen Grows better in air by completely respiring glucose oral flora Lagier2016 Bacteroidetes Flavobacteriia Flavobacteriaceae neg FANA Gliding Rod No spore 35-41
Capnocytophaga granulosa 2 Rare Known Commensal Opportunistic Pathogen human faeces, and human dental plaque Bik2006, RajilicStojanovic2014, Lagier2016, Yang2020 Bacteroidetes Flavobacteriia Flavobacteriaceae neg ANA Gliding Rod No spore 41.7 10(neg)
Capnocytophaga leadbetteri 1 Opportunistic in immunocompromised patients Rare Possible Commensal Opportunistic Pathogen All strains cleave human IgA1 in the hinge region. the oral cavity Byrd2020 Bacteroidetes Flavobacteriia Flavobacteriaceae neg FANA Gliding Rod No spore 41.3
Capnocytophaga ochracea Bacteroides ochraceus 2 Rare Possible Commensal Opportunistic Pathogen dental disease and human faeces RajilicStojanovic2014, Lagier2016, De2020 Bacteroidetes Flavobacteriia Flavobacteriaceae neg FANA Gliding Rod No spore 38-39
Capnocytophaga sputigena 2 Rare Possible Commensal Opportunistic Pathogen dental disease, clinical sources (blood, infection - CCUG) and human faeces RajilicStojanovic2014, Lagier2016, De2020, Zeller2014 Bacteroidetes Flavobacteriia Flavobacteriaceae neg ANA Gliding Rod No spore 38-40
Capnocytophaga stomatis Unlikely Transient Non/unknown Pathogen New2022 Bacteroidetes Flavobacteriia Flavobacteriaceae neg Fusiform No spore
Caproicibacter fermentans Rare Transient Non/unknown Pathogen Produces caproate. a biogas reactor New2022 Firmicutes Clostridia Oscillospiraceae neg SANA Sessile Rod Endospore 51.3
Cardiobacterium hominis 2 Rare Possible Commensal Opportunistic Pathogen human faeces, nasal cavity and clinical specimens (blood - CCUG) Yang2020, New2022, Zeller2014 Proteobacteria Gammaproteobacteria Cardiobacteriaceae neg FANA Sessile Pleiomorphic No spore 59-60
Cardiobacterium valvarum 2 Rare Unknown Opportunistic Pathogen In 1% of Europeans (unseenbio.com). Rare coloniser. the blood of a patient with endocarditis Vachida2019 Proteobacteria Gammaproteobacteria Cardiobacteriaceae neg AER Rod No spore
Carnobacterium divergens Lactobacillus divergens 1 Non Transient Non/unknown Pathogen vacuum-packaged meats Lagier2016, Byrd2020 Firmicutes Bacilli Carnobacteriaceae + FANA Sessile Rod No spore 33.0-36.4
Carnobacterium inhibens Mixed 1 Rare Possible Commensal Opportunistic Infection human faeces, clinical sources (plasma, pus) and salmon Yang2020 Firmicutes Bacilli Carnobacteriaceae + FANA Swimming Rod No spore 35.1
Carnobacterium maltaromaticum Lactobacillus piscicola 2 Opportunistic in immunocompromised patients Unlikely Transient Non/unknown Pathogen Produces 2-methylpropanal, 2-methylpropanol, 3-methylbutanal, and 3-methylbutanol from skim milk. These compounds are probably responsible for a malt smell produced. buttermilk Lagier2016, Byrd2020, Vachida2019 Firmicutes Bacilli Carnobacteriaceae + FANA Sessile Rod No spore 33.7-36.4
Carnobacterium mobile 1 Non Transient Non/unknown Pathogen chicken meat Lagier2016 Firmicutes Bacilli Carnobacteriaceae + FANA Swimming Rod No spore 35.5-37.2
Casaltella massiliensis Rare Possible Commensal Non/unknown Pathogen human faeces (detected - Bilen2018) Lagier2016 Firmicutes Clostridia Eubacteriales Family XIII. Incertae Sedis neg Rod
Catenibacillus scindens Rare Possible Commensal Non/unknown Pathogen human faeces (CCUG) Firmicutes Clostridia Lachnospiraceae + ANA Sessile Oval-shaped No spore 47.1
Catenibacterium mitsuokai 1 Moderate Known Commensal Non/unknown Pathogen human faeces Walker2011, Zupancic2012, Tyakht2013, Nielsen2014, RajilicStojanovic2014, Salonen2014, Browne2016, Lagier2016, Rothschild2018, Forster2019, Byrd2020, De2020, Yang2020, Chen2020, Dubinkina2017, Hu2019, Jie2017, Vachida2019, Qin2012, Minerbi2019, Karlsson2013 Firmicutes Erysipelotrichia Coprobacillaceae + SANA Sessile Rod No spore 36-39
Catenulispora acidiphila 1 Unlikely Transient Non/unknown Pathogen Aerobic, optimum growth temperature of 22-28C and preferred acidity <7 suggests this is an unlikely gut coloniser. temperate forest soil Zeller2014 Actinobacteria Actinomycetia Catenulisporaceae + AER Sessile Filamentous Exospore 71.5
Catonella morbi 2 Rare Possible Commensal Opportunistic Pathogen the gingival crevices of humans with adult periodontitis Byrd2020, Zeller2014, Vachida2019 Firmicutes Clostridia Lachnospiraceae neg SANA Sessile Rod No spore 34 S(20)
Caulobacter vibrioides 1 Unlikely Transient Non/unknown Pathogen Vitamin B2 is essential for growth. Obligate aerobe; unlikely to be a gut coloniser. a freshwater pond Byrd2020, Yang2020, Zeller2014 Proteobacteria Alphaproteobacteria Caulobacteraceae neg SAER Swimming Vibrio No spore 64-65
Cedecea davisae 2 Rare Known Commensal Opportunistic Pathogen human faeces, and clinical sources RajilicStojanovic2014, Lagier2016, Forster2019, Byrd2020, Vachida2019 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Swimming Rod No spore 49-50
Cedecea lapagei 2 Rare Possible Commensal Possible Pathogen human faeces (Alkhalil2017 - ulcerative colitis patient), respiratory tract (throat, sputum) and ticks Lagier2016 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Swimming Rod No spore 48-52
Cedecea neteri 2 Rare Possible Commensal Opportunistic Pathogen human faeces (Alkhalil2017 - ulcerative colitis patient) and clinical sources (blood, wound, sputum) Lagier2016 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Swimming Rod No spore
Cellulomonas carbonis Unlikely Transient Non/unknown Pathogen Aerobic and optimum growth temperature of 28C suggests this is an unlikely gut coloniser. coal mine soil, China Byrd2020 Actinobacteria Actinobacteria Cellulomonadaceae + AER Swimming Rod No spore 74.4
Cellulomonas composti 1 Rare Possible Commensal Non/unknown Pathogen Able to digest cellulose compost and human faeces RajilicStojanovic2014, Lagier2016 Actinobacteria Actinomycetia Cellulomonadaceae + FANA Sessile Rod No spore 73.7
Cellulomonas denverensis 1 Opportunistic in immunocompromised patients Rare Possible Commensal Rare Opportunist clinical sources (blood - CCUG) and human faeces RajilicStojanovic2014, Lagier2016 Actinobacteria Actinomycetia Cellulomonadaceae + AER Swimming Short Rod No spore 68.5
Cellulomonas fimi 1 Rare Possible Commensal Non/unknown Pathogen dung Zeller2014 Actinobacteria Actinomycetia Cellulomonadaceae + AER Swimming Rod No spore 71.3-72.0
Cellulomonas flavigena Empedobacter flavigena 1 Rare Possible Commensal Non/unknown Pathogen Can digest cellulose soil Lagier2016, Zeller2014 Actinobacteria Actinomycetia Cellulomonadaceae + AER Swimming Rod No spore 72.7-74.8
Cellulomonas hominis 1 Opportunistic in immunocompromised patients Rare Possible Commensal Opportunistic Pathogen Doesn't degrade cellulose clinical sources (cerebrospinal fluid) Lagier2016 Actinobacteria Actinomycetia Cellulomonadaceae + Swimming Short Rod No spore 73-76
Cellulomonas massiliensis Positive Rare Known Commensal Non/unknown Pathogen human faeces RajilicStojanovic2014, Lagier2016, Forster2019 Actinobacteria Actinomycetia Cellulomonadaceae + AER Swimming Rod No spore 71.2
Cellulomonas parahominis Rare Possible Commensal Non/unknown Pathogen human faeces RajilicStojanovic2014, Lagier2016 Actinobacteria Actinomycetia Cellulomonadaceae + AER Swimming Rod No spore
Cellulomonas timonensis Rare Possible Commensal Non/unknown Pathogen the faeces of an obese patient (Ndongo2018a) Lagier2016 Actinobacteria Actinomycetia Cellulomonadaceae + FANA Swimming Rod Spore reported 72.4
Cellulosilyticum lentocellum Clostridium lentocellum 1 Rare Possible Commensal Non/unknown Pathogen Cellulolytic. human faeces, and domestic effluent and mud RajilicStojanovic2014, Byrd2020, New2022, Zeller2014, Vachida2019, Qin2012 Firmicutes Clostridia Lachnospiraceae neg SANA Swimming Rod - curved Endospore 36
Cellulosilyticum ruminicola Rare Possible Commensal Non/unknown Pathogen the rumen contents of a yak, Tibet Firmicutes Clostridia Lachnospiraceae neg SANA Sessile Rod Endospore 33.7
Cellulosimicrobium cellulans 1 Rare Known Commensal Possible Pathogen Cellulolytic. human faeces and clinical sources (CCUG) Pfleiderer2013, RajilicStojanovic2014, Lagier2016 Actinobacteria Actinomycetia Promicromonosporaceae + FANA Sessile Club rod No spore 74
Centipeda periodontii 2 Rare Possible Commensal Opportunistic Infection periodontal lesions Zeller2014, Vachida2019 Firmicutes Negativicutes Selenomonadaceae neg SANA Swimming Rod - curved No spore 52-54
Cerasibacillus quisquiliarum 1 Non Transient Non/unknown Pathogen Doesn't oxidise glucose or most common carbohydrates. Has a very high optimum growth temp (50C), so likely to be a gut non-coloniser. decomposing kitchen refuse Lagier2016 Firmicutes Bacilli Bacillaceae + SAER Swimming Rod Endospore 35.5
Cetobacterium somerae 1 Rare Known Commensal Non/unknown Pathogen human faeces RajilicStojanovic2014, Lagier2016, Forster2019, Vachida2019 Fusobacteria Fusobacteriia Fusobacteriaceae neg Micr Sessile Fusobacterium No spore 31 20(+)
Chelatococcus asaccharovorans 1 Unlikely Transient Non/unknown Pathogen Unable to grow with sugars. Strict aerobe, so unlikely to be a gut coloniser. wastewater and soil Frank2007 Proteobacteria Alphaproteobacteria Chelatococcaceae neg SAER Sessile Coccus No spore 63.3-63.5
Chitinophaga agri Unlikely Possible Commensal Non/unknown Pathogen the soil of reclaimed land, Korea New2022 Bacteroidetes Chitinophagia Chitinophagaceae neg AER Rod No spore 46.2
Chlamydia trachomatis Rickettsia trachomatis 2 Non Transient Known Pathogen C. trachomatis is an obligate intracellular parasite that synthesises and accumulates glycogen. Survives outside the cell by producing infectious and resistant elementary bodies ('EB'). clinical sources (sexually transmitted disease, arthritis) Lagier2016 Chlamydiae Chlamydiia Chlamydiaceae neg SANA Sessile No spore
Chloracidobacterium thermophilum Non Transient Non/unknown Pathogen Cells have chlorosomes used for photosynthesis. High minimum growth temperature suggests it is not a gut coloniser a geyser sprint, Yellowstone National Park, USA Acidobacteria Blastocatellia neg Micr Sessile Rod Unknown 61.3
Christensenella hongkongensis Catabacter hongkongensis Minor Possible Commensal Opportunistic Pathogen In 27% of Europeans (unseenbio.com). Minor coloniser. clinical sources and human faeces Walker2011, Pfleiderer2013, RajilicStojanovic2014, Lagier2016, Byrd2020, Jeong2021 Firmicutes Clostridia Christensenellaceae + SANA vr Coccobacillus No spore 48.5-48.8
Christensenella massiliensis Rare Possible Commensal Non/unknown Pathogen human faeces (Ndongo2016) Lagier2016, Byrd2020, De2020 Firmicutes Clostridia Christensenellaceae neg SANA Sessile Rod No spore
Christensenella minuta Positive Minor Possible Commensal Non/unknown Pathogen In 52% of Europeans (unseenbio.com). A minor coloniser. human faeces RajilicStojanovic2014, Lagier2016, Byrd2020, New2022, Jeong2021 Firmicutes Clostridia Christensenellaceae neg SANA Sessile Rod No spore 51.3 20(+)
Christensenella timonensis Minor Possible Commensal Non/unknown Pathogen In 15% of Europeans (unseenbio.com). Minor coloniser. human faeces (Ndongo2016a) Lagier2016, Byrd2020 Firmicutes Clostridia Christensenellaceae neg SANA Sessile Rod No spore
Chromobacterium violaceum 2 Human and animal pathogen Unlikely Possible Commensal Known Pathogen soil and water; clinical sources (septicemic infections) Lagier2016, Zeller2014 Proteobacteria Betaproteobacteria Chromobacteriaceae neg AER Swimming Rod No spore 65-68
Chromohalobacter japonicus 1 Unlikely Transient Non/unknown Pathogen Requires at least 5% salt to grow, so unlikely gut coloniser. Japanese salty food Lagier2016 Proteobacteria Gammaproteobacteria Halomonadaceae neg SAER Swimming Rod No spore 62.9
Chromohalobacter salexigens 1 Unlikely Transient Non/unknown Pathogen salterns Cassir2015, Zeller2014 Proteobacteria Gammaproteobacteria Halomonadaceae neg SAER Swimming Rod No spore 64.2-66.0
Chryseobacterium gallinarum Unlikely Possible Commensal Non/unknown Pathogen a chicken pharyngeal scrape, Germany Byrd2020, New2022 Bacteroidetes Flavobacteriia Weeksellaceae neg AER Sessile Rod No spore 37.3
Chryseobacterium gleum Flavobacterium gleum 2 Unlikely Transient Opportunistic Pathogen Obligate aerobe; unlikely to be a gut coloniser. clinical sources (vagina, sputum, wound, abdominal tap) Lagier2016 Bacteroidetes Flavobacteriia Weeksellaceae neg SAER Sessile Rod No spore 37.6
Chryseobacterium hominis 2 Rare Possible Commensal Possible Pathogen clinical sources (blood, wound - CCUG) and human faeces Pfleiderer2013, RajilicStojanovic2014, Lagier2016 Bacteroidetes Flavobacteriia Weeksellaceae neg AER Sessile Rod No spore 36.5
Chryseobacterium indologenes Flavobacterium indologenes 2 Human and animal pathogen Rare Possible Commensal Known Pathogen clinical sources (sputum, pus, urine, pharynx) Lagier2016 Bacteroidetes Flavobacteriia Weeksellaceae neg FANA Sessile Rod No spore 37.3-38.3
Chryseobacterium oranimense Rare Possible Commensal Non/unknown Pathogen human faeces (CCUG), and milk Bacteroidetes Flavobacteriia Weeksellaceae neg AER Sessile Rod No spore
Chryseobacterium taklimakanense Planobacterium taklimakanense Rare Possible Commensal Non/unknown Pathogen desert soil, China Lagier2016 Bacteroidetes Flavobacteriia Weeksellaceae neg FANA Swimming Rod No spore 41.5
Chryseobacterium viscerum Non Transient Non/unknown Pathogen An aerobe that can't grow at 37C suggests this is a non-coloniser of the gut. the gills and livers of five diseased rainbow trout Byrd2020 Bacteroidetes Flavobacteriia Flavobacteriaceae neg AER Sessile Rod No spore 38.6
Chryseomicrobium amylolyticum Rare Possible Commensal Non/unknown Pathogen human faeces and soil Yang2020 Firmicutes Bacilli Planococcaceae + AER Sessile Rod No spore 57.6
Citrobacter amalonaticus Levinea amalonatica 2 Rare Known Commensal Opportunistic Pathogen human faeces, clinical sources (ear, urine- CCUG), animals and soil RajilicStojanovic2014, Lagier2016, Byrd2020, De2020 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Swimming Rod No spore 51-52
Citrobacter braakii Negative 2 Rare Possible Commensal Opportunistic Pathogen human faeces (Alkhalil2017 - high load in several ulcerative colitis patients) and animals RajilicStojanovic2014, Lagier2016, Forster2019, Byrd2020 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Swimming Rod No spore
Citrobacter europaeus Rare Possible Commensal Non/unknown Pathogen human faeces (Ribeiro2017) Byrd2020 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Swimming Rod No spore 52.0
Citrobacter farmeri 2 Minor Possible Commensal Possible Pathogen In 14% of Europeans (unseenbio.com). Minor coloniser. human faeces, urine, and clinical sources RajilicStojanovic2014, Lagier2016, Byrd2020 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Swimming Rod No spore
Citrobacter freundii Negative 2 Minor Known Commensal Opportunistic Pathogen In 6% of Europeans (unseenbio.com), i.e., a minor coloniser. human faeces (high load in several ulcerative colitis patients), sewage, animals and clinical sources (blood, wound, urine - CCUG) Finegold1977, Benno1984, Benno1986, Benno1989, Pfleiderer2013, RajilicStojanovic2014, Lagier2016, Zou2019, Almeida2019, Forster2019, King2019, Byrd2020, New2022, Chen2020, Dubinkina2017, Hu2019, Jie2017, Vachida2019, Wang2020a Proteobacteria Gammaproteobacteria Enterobacteriaceae neg AER Swimming Rod No spore 50-51
Citrobacter gillenii Citrobacter genomospecies 10 2 Rare Possible Commensal Possible Pathogen human faeces, urine, clinical sources and the environment RajilicStojanovic2014, Lagier2016, Yang2020 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Swimming Rod No spore
Citrobacter intermedius Unlikely Possible Commensal Non/unknown Pathogen human faeces RajilicStojanovic2014, Lagier2016 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Swimming Rod No spore
Citrobacter koseri 2 Minor Known Commensal Opportunistic Pathogen human faeces, clinical sources (blood, wound, urine - CCUG) and the environment Walker2011, RajilicStojanovic2014, Lagier2016, Byrd2020, New2022, Dubinkina2017, Zeller2014, Vachida2019 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Swimming Rod No spore 51-52
Citrobacter murliniae Negative 2 Rare Possible Commensal Opportunistic Pathogen human faeces (high load in several ulcerative colitis patients), clinical sources (blood, urine - CCUG) and food Pandey2012, RajilicStojanovic2014, Lagier2016 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Swimming Rod No spore
Citrobacter pasteurii Rare Possible Commensal Non/unknown Pathogen human faeces (diarrhoea patient - Clermont2015) Forster2019, Byrd2020 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Swimming Rod No spore 51.80
Citrobacter portucalensis Citrobacter sp. 30_2 Rare Transient Non/unknown Pathogen In 9% of Europeans (unseenbio.com). Rare coloniser. a water well, Portugal Byrd2020, New2022, Jie2017 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Swimming Rod No spore 52
Citrobacter rodentium Citrobacter species 9 2 Opportunistic in immunocompromised patients Rare Possible Commensal Possible Pathogen rodents Byrd2020, Zeller2014 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Sessile Rod No spore
Citrobacter sedlakii 2 Rare Possible Commensal Possible Pathogen human faeces and clinical sources (blood, urine - CCUG) RajilicStojanovic2014, Lagier2016, Byrd2020 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Swimming Rod No spore
Citrobacter werkmanii Negative 2 Rare Known Commensal Possible Pathogen human faeces (high load in several ulcerative colitis patients), clinical sources (blood - CCUG) and soil RajilicStojanovic2014, Lagier2016, Byrd2020, Yang2020, Wang2020a Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Swimming Rod No spore
Citrobacter youngae Negative 2 Rare Known Commensal Opportunistic Pathogen human faeces (high load in several ulcerative colitis patients), clinical sources, food, animals and soil Tyakht2013, RajilicStojanovic2014, Lagier2016, Dubinkina2017, Zeller2014 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Swimming Rod No spore
Citroniella saccharovorans Rare Possible Commensal Non/unknown Pathogen human faeces (CCUG) Firmicutes Clostridia Peptoniphilaceae + SANA Sessile Coccus No spore 29.9
Cloacibacillus evryensis Minor Known Commensal Possible Pathogen human faeces, and wastewater RajilicStojanovic2014, Lagier2016, Forster2019, Byrd2020, Yang2020, Jie2017, Minerbi2019 Synergistetes Synergistia Synergistaceae neg SANA Sessile Rod No spore 55.8
Cloacibacillus porcorum Rare Possible Commensal Possible Pathogen Ferments mucin to formate, acetate and propionate. human faeces (Bilen2018e), clinical sources (blood - CCUG) and pig intestines Lagier2016, Byrd2020, Yang2020, New2022, Jeong2021, Wang2020a Synergistetes Synergistia Synergistaceae neg SANA Sessile Rod - curved No spore 55.1
Cloacibacterium normanense 1 Rare Possible Commensal Non/unknown Pathogen human faeces, wastewater, and human gut RajilicStojanovic2014, Cassir2015, Byrd2020 Bacteroidetes Flavobacteriia Weeksellaceae neg FANA Sessile Pleiomorph rod No spore 31
Clostridioides difficile Clostridium difficile Negative 2 Human and animal pathogen Widespread Known Commensal Causes Illness Produces 5-aminovalerate and 2-aminobutyrate. Also appears to uniquely produce p-cresol as a breakdown product of tyrosine metabolism, which gives the diarrhoea a distinct odour. human faeces, soil, clinical specimens (rare), and other animals Finegold1974, Benno1984, Benno1989, Woodmansey2004, Walker2011, Pandey2012, Zupancic2012, Tyakht2013, Aujoulat2014, RajilicStojanovic2014, Salonen2014, Cassir2015, Lagier2016, Almeida2019, Forster2019, King2019, Byrd2020, Byrd2020, De2020, New2022, Dubinkina2017, Hu2019, Zeller2014, Vachida2019, Wang2020a, LeChatelier2013, PerezBrocal2015 Firmicutes Clostridia Peptostreptococcaceae + SANA Swimming Rod Endospore 28.0
Clostridioides mangenotii Clostridium mangenotii 1 Rare Known Commensal Known Pathogen Produces 5-aminovalerate and 2-aminobutyrate. human faeces (Rainey2011fBergey), soil and marine sediments Lagier2016 Firmicutes Clostridia Peptostreptococcaceae + SANA Sessile Rod Endospore 31.6 20(neg)
Clostridium acetobutylicum Positive 1 Rare Known Commensal Non/unknown Pathogen human faeces, soil, water sources and animals Taylor1985, RajilicStojanovic2014, Lagier2016, New2022, Qin2012 Firmicutes Clostridia Clostridiaceae + SANA Swimming Rod Endospore 28-29 20(neg)
Clostridium amazonense Rare Possible Commensal Non/unknown Pathogen human faeces (CCUG) Firmicutes Clostridia Clostridiaceae + SANA Rod Endospore 31.6
Clostridium amazonitimonense Rare Possible Commensal Non/unknown Pathogen human faeces (CCUG, Alou2018) Lagier2016 Firmicutes Clostridia Clostridiaceae + SANA Swimming Rod Endospore 30.6
Clostridium aminobutyricum Rare Possible Commensal Non/unknown Pathogen swamp mud, USA Firmicutes Clostridia Clostridiaceae + SANA Swimming Short Rod Endospore
Clostridium aminophilum 1 Rare Possible Commensal Non/unknown Pathogen Asaccharolytic. Sodium is essential for growth fistulated cattle Firmicutes Clostridia Lachnospiraceae + SANA Sessile Rod Endospore 52.5
Clostridium amylolyticum Rare Possible Commensal Non/unknown Pathogen a upflow anaerobic blanket digestion reactor Lagier2016 Firmicutes Clostridia Clostridiaceae + SANA Swimming Rod No spore 33.1
Clostridium anorexicamassiliense Rare Possible Commensal Non/unknown Pathogen human faeces Pfleiderer2013, RajilicStojanovic2014 Firmicutes Clostridia Clostridiaceae + SANA Sessile Rod
Clostridium argentinense 2 Rare Possible Commensal Opportunistic Pathogen Produces phenylacetic acid as a fermentation byproduct; doesn't ferment sugars. May produce neuroparalytic toxins (botulinum toxin). Doesn't produce indole but can produce an indole derivative. soil, amniotic fluid, autopsy specimens, blood and wounds, Argentina New2022 Firmicutes Clostridia Clostridiaceae + ANA Swimming Rod Endospore 28-30
Clostridium aurantibutyricum Positive 1 Rare Known Commensal Non/unknown Pathogen human faeces (Rainey2011aBergey), rotting vegetation and sewage sludge Firmicutes Clostridia Clostridiaceae + SANA Swimming Rod Endospore 27 20(neg)
Clostridium autoethanogenum Rare Possible Commensal Non/unknown Pathogen Ferments CO, H2 and CO2 to ethanol and acetate. rabbit faeces New2022 Firmicutes Clostridia Clostridiaceae + SANA Swimming Rod Endospore 26
Clostridium baratii Clostridium paraperfringens 2 Zoonotic pathogen Minor Known Commensal Opportunistic Pathogen human faeces, human gut, and wounds Finegold1974, Finegold1977, Benno1984, Woodmansey2004, Pfleiderer2013, RajilicStojanovic2014, Browne2016, Lagier2016, Byrd2020, New2022 Firmicutes Clostridia Clostridiaceae + SANA Sessile Rod Endospore 28 20(neg)
Clostridium beijerinckii Clostridium rubrum 1 Minor Known Commensal Opportunistic Pathogen human faeces, and soil Finegold1977, Benno1984, Benno1986, Benno1989, RajilicStojanovic2014, Lagier2016, Byrd2020, New2022, Zeller2014 Firmicutes Clostridia Clostridiaceae + SANA Swimming Rod Endospore 26-28 20(neg)
Clostridium boliviensis Rare Possible Commensal Non/unknown Pathogen Unpublished thus far. human faeces and sludge, Bolivia Forster2019 Firmicutes Clostridia Clostridiaceae + ANA
Clostridium bornimense Rare Possible Commensal Non/unknown Pathogen a biogas reactor Byrd2020, New2022 Firmicutes Clostridia Clostridiaceae vr ANA Rod Rare 29.6
Clostridium botulinum Gp I Negative 2 Unlikely Possible Commensal Causes Illness Causes illness; unlikely to be a coloniser of a healthy microbiome. human gut, soil, food and animal intestines Benno1984, RajilicStojanovic2014, Lagier2016, King2019, New2022, Zeller2014, Qin2012 Firmicutes Clostridia Clostridiaceae + SANA Swimming Rod - curved Endospore 26-28 20(neg)
Clostridium botulinum Gp II Negative 2 Unlikely Possible Commensal Opportunistic Pathogen Causes illness; unlikely to be a coloniser of a healthy microbiome. human faeces, soil, marine, and animals Finegold1974, Benno1984, RajilicStojanovic2014, Lagier2016, King2019 Firmicutes Clostridia Clostridiaceae + ANA Swimming Rod Endospore 27-29 20(neg)
Clostridium botulinum Gp III 2 Unlikely Possible Commensal Opportunistic Pathogen Causes illness; unlikely to be a coloniser of a healthy microbiome. faeces and carcasses Benno1984, RajilicStojanovic2014, Lagier2016, King2019 Firmicutes Clostridia Clostridiaceae + ANA Swimming Rod Endospore 26-28 20(neg)
Clostridium botulinum Gp IV 2 Unlikely Possible Commensal Opportunistic Pathogen Causes illness; unlikely to be a coloniser of a healthy microbiome. soil, human autopsy Benno1984, RajilicStojanovic2014, Lagier2016, King2019 Firmicutes Clostridia Clostridiaceae + ANA Swimming Rod No spore 20(neg)
Clostridium budayi Eubacterium budayi 1 Rare Transient Non/unknown Pathogen human faeces, cadaver and soil Finegold1977, RajilicStojanovic2014, Lagier2016 Firmicutes Clostridia Clostridiaceae + SANA Sessile Rod
Clostridium butyricum Positive 2 Zoonotic pathogen Widespread Known Commensal Opportunistic Pathogen human faeces, soil, clinical sources (blood, tissue - CCUG) and water sources Finegold1977, Benno1984, Benno1986, Woodmansey2004, McLaughlin2010, Walker2011, Zupancic2012, Pfleiderer2013, Aujoulat2014, RajilicStojanovic2014, Cassir2015, Lagier2016, Zou2019, Almeida2019, Byrd2020, Yang2020, New2022, Dubinkina2017, Hu2019, Jeong2021, Zeller2014, Vachida2019, PerezBrocal2015 Firmicutes Clostridia Clostridiaceae + ANA Swimming Rod Endospore 27-28
Clostridium cadaveris 2 Rare Known Commensal Opportunistic Pathogen human faeces, clinical sources (abscesses, wounds and blood - CCUG), soil and animals Finegold1977, RajilicStojanovic2014, Lagier2016, Byrd2020 Firmicutes Clostridia Clostridiaceae + SANA Swimming Rod Endospore 27 20(d(neg))
Clostridium cagae Rare Possible Commensal Non/unknown Pathogen human faeces (Tall2020a) Firmicutes Clostridia Clostridiaceae + SANA Sessile Rod Endospore 36.6
Clostridium carboxidivorans 1 Rare Possible Commensal Non/unknown Pathogen Consumes H2/CO2 or CO autotrophically. Cellulolytic. Homoacetogen. settling lagoon Lagier2016, New2022, Qin2012 Firmicutes Clostridia Clostridiaceae + SANA Swimming Rod Rare 31-32
Clostridium carnis 2 Rare Known Commensal Opportunistic Pathogen human faeces (Rainey2011aBergey), clinical specimens, soil and putrefying meat Firmicutes Clostridia Clostridiaceae + SANA Swimming Rod Endospore 28 20(neg)
Clostridium celatum Positive 1 Minor Known Commensal Non/unknown Pathogen human faeces Benno1986, RajilicStojanovic2014, Lagier2016, Byrd2020, Chen2020, Dubinkina2017, Hu2019, Vachida2019 Firmicutes Clostridia Clostridiaceae + SANA Sessile Rod Endospore 20(neg)
Clostridium cellulosi 1 Unlikely Transient Non/unknown Pathogen Cellulolytic. High optimum growth temperature so unlikely to be a gut coloniser. human faeces and cow manure Salonen2014 Firmicutes Clostridia Clostridiaceae neg SANA Swimming Rod Endospore 35
Clostridium cellulovorans Positive 1 Rare Possible Commensal Non/unknown Pathogen Can't utilise starch or proteolyse protein. batch methanogenic fermentation Byrd2020, New2022 Firmicutes Clostridia Clostridiaceae neg SANA Sessile Rod Endospore 26-27
Clostridium chartatabidum 1 Rare Known Commensal Non/unknown Pathogen Cellulolytic. human faeces, and rumen of sheep and cattle Walker2011, RajilicStojanovic2014, Yang2020 Firmicutes Clostridia Clostridiaceae + SANA Swimming Rod Endospore 31
Clostridium chauvoei 2 Human and animal pathogen Rare Transient Opportunistic Pathogen human faeces, soil, and various animal gut RajilicStojanovic2014, Byrd2020, New2022 Firmicutes Clostridia Clostridiaceae + SANA Swimming Pleiomorphic Endospore 27 20(neg)
Clostridium cochlearium 1 Opportunistic in immunocompromised patients Minor Known Commensal Opportunistic Pathogen human faeces and clinical sources (wounds) Finegold1974, Finegold1977, Benno1984, Taylor1985, Benno1986, Benno1989, RajilicStojanovic2014, Lagier2016, Byrd2020, New2022 Firmicutes Clostridia Clostridiaceae + SANA Swimming Rod Endospore 27-28 20(neg)
Clostridium cocleatum 1 Opportunistic in immunocompromised patients Rare Known Commensal Opportunistic Infection human faeces Benno1984, Benno1986, Woodmansey2004, Walker2011, RajilicStojanovic2014, PerezBrocal2015 Firmicutes Clostridia Clostridiaceae + ANA Sessile Corkscrew Endospore 28-29 20(neg)
Clostridium colicanis 1 Rare Possible Commensal Non/unknown Pathogen canine faeces Firmicutes Clostridia Clostridiaceae neg ANA Sessile Rod Endospore 37.1
Clostridium colinum 2 Animal pathogen Rare Possible Commensal Possible Pathogen birds, and is an avian pathogen. Has been detected in human faeces Salonen2014, PerezBrocal2015 Firmicutes Clostridia Clostridiaceae + ANA Swimming Rod Endospore 43
Clostridium combesii Eubacterium combesii 2 Rare Transient Rare Opportunist infections and soil, Africa Finegold1977 Firmicutes Clostridia Clostridiaceae + SANA vr Rod No spore 28.1
Clostridium culturomicium Rare Possible Commensal Non/unknown Pathogen human faeces (obese) Firmicutes Clostridia Clostridiaceae + SANA Sessile Rod Endospore 32.2
Clostridium dakarense Rare Possible Commensal Non/unknown Pathogen human faeces (Lo2013) Lagier2016 Firmicutes Clostridia Clostridiaceae + SANA Swimming Rod Endospore 28.0
Clostridium diolis 1 Rare Possible Commensal Non/unknown Pathogen Produces 1,3-propanediol from glycerol. decaying straw Lagier2016 Firmicutes Clostridia Clostridiaceae + SANA Swimming Rod Endospore
Clostridium disporicum 1 Minor Known Commensal Non/unknown Pathogen Borderline cold mesophile human faeces, and rat faeces Mangin2004, McLaughlin2010, Walker2011, Aujoulat2014, RajilicStojanovic2014, Browne2016, Lagier2016, Byrd2020, Yang2020 Firmicutes Clostridia Clostridiaceae + SANA Sessile Rod Endospore 40-41
Clostridium drakei 1 Unlikely Transient Non/unknown Pathogen Can grow autotrophically with H2/CO2 or CO. Homoacetogen. an acidic coal-mine pond, Germany New2022 Firmicutes Clostridia Clostridiaceae + SANA Swimming Rod Endospore 30-32
Clostridium estertheticum 1 Unlikely Transient Non/unknown Pathogen Low optimum growth temperature (6-8C) so unlikely to be a gut coloniser. chill-stored vacuum-packed beef New2022 Firmicutes Clostridia Clostridiaceae + SANA Swimming Rod Endospore 32.4-33.9
Clostridium fallax Bacillus fallax 2 Human and animal pathogen Rare Known Commensal Opportunistic Pathogen Found in human breast milk (Jeurink2013). human faeces, clinical sources and animals Finegold1974, RajilicStojanovic2014, Lagier2016, Byrd2020 Firmicutes Clostridia Clostridiaceae + SANA Swimming Rod Endospore 26 20(neg)
Clostridium felsineum 1 Rare Known Commensal Non/unknown Pathogen human faeces, rotting vegetation and soil Finegold1974, RajilicStojanovic2014, Salonen2014, Byrd2020 Firmicutes Clostridia Clostridiaceae + SANA Swimming Endospore 26 20(neg)
Clostridium fessum Rare Possible Commensal Non/unknown Pathogen human faeces (Seo2021) Firmicutes Clostridia Clostridiaceae + SANA Swimming Rod Endospore 48.3
Clostridium gasigenes 1 Unlikely Transient Non/unknown Pathogen Psychrophilic. Optimum growth temp is low (20-22C), so unlikely to be a gut coloniser. vacuum-packed, chilled lamb ('brown pack' spoilage) Byrd2020, New2022 Firmicutes Clostridia Clostridiaceae + Swimming Endospore 28.3-29.4
Clostridium haemolyticum 2 Human and animal pathogen Rare Known Commensal Opportunistic Pathogen human faeces (Rainey2011aBergey), clinical sources and animal muscle Firmicutes Clostridia Clostridiaceae + SANA Swimming Rod Endospore 26-27 20(neg)
Clostridium herbivorans 1 Rare Possible Commensal Non/unknown Pathogen human faeces, and pig intestine Nam2008a, Walker2011, RajilicStojanovic2014 Firmicutes Clostridia Clostridiaceae + SANA Swimming Rod Endospore 38
Clostridium hylemonae Positive 1 Minor Known Commensal Non/unknown Pathogen human faeces Tyakht2013, RajilicStojanovic2014, Lagier2016, New2022, Dubinkina2017, Hu2019, Jie2017, Zeller2014, Vachida2019, Qin2012 Firmicutes Clostridia Clostridiaceae + SANA Sessile Rod - curved Endospore 48.6
Clostridium ihumii Rare Possible Commensal Non/unknown Pathogen human faeces (Merhej2015) Lagier2016, Byrd2020 Firmicutes Clostridia Clostridiaceae + SANA Swimming Rod Endospore 26.7
Clostridium innocuum 2 Widespread Known Commensal Opportunistic Pathogen human faeces and clinical sources (blood, appendix - CCUG) Moore1974, Holdeman1976, Finegold1974, Finegold1977, Benno1984, Benno1986, Benno1989, Mangin2004, MacFarlane2004, Woodmansey2004, Nam2008a, Walker2011, Zupancic2012, Pfleiderer2013, Aujoulat2014, Nielsen2014, RajilicStojanovic2014, Browne2016, Lagier2016, Rothschild2018, Zou2019, Yang2020, New2022, Chen2020, Hu2019, Vachida2019 Firmicutes Clostridia Clostridiaceae + SANA Sessile Rod Endospore 43-44
Clostridium intestinale Clostridium intestinalis 1 Rare Transient Non/unknown Pathogen pig, cattle faeces and human large intestine (Elsayed2005) Byrd2020, New2022 Firmicutes Clostridia Clostridiaceae + FANA Swimming Rod Endospore 26-28
Clostridium isatidis 1 Unlikely Possible Commensal Non/unknown Pathogen Indigo is reduced. High optimum growth temperature so unlikely to be a gut coloniser. a woad vat New2022 Firmicutes Clostridia Clostridiaceae + ANA Swimming Rod Endospore 27
Clostridium jeddahense Rare Possible Commensal Non/unknown Pathogen human faeces (Lagier2014) Lagier2016, Byrd2020 Firmicutes Clostridia Clostridiaceae + SANA Swimming Rod Endospore 52.0
Clostridium jeddahitimonense Rare Possible Commensal Non/unknown Pathogen human faeces (obese) Firmicutes Clostridia Clostridiaceae + SANA Sessile Rod Endospore 29.2
Clostridium kluyveri 1 Unlikely Transient Non/unknown Pathogen Caproate produced but doesn't attack carbohydrates. Prefers yeast autolysate and ethanol. fresh water, marine muds and decaying plants New2022, Qin2012 Firmicutes Clostridia Clostridiaceae vr SANA Swimming Rod Endospore 30
Clostridium leptum Positive 1 Widespread Known Commensal Non/unknown Pathogen human faeces McLaughlin2010, Walker2011, Zupancic2012, Tyakht2013, Nielsen2014, RajilicStojanovic2014, Salonen2014, Lagier2016, Rothschild2018, Zou2019, Byrd2020, De2020, Yang2020, Chen2020, Dubinkina2017, Hu2019, Jeong2021, Jie2017, Zeller2014, Wang2018, Vachida2019, Wang2020a, Urban2020, Qin2012, Minerbi2019, Karlsson2013 Firmicutes Clostridia Clostridiaceae + SANA Sessile Rod - curved Endospore 51-52 20(neg)
Clostridium magnum 1 Rare Possible Commensal Non/unknown Pathogen Homoacetogen. anoxic freshwater sediments De2020 Firmicutes Clostridia Clostridiaceae neg SANA Swimming Rod Endospore 29.1
Clostridium malenominatum Bacillus malenominatus 2 Rare Known Commensal Opportunistic Pathogen human faeces, soil and clinical sources Finegold1974, Taylor1985, MacFarlane2004, Woodmansey2004, RajilicStojanovic2014, Lagier2016 Firmicutes Clostridia Clostridiaceae + SANA Swimming Rod Endospore 28 20(neg)
Clostridium manihotivorum Rare Possible Commensal Non/unknown Pathogen pulp landfill, Thailand New2022 Firmicutes Clostridia Clostridiaceae + ANA Sessile Rod Endospore 32
Clostridium massiliamazoniense Clostridium massilioamazoniense Rare Possible Commensal Non/unknown Pathogen the human gut Pfleiderer2013, Lagier2016 Firmicutes Clostridia Clostridiaceae + SANA Sessile Rod Endospore 27.6
Clostridium massiliodielmoense Rare Possible Commensal Non/unknown Pathogen human faeces (Alou2016a) Lagier2016, Byrd2020 Firmicutes Clostridia Clostridiaceae + SANA Sessile Rod Endospore 28.3
Clostridium mediterraneense Clostridium mediterraneense Rare Possible Commensal Non/unknown Pathogen the faeces of a man with diabetes Lagier2016, Byrd2020 Firmicutes Clostridia Clostridiaceae + SANA Swimming Rod Endospore
Clostridium merdae Rare Possible Commensal Non/unknown Pathogen human faeces (Alou2018) Firmicutes Clostridia Clostridiaceae + SANA Swimming Rod Endospore 45.3
Clostridium metallolevans Rare Possible Commensal Non/unknown Pathogen Produces volatile metalloids from As, Sb, Se, Te, Bi and Hg. Butyraldehyde is also a product of fermentation. Zupancic2012 Firmicutes Clostridia Clostridiaceae + SANA Rod Endospore
Clostridium methoxybenzovorans 1 Rare Possible Commensal Non/unknown Pathogen Methoxyaryl demethylation occurs. Homoacetogen. Able to use the following electron donors: methanol, sugars, lactate, methoxylated aromatics. human faeces, and an anaerobic digester RajilicStojanovic2014 Firmicutes Clostridia Clostridiaceae + SANA Sessile Rod Endospore 44
Clostridium methylpentosum Positive 1 Moderate Known Commensal Non/unknown Pathogen Seen in 83% of subjects in study by Qin2010, but at low levels. Moderate coloniser. human faeces Walker2011, Zupancic2012, Tyakht2013, RajilicStojanovic2014, Lagier2016, Dubinkina2017, Jie2017, Zeller2014, Vachida2019, Qin2012, PerezBrocal2015 Firmicutes Clostridia Clostridiaceae + SANA Sessile Rod - curved Endospore 46 20(+)
Clostridium minihomine Rare Possible Commensal Non/unknown Pathogen human faeces (CCUG) Byrd2020 Firmicutes Clostridia Clostridiaceae + SANA Rod
Clostridium moniliforme Eubacterium moniliforme 2 Rare Known Commensal Opportunistic Infection human faeces, soil and clinical samples (blood and various infections) Finegold1974, Finegold1977, RajilicStojanovic2014, Lagier2016 Firmicutes Clostridia Clostridiaceae + SANA Swimming Rod No spore 20(+)
Clostridium neonatale Minor Possible Commensal Rare Opportunist human faeces and clinical sources (blood - CCUG) Favier2002, Aujoulat2014, RajilicStojanovic2014, Cassir2015, Lagier2016, Byrd2020, Li2019b Firmicutes Clostridia Clostridiaceae + SANA Swimming Rod Endospore 28.5
Clostridium niameyense Rare Possible Commensal Non/unknown Pathogen human faeces (anorexic person with marasmus) Lagier2016, Byrd2020 Firmicutes Clostridia Clostridiaceae + SANA Swimming Rod No spore 27
Clostridium nigeriense Rare Possible Commensal Non/unknown Pathogen human faeces (Alou2018) Lagier2016, Byrd2020 Firmicutes Clostridia Clostridiaceae + FANA Swimming Rod Endospore 28.2
Clostridium nitritogenes Eubacterium nitritogenes 2 Rare Transient Opportunistic Infection human faeces, soil and clinical sources (infections) Finegold1974, RajilicStojanovic2014, Lagier2016 Firmicutes Clostridia Clostridiaceae + SANA Sessile Rod
Clostridium novyi A Negative 2 Human and animal pathogen Rare Transient Opportunistic Pathogen human faeces (possibly transient), clinical (blood - CCUG) and animal sources Woodmansey2004, Lagier2016, New2022 Firmicutes Clostridia Clostridiaceae + SANA Swimming Rod Endospore 29 20(neg)
Clostridium oceanicum Positive 1 Rare Known Commensal Non/unknown Pathogen human faeces (Rainey2011aBergey) and marine sediments Firmicutes Clostridia Clostridiaceae + ANA Swimming Rod Endospore 26-28 20(neg)
Clostridium paraputrificum 2 Moderate Known Commensal Opportunistic Pathogen human faeces, animal faeces and clinical sources (peritoneal fluid, wounds, and appendicitis) Finegold1974, Finegold1977, Benno1984, Taylor1985, Benno1986, Benno1989, McLaughlin2010, Walker2011, Zupancic2012, Pfleiderer2013, Aujoulat2014, RajilicStojanovic2014, Browne2016, Cassir2015, Lagier2016, Byrd2020, Yang2020 Firmicutes Clostridia Clostridiaceae + SANA Swimming Rod Endospore 26-27 20(+)
Clostridium pasteurianum 1 Rare Possible Commensal Non/unknown Pathogen soil New2022 Firmicutes Clostridia Clostridiaceae + ANA vr Rod Endospore 26-28 20(neg)
Clostridium perfringens 2 Human and animal pathogen Widespread Known Commensal Known Pathogen human faeces, clinical sources (blood, wound - CCUG) and human gut Finegold1974, Finegold1977, Benno1984, Taylor1985, Benno1986, Benno1989, Mangin2004, Woodmansey2004, McLaughlin2010, Walker2011, Zupancic2012, deGoffau2013, Pfleiderer2013, Tyakht2013, Aujoulat2014, RajilicStojanovic2014, Cassir2015, Browne2016, Lagier2016, Zou2019, Almeida2019, Byrd2020, Yang2020, New2022, Dubinkina2017, Hu2019, Jie2017, Zeller2014, Vachida2019, Wang2020a, Moore1995, Li2019b, PerezBrocal2015 Firmicutes Clostridia Clostridiaceae + SANA Sessile Rod Endospore 27
Clostridium phoceensis Rare Possible Commensal Non/unknown Pathogen human faeces (Hosny2019) Lagier2016, Minerbi2019 Firmicutes Clostridia Clostridiaceae neg SANA Sessile Rod Endospore 59.3
Clostridium polyendosporum Anaerobacter polyendosporus 1 Rare Transient Non/unknown Pathogen human faeces (probably transient) and soil Forster2019 Firmicutes Clostridia Clostridiaceae + SANA Sessile Pleiomorphic Endospore 29
Clostridium polynesiense Rare Possible Commensal Non/unknown Pathogen human faeces (Sankar2015) Lagier2016 Firmicutes Clostridia Clostridiaceae + SANA Swimming Rod Endospore 34
Clostridium polysaccharolyticum Fusobacterium polysaccharolyticum 1 Rare Possible Commensal Non/unknown Pathogen Cellulolytic. human faeces and sheep rumen Walker2011, Byrd2020, De2020 Firmicutes Clostridia Clostridiaceae neg SANA Swimming Rod Endospore 41.6
Clostridium populeti 1 Rare Possible Commensal Non/unknown Pathogen Cellulolytic. human faeces, and Poplar wood digestion Nam2008a, RajilicStojanovic2014, Byrd2020 Firmicutes Clostridia Clostridiaceae neg SANA Swimming Rod Endospore 28
Clostridium punense Rare Possible Commensal Non/unknown Pathogen human faeces (CCUG) Firmicutes Clostridia Clostridiaceae + SANA Sessile Rod Endospore 44.1
Clostridium putrefaciens 1 Opportunistic in immunocompromised patients Minor Transient Opportunistic Infection Low optimum growth temp, so unlikely gut coloniser. human faeces, bacteriuria and rotting meat Finegold1974, Finegold1977, Benno1984, Taylor1985, Benno1989, RajilicStojanovic2014, Lagier2016 Firmicutes Clostridia Clostridiaceae + ANA Sessile Rod Endospore 22-25 20(neg)
Clostridium rectalis Rare Possible Commensal Non/unknown Pathogen human faeces (Tall2020a) Firmicutes Clostridia Clostridiaceae + SANA Sessile Rod Endospore 28.1
Clostridium roseum 1 Rare Possible Commensal Non/unknown Pathogen German maize Firmicutes Clostridia Clostridiaceae + SANA Swimming Rod Endospore
Clostridium saccharobutylicum 1 Unlikely Transient Non/unknown Pathogen Doesn't produce riboflavin when grown in milk. Patented industrial strains used to produce solvents (acetone and butanol). commercial solvent production Byrd2020, New2022 Firmicutes Clostridia Clostridiaceae + ANA Swimming Rod Endospore 28-32
Clostridium saccharoperbutylacetonicum 1 Rare Possible Commensal Non/unknown Pathogen human faeces RajilicStojanovic2014, Cassir2015, Byrd2020, New2022 Firmicutes Clostridia Clostridiaceae + SANA Swimming Rod Endospore 31
Clostridium sardiniense Clostridium absonum 2 Rare Known Commensal Possible Pathogen human faeces (infants) Woodmansey2004, RajilicStojanovic2014, Lagier2016, Zou2019, Yang2020 Firmicutes Clostridia Clostridiaceae + SANA Sessile Rod Endospore
Clostridium sartagoforme 1 Minor Known Commensal Non/unknown Pathogen human faeces and oral cavity Finegold1974, Finegold1977, Benno1984, Benno1986, Benno1989, RajilicStojanovic2014, Lagier2016, Byrd2020 Firmicutes Clostridia Clostridiaceae + SANA Swimming Rod Endospore 28 20(neg)
Clostridium saudiense Clostridium saudii Minor Possible Commensal Rare Opportunist In 54% of Europeans (unseenbio.com). Minor coloniser. human faeces and clinical sources (blood - CCUG) Chung2016, Lagier2016, Byrd2020, Minerbi2019 Firmicutes Clostridia Clostridiaceae + SANA Swimming Rod Endospore 28
Clostridium scatologenes 1 Opportunistic in immunocompromised patients Rare Known Commensal Opportunistic Infection Homoacetogen. Able to use the following donors: ethanol, butanol, glycerol, sugars, methoxylated aromatics. human faeces (undersized infants - Rainey2011aBergey) Firmicutes Clostridia Clostridiaceae + SANA Swimming Rod Endospore 27 20(neg)
Clostridium schirmacherense 1 Unlikely Transient Non/unknown Pathogen Optimum growth temperature is 5-10C; unlikely to be a gut coloniser. cold lake sediment Lagier2016 Firmicutes Clostridia Clostridiaceae + SANA Swimming Rod Endospore 24
Clostridium scindens Positive 1 Moderate Known Commensal Non/unknown Pathogen Capable of bile acid 7α-dehydroxylation which produces toxic secondary bile acids. These metabolites inhibit Clostridioides difficile growth. 50% of Europeans have it (unseenbio.com). human faeces Pfleiderer2013, Tyakht2013, RajilicStojanovic2014, Lagier2016, Yang2020, New2022, Dubinkina2017, Hu2019, Jie2017, Zeller2014, Vachida2019, Wang2020a, Qin2012, Minerbi2019, Karlsson2013 Firmicutes Clostridia Clostridiaceae + SANA Sessile Endospore 45
Clostridium senegalense Rare Possible Commensal Non/unknown Pathogen human faeces, and human gut RajilicStojanovic2014, Lagier2016, Byrd2020 Firmicutes Clostridia Clostridiaceae + SANA Swimming Rod Endospore 26.8
Clostridium septicum 2 Rare Known Commensal Opportunistic Pathogen human faeces, soil, animals and clinical sources (bacteremia, gas gangrene, other infections) Finegold1974, Finegold1977, RajilicStojanovic2014, Lagier2016, Byrd2020, New2022 Firmicutes Clostridia Clostridiaceae + SANA Swimming Endospore 24
Clostridium sporogenes Negative 2 Minor Known Commensal Opportunistic Pathogen human faeces, soil, animals and clinical sources (bacteremia, wounds, abscesses and atherosclerotic plaques) Taylor1985, Woodmansey2004, Pfleiderer2013, Tyakht2013, RajilicStojanovic2014, Lagier2016, Almeida2019, Jeong2021, Wang2020a Firmicutes Clostridia Clostridiaceae + SANA Swimming Rod Endospore 26 20(d)
Clostridium sporosphaeroides 1 Minor Known Commensal Non/unknown Pathogen human faeces and canned food Moore1974, Finegold1974, Benno1984, Woodmansey2004, PerisBondia2011, RajilicStojanovic2014, Lagier2016, Byrd2020 Firmicutes Clostridia Clostridiaceae + SANA Sessile Endospore 27 20(neg)
Clostridium subterminale 2 Rare Known Commensal Opportunistic Infection human faeces, soil, animals and clinical sources (diarrhoea, rare infections) Taylor1985, McLaughlin2010, RajilicStojanovic2014, Lagier2016 Firmicutes Clostridia Clostridiaceae + SANA Swimming Rod Endospore 28 20(neg)
Clostridium sulfidigenes Rare Possible Commensal Non/unknown Pathogen pond sediment and human faeces Lagier2016 Firmicutes Clostridia Clostridiaceae + SANA Swimming Rod Endospore 32.3
Clostridium symbiosum 2 Widespread Known Commensal Opportunistic Pathogen human faeces and clinical sources (blood, liver abscess, bowel infections) Walker2011, Pfleiderer2013, Tyakht2013, Aujoulat2014, Nielsen2014, RajilicStojanovic2014, Salonen2014, Lagier2016, Rothschild2018, Zou2019, Almeida2019, Byrd2020, Yang2020, Chen2020, Dubinkina2017, Hu2019, Jie2017, Zeller2014, Wang2018, Vachida2019, Wang2020a, Urban2020, Qin2012, LeChatelier2013, Karlsson2013 Firmicutes Clostridia Clostridiaceae neg SANA Swimming Rod Endospore 46.2 20(neg)
Clostridium taeniosporum Unlikely Transient Non/unknown Pathogen Closely related to C. botulinum but doesn't produce the toxin. lake silt, Crimea Byrd2020, New2022 Firmicutes Clostridia Clostridiaceae + ANA Swimming Rod Endospore
Clostridium tertium 2 Human and animal pathogen Moderate Known Commensal Opportunistic Pathogen human faeces and appendix, clinical sources (blood, bowel infections, brain abscess) Finegold1977, Benno1984, Taylor1985, Benno1986, Benno1989, Woodmansey2004, Walker2011, Pfleiderer2013, Aujoulat2014, RajilicStojanovic2014, Lagier2016, Zou2019, Byrd2020, Yang2020, Minerbi2019 Firmicutes Clostridia Clostridiaceae + ANA Swimming Rod Endospore 24-26 20(neg)
Clostridium tetani Negative 2 Toxin produced; vaccine available, human and animal pathogen Unlikely Known Commensal Known Pathogen human faeces (Rainey2011aBergey), animal faeces, soil, clinical sources (wounds, infected gums, infections) Lagier2016, New2022, Zeller2014 Firmicutes Clostridia Clostridiaceae + SANA Swimming Rod Endospore 25-26 20(neg)
Clostridium thermarum Unlikely Transient Non/unknown Pathogen hot springs, China New2022 Firmicutes Clostridia Clostridiaceae + SANA Swimming Rod Endospore 36.3-36.6
Clostridium thermobutyricum 1 Rare Possible Commensal Non/unknown Pathogen horse manure compost containing straw and wood shavings Byrd2020 Firmicutes Clostridia Clostridiaceae vr ANA Swimming Rod Endospore 37
Clostridium thiosulfatireducens 1 Rare Possible Commensal Non/unknown Pathogen upflow anerobic sludge blanket digestors Lagier2016 Firmicutes Clostridia Clostridiaceae + ANA Swimming Rod Endospore 31.4
Clostridium transplantifaecale Rare Possible Commensal Non/unknown Pathogen Virtually all 50 carbohydrates tested (API50) were positive; this result is rather surprising. human faeces (Clostridioides difficile infection) Firmicutes Clostridia Clostridiaceae + ANA Sessile Rod 48.1
Clostridium tyrobutyricum Positive 1 Rare Known Commensal Non/unknown Pathogen human faeces Taylor1985, Benno1986, RajilicStojanovic2014, Lagier2016, Byrd2020, New2022 Firmicutes Clostridia Clostridiaceae + SANA Swimming Rod Endospore 28 20(neg)
Clostridium vincentii 1 Rare Transient Non/unknown Pathogen Can't grow at 31C or above. In 1% of Europeans (unseenbio.com). human faeces, and low-temperature anaerobic sediment RajilicStojanovic2014, Byrd2020 Firmicutes Clostridia Clostridiaceae + SANA Swimming Rod - curved Endospore 33
Clostridium viride 1 Rare Possible Commensal Non/unknown Pathogen human faeces, and anaerobic sewage sludge Walker2011, Zupancic2012, RajilicStojanovic2014 Firmicutes Clostridia Clostridiaceae + SANA Swimming Oval-shaped Unknown 41.5
Colibacter massiliensis Rare Possible Commensal Non/unknown Pathogen human faeces (Anani2019) Firmicutes Negativicutes Veillonellaceae + SANA Sessile Diplococci No spore 50.2
Colidextribacter massiliensis Rare Possible Commensal Non/unknown Pathogen human colon and human faeces (obese patient - Ricaboni2016c) De2020, Minerbi2019 Firmicutes Clostridia Eubacteriales incertae sedis neg SANA Coccus No spore
Collinsella aerofaciens Eubacterium aerofaciens Positive 2 Widespread Known Commensal Opportunistic Pathogen human faeces Moore1974, Holdeman1976, Finegold1974, Finegold1977, Benno1984, Benno1986, Benno1989, MacFarlane2004, Woodmansey2004, McLaughlin2010, Walker2011, Zupancic2012, Pfleiderer2013, Tyakht2013, Nielsen2014, RajilicStojanovic2014, Browne2016, Lagier2016, Rothschild2018, Zou2019, Chung2019, Forster2019, King2019, Byrd2020, De2020, Yang2020, New2022, Chen2020, Dubinkina2017, Hu2019, Jie2017, Zeller2014, Vachida2019, Wang2020a, Minerbi2019, Moore1995, Li2019b, Karlsson2013, PerezBrocal2015 Actinobacteria Coriobacteriia Coriobacteriaceae + SANA Sessile Coccus No spore 60-61
Collinsella bouchesdurhonensis Minor Possible Commensal Non/unknown Pathogen In 26% of Europeans (unseenbio.com). Minor coloniser. human faeces (CCUG) Byrd2020, De2020, Minerbi2019 Actinobacteria Coriobacteriia Coriobacteriaceae + SANA Sessile Rod No spore 57.9
Collinsella ihumii Collinsella ihuae Rare Possible Commensal Non/unknown Pathogen human faeces (healthy volunteer) Lagier2016, Byrd2020, De2020 Actinobacteria Coriobacteriia Coriobacteriaceae + SANA Sessile Rod No spore 64.1
Collinsella intestinalis 1 Moderate Known Commensal Non/unknown Pathogen human faeces Tyakht2013, Nielsen2014, RajilicStojanovic2014, Lagier2016, Zou2019, Forster2019, Byrd2020, Yang2020, Dubinkina2017, Hu2019, Jeong2021, Zeller2014, Vachida2019, Wang2020a, Minerbi2019 Actinobacteria Coriobacteriia Coriobacteriaceae + SANA Sessile Rod No spore 64.4
Collinsella massiliensis Rare Possible Commensal Non/unknown Pathogen human faeces (Padmanabhan2014) Lagier2016 Actinobacteria Coriobacteriia Coriobacteriaceae + SANA Sessile Rod No spore 65.8
Collinsella phocaeensis Rare Possible Commensal Non/unknown Pathogen human faeces (Bilen2018e) Byrd2020, De2020 Actinobacteria Coriobacteriia Coriobacteriaceae neg SANA Sessile Rod No spore
Collinsella provencensis Rare Possible Commensal Non/unknown Pathogen human faeces (CCUG) Byrd2020 Actinobacteria Coriobacteriia Coriobacteriaceae + ANA Sessile Rod No spore
Collinsella stercoris 1 Minor Known Commensal Non/unknown Pathogen human faeces Zupancic2012, Tyakht2013, Nielsen2014, RajilicStojanovic2014, Lagier2016, Forster2019, Byrd2020, Dubinkina2017, Zeller2014, Vachida2019, Minerbi2019, Li2019b, PerezBrocal2015 Actinobacteria Coriobacteriia Coriobacteriaceae + SANA Sessile Rod No spore 61.2
Collinsella tanakaei Minor Known Commensal Non/unknown Pathogen human faeces RajilicStojanovic2014, Lagier2016, Zou2019, Forster2019, Byrd2020, Dubinkina2017, Hu2019, Jie2017, Vachida2019, Qin2012, Minerbi2019 Actinobacteria Coriobacteriia Coriobacteriaceae + SANA Sessile Rod No spore 60.8 20(+)
Collinsella vaginalis Rare Possible Commensal Non/unknown Pathogen the vagina Byrd2020 Actinobacteria Coriobacteriia Coriobacteriaceae + SANA Sessile Rod No spore
Comamonas aquatica Aquaspirillum aquaticum 2 Non Transient Opportunistic Pathogen water sources De2020 Proteobacteria Betaproteobacteria Comamonadaceae neg AER Swimming Rod No spore 62.8-66.7
Comamonas denitrificans 1 Rare Possible Commensal Non/unknown Pathogen human faeces and activated sludge Yang2020 Proteobacteria Betaproteobacteria Comamonadaceae neg FANA Swimming Rod No spore 60.4-60.8
Comamonas kerstersii 2 Rare Possible Commensal Opportunistic Pathogen human faeces and clinical sources (blood, appendix - CCUG) RajilicStojanovic2014, Lagier2016, Byrd2020, Yang2020 Proteobacteria Betaproteobacteria Comamonadaceae neg AER Swimming Rod No spore 59.7-63.3
Comamonas koreensis 1 Unlikely Transient Non/unknown Pathogen Non-fermentative. a wetland sample, Korea New2022 Proteobacteria Betaproteobacteria Comamonadaceae neg FANA Sessile Rod No spore 66
Comamonas terrigena 2 Unlikely Transient Rare Opportunist Obligate aerobe; unlikely to be a gut coloniser. human faeces (CCUG), soil, and clinical sources (blood - CCUG) Yang2020 Proteobacteria Betaproteobacteria Comamonadaceae neg SAER Swimming Rod No spore 59.7-63.3
Comamonas testosteroni Pseudomonas testosteroni 1 Opportunistic in immunocompromised patients Rare Possible Commensal Rare Opportunist Metabolises testosterone. human faeces and clinical sources (blood - CCUG) Bik2006, McLaughlin2010, RajilicStojanovic2014, De2020, Zeller2014 Proteobacteria Betaproteobacteria Comamonadaceae neg FANA Swimming Rod No spore 61.0-62.1
Comamonas thiooxydans Rare Possible Commensal Non/unknown Pathogen Utilises thiosulfate as an electron acceptor. sulfur spring sediment Pandey2012, Yang2020 Proteobacteria Betaproteobacteria Comamonadaceae neg AER Swimming Rod No spore 61.4
Companilactobacillus alimentarius Lactobacillus alimentarius Positive 1 Rare Transient Non/unknown Pathogen human faeces and food (meat, fish, sourdough) MacFarlane2004, RajilicStojanovic2014, Lagier2016, Byrd2020 Firmicutes Bacilli Lactobacillaceae + Micr Sessile Rod No spore 36–37
Companilactobacillus farciminis Lactobacillus farciminis 1 Rare Transient Non/unknown Pathogen In 1% of Europeans (unseenbio.com). Rare coloniser. raw sausages and sourdough Yang2020, Hu2019, Zeller2014 Firmicutes Bacilli Lactobacillaceae + Micr Sessile Rod No spore 34-36
Companilactobacillus mindensis Lactobacillus mindensis 1 Unlikely Transient Non/unknown Pathogen human faeces and rye flour sourdough fermentation Yang2020 Firmicutes Bacilli Lactobacillaceae + FANA Sessile Rod No spore 37.5
Companilactobacillus versmoldensis Lactobacillus versmoldensis Positive 1 Unlikely Transient Non/unknown Pathogen raw fermented sausage Byrd2020 Firmicutes Bacilli Lactobacillaceae + FANA Sessile Rod No spore 40.5
Conexibacter woesei 1 Rare Possible Commensal Non/unknown Pathogen temperate forest soil Frank2007, Zeller2014 Actinobacteria Thermoleophilia Conexibacteraceae + AER Swimming Short Rod No spore 71
Congobacterium massiliense Rare Possible Commensal Non/unknown Pathogen human faeces (CCUG) Firmicutes Clostridia Eubacteriales Family XIII. Incertae Sedis + Rod
Coprobacillus cateniformis Coprobacillus sp 29 1 1 Moderate Known Commensal Non/unknown Pathogen human faeces (CCUG) Zupancic2012, Pfleiderer2013, RajilicStojanovic2014, Salonen2014, Lagier2016, Zou2019, Forster2019, Byrd2020, Yang2020, Chen2020, Wang2018, Vachida2019, Wang2020a, LeChatelier2013, PerezBrocal2015 Firmicutes Erysipelotrichia Coprobacillaceae + SANA Sessile Coccus No spore 32-34 20(neg)
Coprobacter fastidiosus Moderate Possible Commensal Non/unknown Pathogen In 87% of Europeans (unseenbio.com). human faeces (Shkoporov2013) Lagier2016, Rothschild2018, Zou2019, Forster2019, Byrd2020, Yang2020, Chen2020, Hu2019, Vachida2019, Minerbi2019 Bacteroidetes Bacteroidia Porphyromonadaceae neg SANA Sessile Rod No spore 38.5 2(+)
Coprobacter secundus Moderate Transient Non/unknown Pathogen In 73% of Europeans (unseenbio.com). human faeces (Shkoporov2015) Byrd2020, Yang2020 Bacteroidetes Bacteroidia Barnesiellaceae neg SANA Sessile Rod No spore 37.8 20(+)
Coprobacter secundus subsp. similis Rare Possible Commensal Non/unknown Pathogen human faeces New2022 Bacteroidetes Bacteroidia Barnesiellaceae neg SANA Sessile Rod No spore 38.4 20(+)
Coprococcus catus Positive 1 Widespread Known Commensal Non/unknown Pathogen human faeces Moore1974, PerisBondia2011, Walker2011, Zupancic2012, Tyakht2013, RajilicStojanovic2014, Lagier2016, Rothschild2018, Zou2019, Chung2019, Forster2019, King2019, De2020, Chen2020, Dubinkina2017, Hu2019, Jie2017, Zeller2014, Wang2018, Vachida2019, Wang2020a, LeChatelier2013, Karlsson2013, PerezBrocal2015 Firmicutes Clostridia Lachnospiraceae + SANA Sessile Coccus 41 20(+)
Coprococcus comes Positive 1 Opportunistic in immunocompromised patients Widespread Known Commensal Opportunistic Infection human faeces Moore1974, Holdeman1976, Finegold1977, Benno1986, Benno1989, McLaughlin2010, PerisBondia2011, Walker2011, Tyakht2013, Nielsen2014, RajilicStojanovic2014, Browne2016, Lagier2016, Rothschild2018, Zou2019, Chung2019, Forster2019, Byrd2020, Yang2020, New2022, Chen2020, Dubinkina2017, Hu2019, Jeong2021, Jie2017, Zeller2014, Wang2018, Vachida2019, Wang2020a, Urban2020, Qin2012, Minerbi2019, Moore1995, LeChatelier2013, Karlsson2013 Firmicutes Clostridia Lachnospiraceae + SANA Sessile Coccus Endospore 40 20(neg)
Coprococcus eutactus Positive 1 Widespread Known Commensal Non/unknown Pathogen human faeces Moore1974, Benno1986, PerisBondia2011, Walker2011, Zupancic2012, Tyakht2013, Nielsen2014, RajilicStojanovic2014, Salonen2014, Browne2016, Lagier2016, Rothschild2018, Zou2019, Forster2019, Byrd2020, Chen2020, Dubinkina2017, Hu2019, Jeong2021, Jie2017, Zeller2014, Wang2018, Vachida2019, Minerbi2019, Li2019b, LeChatelier2013, Karlsson2013, PerezBrocal2015 Firmicutes Clostridia Lachnospiraceae + SANA Sessile Coccus Endospore 41
Coprococcus phoceensis Rare Possible Commensal Non/unknown Pathogen human faeces (Crohn's) Firmicutes Clostridia Lachnospiraceae vr SANA Sessile Rod No spore 40.2
Coraliomargarita akajimensis 1 Non Transient Non/unknown Pathogen Obligate aerobe and low optimum temperature suggest it is not a gut coloniser. sea water, Japan Qin2012 Verrucomicrobia Opitutae Puniceicoccaceae neg SAER Sessile Coccus No spore 53.9
Coriobacterium glomerans 1 Unlikely Transient Non/unknown Pathogen the intestinal tracts of bugs Byrd2020, New2022, Zeller2014 Actinobacteria Coriobacteriia Coriobacteriaceae + SANA Sessile Pleiomorph rod No spore 61
Corynebacterium accolens 2 Rare Possible Commensal Opportunistic Pathogen clinical sources (inflammatory foci, blood, wound, vaginal discharge - CCUG). Has been detected in human faeces (Bilen2018e) Lagier2016, De2020, Zeller2014, Vachida2019 Actinobacteria Actinomycetia Corynebacteriaceae + FANA Sessile Rod No spore 58.2
Corynebacterium afermentans 2 Rare Known Commensal Opportunistic Pathogen Nonlipophilic. human faeces, clinical sources (blood, various - CCUG) and skin Pfleiderer2013, RajilicStojanovic2014, Lagier2016 Actinobacteria Actinomycetia Corynebacteriaceae + AER Sessile Pleiomorph rod No spore 66
Corynebacterium ammoniagenes Brevibacterium ammoniagenes 1 Opportunistic in immunocompromised patients Rare Possible Commensal Opportunistic Infection piggery waste and human faeces Tyakht2013, RajilicStojanovic2014, Lagier2016, Forster2019, Zeller2014 Actinobacteria Actinomycetia Corynebacteriaceae + FANA Sessile Rod No spore 53.7
Corynebacterium amycolatum 2 Human and animal pathogen Rare Known Commensal Opportunistic Pathogen Nonlipophilic. human faeces and clinical sources (blood, urine, pus, sputum, wound, other - CCUG) Hoyles2012, Pfleiderer2013, RajilicStojanovic2014, Lagier2016, Forster2019, Zeller2014 Actinobacteria Actinomycetia Corynebacteriaceae + FANA Sessile Pleiomorph rod No spore 61
Corynebacterium appendicis 1 Opportunistic in immunocompromised patients Rare Known Commensal Opportunistic Pathogen Lipophilic. an appendix and human faeces RajilicStojanovic2014, Lagier2016 Actinobacteria Actinomycetia Corynebacteriaceae + FANA Sessile Rod No spore 65.8
Corynebacterium argentoratense 2 Rare Possible Commensal Possible Pathogen the throats of patients suffering from tonsillitis Byrd2020 Actinobacteria Actinobacteria Corynebacteriaceae + FANA Sessile Pleiomorph rod No spore 60-61
Corynebacterium aurimucosum 1 Opportunistic in immunocompromised patients Rare Known Commensal Opportunistic Pathogen human faeces and various clinical specimens RajilicStojanovic2014, Lagier2016, Zeller2014 Actinobacteria Actinomycetia Corynebacteriaceae + FANA Sessile Coryneform No spore 63.7
Corynebacterium bouchesdurhonense Rare Possible Commensal Non/unknown Pathogen human faeces (Ndongo2017) and blood Lagier2016 Actinobacteria Actinomycetia Corynebacteriaceae + FANA Sessile Rod No spore
Corynebacterium bovis 2 Human and animal pathogen Rare Possible Commensal Opportunistic Pathogen Lipophilic irregular rods. commensal on cow's udder De2020 Actinobacteria Actinomycetia Corynebacteriaceae + AER Sessile Club rod No spore 67.8-69.7
Corynebacterium callunae 1 Unlikely Transient Non/unknown Pathogen Fermentative, non-lipophilic. heather New2022 Actinobacteria Actinomycetia Corynebacteriaceae + FANA Sessile Short Rod No spore 51.2
Corynebacterium casei 1 Rare Possible Commensal Non/unknown Pathogen the surface of a smear-ripened cheese Byrd2020 Actinobacteria Actinobacteria Corynebacteriaceae + FANA Sessile Pleiomorph rod No spore 51
Corynebacterium coyleae 2 Rare Known Commensal Opportunistic Pathogen Nonlipophilic. human faeces and clinical sources (blood, wound, vagina - CCUG) RajilicStojanovic2014, Lagier2016 Actinobacteria Actinomycetia Corynebacteriaceae + FANA Sessile Diphtheroidal No spore 62-64
Corynebacterium cystitidis 2 Animal pathogen Rare Possible Commensal Opportunistic Pathogen bovine sources De2020 Actinobacteria Actinomycetia Corynebacteriaceae + FANA Sessile Rod No spore 52.6-53.9
Corynebacterium diphtheriae 2 Toxin produced; vaccine available Non Transient Known Pathogen clinical sources Lagier2016 Actinobacteria Actinomycetia Corynebacteriaceae vr ANA Sessile Rod No spore 52-55
Corynebacterium doosanense Rare Possible Commensal Non/unknown Pathogen activated sludge Lagier2016, De2020 Actinobacteria Actinomycetia Corynebacteriaceae + AER Sessile Club rod No spore 53.5
Corynebacterium durum 1 Opportunistic in immunocompromised patients Minor Known Commensal Opportunistic Pathogen human faeces and clinical sources (sputum, abscess, lesion - CCUT) McLaughlin2010, RajilicStojanovic2014, Cassir2015, Lagier2016, Byrd2020, De2020, Jeong2021, Vachida2019, Li2019b, PerezBrocal2015 Actinobacteria Actinomycetia Corynebacteriaceae + FANA Sessile Pleiomorph rod No spore 55
Corynebacterium efficiens 1 Rare Possible Commensal Non/unknown Pathogen Produces large amounts of L-glutamic acid under aerobic conditions. soil and vegetables Lagier2016, Zeller2014 Actinobacteria Actinomycetia Corynebacteriaceae + FANA Sessile Club rod No spore 59-60.2
Corynebacterium falsenii 2 Rare Possible Commensal Opportunistic Pathogen Nonlipophilic. clinical sources De2020 Actinobacteria Actinomycetia Corynebacteriaceae + FANA Sessile Club rod No spore
Corynebacterium flavescens Microbacterium flavum 1 Rare Possible Commensal Possible Pathogen cheese (CCUG). Has also been detected in human faeces (Bilen2018e) Lagier2016, Byrd2020 Actinobacteria Actinomycetia Corynebacteriaceae vr FANA Sessile Pleiomorph rod No spore 58.3
Corynebacterium freneyi 2 Rare Possible Commensal Opportunistic Pathogen Nonlipophilic. human faeces and clinical sources (cervix, vagina, wound, blood - CCUG) RajilicStojanovic2014, Lagier2016 Actinobacteria Actinomycetia Corynebacteriaceae + FANA Sessile Club rod No spore
Corynebacterium genitalium Rare Possible Commensal Opportunistic Infection industrial sources and clinical specimens Zeller2014 Actinobacteria Actinomycetia Corynebacteriaceae + FANA Sessile Short Rod No spore 62.8
Corynebacterium glaucum 1 Rare Possible Commensal Non/unknown Pathogen human faeces Bik2006, RajilicStojanovic2014, Lagier2016, De2020 Actinobacteria Actinomycetia Corynebacteriaceae + FANA Sessile Coryneform No spore 64.3
Corynebacterium glucuronolyticum 2 Rare Possible Commensal Opportunistic Pathogen Nonlipophilic. clinical sources (prostatitis, cervix, urine, blood, vagina - CCUG) and human faeces Dubourg2013, RajilicStojanovic2014, Lagier2016 Actinobacteria Actinomycetia Corynebacteriaceae + FANA Sessile Coryneform No spore 52-58
Corynebacterium glutamicum 1 Rare Possible Commensal Non/unknown Pathogen Produces large amounts of L-glutamate under aerobic conditions. sewage Zeller2014 Actinobacteria Actinomycetia Corynebacteriaceae + FANA Sessile Short Rod No spore 55-57.7
Corynebacterium ihumii Rare Possible Commensal Non/unknown Pathogen human faeces (Padmanabhan2014a) Lagier2016 Actinobacteria Actinomycetia Corynebacteriaceae + FANA Sessile Rod No spore 65.1
Corynebacterium jeddahense Rare Possible Commensal Non/unknown Pathogen human faeces (Edouard2014) Lagier2016 Actinobacteria Actinomycetia Corynebacteriaceae + FANA Sessile Rod No spore 67.2
Corynebacterium jeikeium 2 Rare Unknown Opportunistic Pathogen clinical specimens (bone marrow, blood, skin, urine, heart valve) Zeller2014 Actinobacteria Actinomycetia Corynebacteriaceae + AER Sessile Pallasades No spore 58-61
Corynebacterium kroppenstedtii 1 Opportunistic in immunocompromised patients Minor Possible Commensal Opportunistic Pathogen clinical sources (wound, sputum - CCUG) and human faeces RajilicStojanovic2014, Lagier2016, De2020, Yang2020, Zeller2014, Vachida2019, PerezBrocal2015 Actinobacteria Actinomycetia Corynebacteriaceae + FANA Sessile Diphtheroidal No spore 62
Corynebacterium lipophiloflavum 1 Opportunistic in immunocompromised patients Rare Possible Commensal Opportunistic Pathogen Slightly lipophilic. clinical specimens (vaginosis) Lagier2016 Actinobacteria Actinomycetia Corynebacteriaceae + FANA Sessile Club rod No spore 65
Corynebacterium lujinxingii Rare Possible Commensal Non/unknown Pathogen human faeces (Zhang2021) Actinobacteria Actinomycetia Corynebacteriaceae + FANA Sessile Rod No spore 61.2–64.4
Corynebacterium matruchotii 2 Unlikely Transient Rare Opportunist plaque deposits in man and primates New2022, Zeller2014, Vachida2019 Actinobacteria Actinomycetia Corynebacteriaceae + FANA Sessile Pleiomorph rod No spore 55-58
Corynebacterium minutissimum 2 Rare Known Commensal Opportunistic Pathogen human faeces and clinical sources (blood, urine, vagina - CCUG) RajilicStojanovic2014, Lagier2016 Actinobacteria Actinomycetia Corynebacteriaceae + FANA Sessile Short Rod No spore 58
Corynebacterium mucifaciens 2 Rare Possible Commensal Rare Opportunist Nonlipophilic. clinical sources (blood - CCUG) and human faeces Bik2006, Pfleiderer2013, RajilicStojanovic2014, Lagier2016 Actinobacteria Actinomycetia Corynebacteriaceae + FANA Sessile Rod No spore 63-65
Corynebacterium neomassiliense Rare Possible Commensal Non/unknown Pathogen human faeces (healthy) Actinobacteria Actinomycetes Corynebacteriaceae + AER Sessile Rod No spore 66.8
Corynebacterium otitidis Turicella otitidis 2 Rare Possible Commensal Opportunistic Infection ear infections Lagier2016, De2020 Actinobacteria Actinomycetia Corynebacteriaceae + FANA Sessile Diphtheroidal No spore 65-72
Corynebacterium pacaense Rare Possible Commensal Non/unknown Pathogen human faeces (Bellali2019) Lagier2016 Actinobacteria Actinomycetia Corynebacteriaceae + AER Sessile Rod - curved No spore 63.7
Corynebacterium propinquum 2 Rare Possible Commensal Rare Opportunist clinical sources (wound, repiratory tract - CCUG) and human faeces RajilicStojanovic2014, Lagier2016, Byrd2020, Vachida2019 Actinobacteria Actinomycetia Corynebacteriaceae + FANA Sessile Rod No spore 57-59
Corynebacterium provencense Rare Possible Commensal Non/unknown Pathogen human faeces (Ndongo2017) Lagier2016, Byrd2020 Actinobacteria Actinomycetia Corynebacteriaceae + FANA Sessile Rod Exospore
Corynebacterium pseudodiphtheriticum 2 Rare Possible Commensal Rare Opportunist human faeces and clinical sources (blood, sputum, wound - CCUG) RajilicStojanovic2014, Lagier2016, Forster2019 Actinobacteria Actinomycetia Corynebacteriaceae + FANA Sessile Club rod No spore 54.9-56.8
Corynebacterium pseudogenitalium Rare Possible Commensal Rare Opportunist the normal flora of the genitourinary tract Lagier2016, Vachida2019 Actinobacteria Actinomycetia Corynebacteriaceae + FANA Sessile Pleiomorph rod No spore
Corynebacterium pyruviciproducens Rare Possible Commensal Opportunistic Infection Lipophilic. clinical sources (groin abscess) Lagier2016, Byrd2020 Actinobacteria Actinomycetia Corynebacteriaceae + FANA Sessile Coryneform No spore 62
Corynebacterium riegelii 2 Rare Possible Commensal Opportunistic Infection clinical sources Lagier2016 Actinobacteria Actinomycetia Corynebacteriaceae + FANA Sessile Club rod No spore
Corynebacterium sanguinis Rare Possible Commensal Opportunistic Pathogen clinical sources (blood, wound - CCUG) and human faeces RajilicStojanovic2014 Actinobacteria Actinomycetia Corynebacteriaceae + FANA Sessile Rod No spore 65
Corynebacterium simulans 2 Rare Known Commensal Possible Pathogen clinical sources and human faeces RajilicStojanovic2014, Lagier2016, De2020 Actinobacteria Actinomycetia Corynebacteriaceae + FANA Sessile Diphtheroidal No spore
Corynebacterium singulare 1 Opportunistic in immunocompromised patients Rare Possible Commensal Non/unknown Pathogen human semen Actinobacteria Actinomycetia Corynebacteriaceae + FANA Sessile Pallasades No spore 62
Corynebacterium stationis Brevibacterium stationis 1 Rare Possible Commensal Rare Opportunist Nonlipophilic. human faeces (infant stools - Bernard2010), clinical sources (blood) and seawater Lagier2016 Actinobacteria Actinomycetia Corynebacteriaceae + FANA Sessile Rod No spore 53.9
Corynebacterium striatum 2 Rare Possible Commensal Known Pathogen Nonlipophilic. clinical sources (blood, wound, infection - CCUG) and human faeces RajilicStojanovic2014, Lagier2016, Zeller2014 Actinobacteria Actinomycetia Corynebacteriaceae + FANA Sessile Club rod No spore 57.6
Corynebacterium suicordis 2 Animal pathogen Rare Possible Commensal Possible Pathogen Nonlipophilic. pig clinical sources Lagier2016 Actinobacteria Actinomycetia Corynebacteriaceae + FANA Sessile Rod No spore
Corynebacterium sundsvallense 2 Rare Possible Commensal Opportunistic Pathogen clinical sources (blood, sinus, vagina - CCUG) and human faeces RajilicStojanovic2014, Lagier2016 Actinobacteria Actinomycetia Corynebacteriaceae + AER Sessile Rod No spore 64
Corynebacterium tuberculostearicum 2 Rare Possible Commensal Opportunistic Pathogen Lipophilic. clinical sources (blood, wound, tissue - CCUG) and human faeces Pfleiderer2013, Aujoulat2014, RajilicStojanovic2014, Lagier2016, Yang2020, Zeller2014 Actinobacteria Actinomycetia Corynebacteriaceae + FANA Sessile Pleiomorph rod No spore 58
Corynebacterium ulcerans 2 Human and animal pathogen Rare Possible Commensal Known Pathogen clinical sources (throat, wound, sinus - CCUG) and human faeces RajilicStojanovic2014 Actinobacteria Actinomycetia Corynebacteriaceae + FANA Sessile Pleiomorph rod No spore 53-55
Corynebacterium urealyticum 2 Human and animal pathogen Rare Possible Commensal Opportunistic Pathogen Lipophilic. urine and clinical sources Lagier2016, Zeller2014 Actinobacteria Actinomycetia Corynebacteriaceae + AER Sessile Rod No spore 61-62
Corynebacterium ureicelerivorans 1 Opportunistic in immunocompromised patients Rare Possible Commensal Rare Opportunist clinical sources (blood - CCUG) and human faeces Pfleiderer2013, RajilicStojanovic2014, Lagier2016 Actinobacteria Actinomycetia Corynebacteriaceae + FANA Sessile Rod No spore
Corynebacterium urinapleomorphum Rare Possible Commensal Non/unknown Pathogen the urine of a baby Byrd2020 Actinobacteria Actinobacteria Corynebacteriaceae + FANA Sessile Pleiomorph rod No spore 63.4
Corynebacterium variabile Corynebacterium mooreparkense 1 Unlikely Transient Possible Pathogen Obligate aerobe; unlikely to be a gut coloniser. animal fodder, cheese and other food. Has been detected in human faeces (Bilen2018e) Lagier2016, Byrd2020, Zeller2014, Li2019b Actinobacteria Actinomycetia Corynebacteriaceae + SAER Sessile Diphtheroidal No spore 65
Corynebacterium wankanglinii Rare Possible Commensal Non/unknown Pathogen human faeces (Zhang2021) Actinobacteria Actinomycetia Corynebacteriaceae + FANA Sessile Rod No spore 61.2–64.4
Corynebacterium xerosis 1 Rare Possible Commensal Opportunistic Pathogen Nonlipophilic. human faeces, clinical sources, and animal sources RajilicStojanovic2014, Lagier2016 Actinobacteria Actinomycetia Corynebacteriaceae + FANA Sessile Club rod No spore 67.3
Crassaminicella thermophila Unlikely Transient Non/unknown Pathogen Optimum growth temperature is 50-55C, so unlikely to be a gut coloniser. a hydrothermal vent chimney New2022 Firmicutes Clostridia Clostridiaceae + ANA Swimming Rod - curved Endospore 30.8
Criibacterium bergeronii Rare Possible Commensal Possible Pathogen a vaginal sample of a woman diagnosed with bacterial vaginosis Byrd2020 Firmicutes Clostridia Peptostreptococcaceae vr ANA Swimming Rod No spore 33.8
Cronobacter condimenti Unlikely Transient Non/unknown Pathogen spiced meat, Slovakia New2022 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Sessile Rod No spore
Cronobacter muytjensii 2 Rare Possible Commensal Non/unknown Pathogen clinical specimens (meningitis) Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Swimming Rod No spore 57
Cronobacter sakazakii Enterobacter sakazakii 2 Minor Known Commensal Opportunistic Pathogen clinical sources (cerebrospinal fluid, sputum - CCUG) and human faeces McLaughlin2010, RajilicStojanovic2014, Lagier2016, Byrd2020, Yang2020, Hu2019, Zeller2014, Vachida2019 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Swimming Rod No spore 56.7-57
Cronobacter turicensis 2 Rare Possible Commensal Opportunistic Infection clinical specimens (neonatal meningitis) Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Swimming Rod No spore 57
Cruoricaptor ignavus Rare Possible Commensal Opportunistic Pathogen a septicaemia patient, Australia New2022 Bacteroidetes Flavobacteriia Weeksellaceae neg Micr Sessile Coccus No spore 45.6
Cryptobacterium curtum 1 Opportunistic in immunocompromised patients Minor Possible Commensal Opportunistic Pathogen dental disease and human faeces Bik2006, RajilicStojanovic2014, Lagier2016, Byrd2020, New2022, Zeller2014, Vachida2019 Actinobacteria Coriobacteriia Eggerthellaceae + SANA Sessile Rod No spore 50-51
Culturomica massiliensis Rare Possible Commensal Non/unknown Pathogen human faeces (Bilen2018e) Lagier2016, Minerbi2019 Bacteroidetes Bacteroidia Odoribacteraceae neg SANA Swimming Rod No spore
Cupriavidus metallidurans Ralstonia metallidurans 1 Unlikely Transient Non/unknown Pathogen Borderline cold mesophile, with optimum growth temp of 27C. Unlikely gut coloniser. human faeces, and wastewater McLaughlin2010, RajilicStojanovic2014 Proteobacteria Betaproteobacteria Burkholderiaceae neg AER Swimming Rod No spore 63.7
Curtobacterium flaccumfaciens 1 Unlikely Transient Non/unknown Pathogen Borderline cold mesophile, so unlikely to be a gut coloniser. human faeces RajilicStojanovic2014, Lagier2016 Actinobacteria Actinomycetia Microbacteriaceae + SAER Swimming Rod No spore 68.3-73.7
Cutibacterium acnes Propionibacterium acnes 2 Moderate Known Commensal Opportunistic Pathogen A significant member of the seeding microbiota that colonises the gut of C-section newborns but also found in breast milk (Jeurink2013). human skin, clinical sources (blood, wound, tissue - CCUG) and human faeces Moore1974, Holdeman1976, Finegold1977, Taylor1985, Woodmansey2004, Walker2011, Dubourg2013, Pfleiderer2013, Aujoulat2014, RajilicStojanovic2014, Cassir2015, Lagier2016, Zou2019, Almeida2019, Forster2019, Byrd2020, Yang2020, New2022, Zeller2014, Vachida2019, Li2019b, PerezBrocal2015 Actinobacteria Actinomycetia Propionibacteriaceae + Micr Sessile Rod No spore 59-64
Cutibacterium acnes subsp. defendens Propionibacterium acnes subsp. defendens Rare Possible Commensal Opportunistic Infection healthy skin, oral cavity and genitourinary tract King2019 Actinobacteria Actinomycetia Propionibacteriaceae + ANA Sessile Pleiomorph rod No spore 60
Cutibacterium avidum Propionibacterium avidum 2 Rare Possible Commensal Opportunistic Pathogen human skin, clinical sources (abscess, wound, tissue - CCUG) and human faeces RajilicStojanovic2014, Cassir2015, Lagier2016, Almeida2019, Forster2019 Actinobacteria Actinomycetia Propionibacteriaceae + ANA Sessile Rod No spore
Cutibacterium granulosum Propionibacterium granulosum 2 Human and animal pathogen Minor Possible Commensal Opportunistic Pathogen human faeces McLaughlin2010, Dubourg2013, RajilicStojanovic2014, Cassir2015, Lagier2016, Yang2020, PerezBrocal2015 Actinobacteria Actinomycetia Propionibacteriaceae + ANA Rod No spore
Cytophaga hutchinsonii 1 Rare Possible Commensal Non/unknown Pathogen human faeces and soil Yang2020 Bacteroidetes Cytophagia Cytophagaceae neg AER Gliding Rod No spore 38.8
Dakarella massiliensis Rare Possible Commensal Possible Pathogen vaginal flora Lagier2016, Byrd2020, Minerbi2019 Proteobacteria Betaproteobacteria Sutterellaceae neg SANA Sessile Rod No spore 57
Dakotella fusiforme Unknown Rare Possible Commensal Non/unknown Pathogen human faeces (healthy) Firmicutes Erysipelotrichia Erysipelotrichaceae + FANA Sessile Rod No spore 32.9
Dehalobacter restrictus 1 Non Transient Non/unknown Pathogen Dechlorinates tetra- and trichlorethane. Non-fermentative. Unlikely gut coloniser. sediment of the Rhine River Byrd2020, New2022 Firmicutes Clostridia Peptococcaceae neg SANA Swimming Rod No spore 45.3
Dehalobacterium formicoaceticum Unlikely Transient Non/unknown Pathogen Uses dichloromethane as an energy and carbon source. dichloromethane-contaminated groundwater New2022 Firmicutes Clostridia Peptococcaceae + SANA Sessile Short Rod 42.7
Dehalococcoides mccartyi Unlikely Transient Non/unknown Pathogen Hydrogenotrophic, organohalide-respiring. Reductive dehalogenation of mono- and polychlorinated and brominated aromatic compounds, alkanes and alkenes. an anaerobic reactor, USA Byrd2020, New2022 Chloroflexi Dehalococcoidia Dehalococcoidaceae unk SANA Sessile Coccus No spore 47-48.9
Deinococcus aquaticus Unlikely Transient Non/unknown Pathogen Obligate aerobe; unlikely to be a gut coloniser. freshwater and human faeces RajilicStojanovic2014, Lagier2016 Deinococcus-Thermus Deinococci Deinococcaceae neg SAER Sessile Rod No spore 68.3
Deinococcus caeni Unlikely Transient Non/unknown Pathogen Obligate aerobe; unlikely to be a gut coloniser. human faeces and activated sludge Yang2020 Deinococcus-Thermus Deinococci Deinococcaceae neg SAER Sessile Rod No spore 68.4
Deinococcus geothermalis 1 Non Transient Non/unknown Pathogen High optimum growth temperature so likely not a gut coloniser. hotsprings De2020, New2022 Deinococcus-Thermus Deinococci Deinococcaceae + AER Sessile Tetrad No spore 65.9
Deinococcus proteolyticus 1 Unlikely Transient Non/unknown Pathogen Resistant to 1.5 Mrad of gamma radiation. New2022, Zeller2014 Deinococcus-Thermus Deinococci Deinococcaceae + SAER Sessile Coccus No spore 65
Deinococcus reticulitermitis Unlikely Transient Non/unknown Pathogen Obligate aerobe; unlikely to be a gut coloniser. termite gut, and human faeces Yang2020 Deinococcus-Thermus Deinococci Deinococcaceae neg SAER Sessile Rod No spore 65.6
Deinococcus wulumuqiensis Unlikely Transient Non/unknown Pathogen Obligate aerobe; unlikely to be a gut coloniser. human faeces and irradiated soil Yang2020 Deinococcus-Thermus Deinococci Deinococcaceae + SAER Sessile Coccus No spore 66.7
Delftia acidovorans 1 Rare Known Commensal Rare Opportunist human faeces, soil, water sources and clinical samples (blood - CCUG) Bik2006, McLaughlin2010, Walker2011, RajilicStojanovic2014 Proteobacteria Betaproteobacteria Comamonadaceae neg SAER Swimming Rod No spore 67–69
Delftia lacustris Unlikely Transient Non/unknown Pathogen Borderline cold mesophile, so unlikely to be a gut coloniser. mesotrophic lake water Yang2020 Proteobacteria Betaproteobacteria Comamonadaceae neg FANA Swimming Rod No spore 65.3
Delftia tsuruhatensis 1 Rare Possible Commensal Non/unknown Pathogen human faeces (Bilen2018e) and activated sludge Lagier2016 Proteobacteria Betaproteobacteria Comamonadaceae neg AER Swimming Rod - curved No spore 66.2
Dellaglioa algida Lactobacillus algidus 1 Rare Possible Commensal Non/unknown Pathogen human faeces (Sanz2007 - healthy children) Byrd2020 Firmicutes Bacilli Lactobacillaceae + FANA Sessile Rod No spore 36.7
Denitrobacterium detoxificans 1 Rare Possible Commensal Non/unknown Pathogen ruminal microbes. Has been detected in human faeces (Alkhalil2017) Byrd2020, New2022 Actinobacteria Coriobacteriia Eggerthellaceae + ANA Sessile Rod No spore 58-60
Dermabacter hominis 1 Opportunistic in immunocompromised patients Rare Known Commensal Opportunistic Pathogen human skin, clinical sources (blood, wound, abscess - CCUG; fatal septicaemia) and human faeces Dubourg2013, Pfleiderer2013, RajilicStojanovic2014, Cassir2015, Lagier2016, Forster2019 Actinobacteria Actinomycetia Dermabacteraceae + FANA Sessile Rod No spore 62
Dermacoccus barathri 1 Non Transient Non/unknown Pathogen Borderline cold mesophile, with optimum growth temp of 28C. Unlikely gut coloniser. deep sea sediment Lagier2016 Actinobacteria Actinomycetia Dermacoccaceae + AER Sessile Coccus No spore 66.8
Dermacoccus nishinomiyaensis Micrococcus nishinomiyaensis 1 Rare Possible Commensal Rare Opportunist human skin, clinical sources (blood - CCUG) and human faeces RajilicStojanovic2014, Lagier2016 Actinobacteria Actinomycetia Dermacoccaceae + AER Sessile Coccus No spore
Desemzia incerta Brevibacterium incertum 1 Rare Possible Commensal Non/unknown Pathogen human faeces and cicadas Lagier2016, Yang2020 Firmicutes Bacilli Carnobacteriaceae + Micr Swimming Rod No spore 40
Desnuesiella massiliensis Rare Possible Commensal Non/unknown Pathogen human faeces (child suffering from kwashiorkor - Hadjadj2016) Lagier2016 Firmicutes Clostridia Clostridiaceae + FANA Swimming Rod No spore 32.1
Desulfitobacterium dichloroeliminans Desulfitobacterium dichloroeliminans strain DCA1 Unlikely Transient Non/unknown Pathogen Enterococcus casseliflavus is isolated with D. dichloroeliminans in a bibacterial commensal relationship. Dechlorinates 1,2-dichloromethane. dichloroethane-contaminated groundwater New2022 Firmicutes Clostridia Peptococcaceae + ANA Swimming Rod - curved No spore
Desulfitobacterium hafniense Desulfitobacterium frappieri Positive 1 Minor Known Commensal Non/unknown Pathogen human faeces, and anaerobic sewage sludge Tyakht2013, RajilicStojanovic2014, Lagier2016, Forster2019, Byrd2020, New2022, Zeller2014, Qin2012 Firmicutes Clostridia Peptococcaceae neg SANA Swimming Rod Endospore 46-47
Desulfococcus multivorans 1 Rare Possible Commensal Non/unknown Pathogen an anaerobic sewage digestor Byrd2020 Proteobacteria Deltaproteobacteria Desulfobacteraceae neg SANA Sessile Coccus No spore 57.4
Desulfocurvibacter africanus Desulfovibrio Africans Unlikely Transient Non/unknown Pathogen well water, Libya New2022 Proteobacteria Deltaproteobacteria Desulfovibrionaceae neg SANA Swimming Rod - curved No spore 61.1
Desulfofarcimen acetoxidans Desulfotomaculum acetoxidans 1 Unlikely Transient Non/unknown Pathogen Doesn't use sugars, lactate or pyruvate as electron donors. sulfide-containing water and mud; faeces of higher animals New2022, Qin2012 Firmicutes Clostridia Peptococcaceae neg SANA Swimming Rod Endospore 41.1-41.6
Desulfomicrobium baculatum Desulfovibrio baculatus 1 Unlikely Unknown Non/unknown Pathogen Sulfate reducing organism; can fix N2. manganese oxide dumps De2020, New2022, Qin2012 Proteobacteria Deltaproteobacteria Desulfovibrionaceae neg SANA Swimming Short Rod No spore 56.8
Desulfomicrobium orale 2 Unlikely Transient Rare Opportunist subgingival dental plaque Byrd2020, New2022 Proteobacteria Deltaproteobacteria Desulfovibrionaceae neg SANA Swimming Rod No spore 59.7
Desulforamulus reducens Desulfotomaculum reducens Unlikely Transient Non/unknown Pathogen Grows with Cr(VI), U(VI), Mn(IV), and Fe(III) as electron acceptors. a shipyard, USA New2022 Firmicutes Clostridia Peptococcaceae + SANA Swimming Rod - curved Endospore 42.3
Desulforudis audaxviator Unlikely Transient Non/unknown Pathogen This organism contains the entire set of genes required for life in the absence of other organisms or light in one genome. High optimum growth temperature so unlikely to be a gut coloniser. 2.8 km below the surface of a gold mine, South Africa New2022 Firmicutes Clostridia Peptococcaceae + Micr Swimming Rod Endospore 60.9
Desulfoscipio gibsoniae Desulfotomaculum gibsoniae 1 Rare Possible Commensal Non/unknown Pathogen fresh water Firmicutes Clostridia Peptococcaceae neg SANA Swimming Rod - curved Endospore 54.8
Desulfosporosinus youngiae Rare Transient Non/unknown Pathogen Fe(III) and arsenate are not electron acceptors and do not support growth a constructed wetland (acidic), USA New2022 Firmicutes Clostridia Peptococcaceae neg Rod - curved Endospore 36.6
Desulfotomaculum ruminis 1 Unlikely Transient Non/unknown Pathogen the rumen New2022, Qin2012 Firmicutes Clostridia Peptococcaceae + SANA Swimming Rod Endospore 47.2
Desulfovibrio desulfuricans 1 Minor Known Commensal Rare Opportunist human faeces, clinical sources (blood - CCUG) and polluted waters RajilicStojanovic2014, Lagier2016, Rothschild2018, Byrd2020, New2022, Chen2020, Hu2019, Zeller2014, Vachida2019 Proteobacteria Deltaproteobacteria Desulfovibrionaceae neg SANA Swimming Vibrio No spore 55.3
Desulfovibrio diazotrophicus Rare Possible Commensal Non/unknown Pathogen Able to respire sulfate using hydrogen, CO or alcohols. Can fix N2. the human faeces (Sayavedra2021) of a healthy adult, China Proteobacteria Deltaproteobacteria Desulfovibrionaceae neg SANA Swimming Rod - curved No spore 62.1
Desulfovibrio fairfieldensis Minor Known Commensal Rare Opportunist clinical sources (blood - CCUG) and human faeces RajilicStojanovic2014, Lagier2016, Forster2019, Byrd2020, New2022, Jeong2021, Wang2020a, Minerbi2019 Proteobacteria Deltaproteobacteria Desulfovibrionaceae neg SANA Swimming Vibrio No spore 62
Desulfovibrio intestinalis 1 Rare Possible Commensal Non/unknown Pathogen a termite hindgut Proteobacteria Deltaproteobacteria Desulfovibrionaceae neg ANA Swimming Vibrio No spore 54.5-55.5
Desulfovibrio legallii Rare Possible Commensal Non/unknown Pathogen human faeces and activated sludge Zou2019, Byrd2020, Yang2020, Minerbi2019 Proteobacteria Deltaproteobacteria Desulfovibrionaceae + SANA Swimming Vibrio No spore 55
Desulfovibrio longreachensis 1 Rare Possible Commensal Non/unknown Pathogen the water of a free-flowing bore of the Great Artesian Basin, Australia Proteobacteria Deltaproteobacteria Desulfovibrionaceae neg ANA Swimming Vibrio No spore 69
Desulfovibrio piger Desulfomonas pigra 1 Moderate Known Commensal Non/unknown Pathogen human faeces Walker2011, Tyakht2013, Nielsen2014, RajilicStojanovic2014, Chung2016, Lagier2016, Rothschild2018, Forster2019, Byrd2020, Yang2020, New2022, Chen2020, Dubinkina2017, Hu2019, Jie2017, Zeller2014, Wang2018, Vachida2019, Wang2020a, Minerbi2019, Karlsson2013 Proteobacteria Deltaproteobacteria Desulfovibrionaceae neg SANA Sessile Rod No spore 64 20(+)
Desulfovibrio trichonymphae Non Transient Non/unknown Pathogen Intracellular mutualist of Trichonympha agilis protist. Suited to H2/SO4 respiration, which prevents the buildup of H2 and subsequent inhibition of the fermentation process in the hindgut. termite gut New2022 Proteobacteria Deltaproteobacteria Desulfovibrionaceae unk ANA Sessile Coccus No spore 54.8
Desulfovibrio vulgaris Desulfovibrio vulgaris subsp. vulgaris 1 Rare Possible Commensal Non/unknown Pathogen Uses sulfate, sulfite and thiosulfate as electron acceptors soil and water sources Lagier2016, New2022, Zeller2014 Proteobacteria Deltaproteobacteria Desulfovibrionaceae neg SANA Swimming Vibrio No spore 61.2
Desulfurispirillum indicum Unlikely Transient Non/unknown Pathogen Dissimilatory selenate- and selenite-respiring bacterium isolated from sediments collected in an estuarine channel in Chepauk in Chennai. A low optimum temperature and fastidious dietary requirements suggests it is not a gut coloniser. an estuarine channel, India Chrysiogenetes Chrysiogenetes Chrysiogenaceae neg SANA Swimming Rod No spore 56.1
Desulfurobacterium thermolithotrophum 1 Non Transient Non/unknown Pathogen Optimum growth temperature is 70C, so likely not a gut coloniser. a deep-sea hydrothermal vent Byrd2020, New2022 Aquificae Aquificae Desulfurobacteriaceae neg ANA Swimming Rod No spore 35
Devosia chinhatensis 1 Rare Possible Commensal Non/unknown Pathogen human faeces and hexachlorocyclohexane contaminated dump site Yang2020 Proteobacteria Alphaproteobacteria Devosiaceae neg AER Swimming Rod No spore
Devosia limi 1 Unlikely Transient Non/unknown Pathogen Obligate aerobe; unlikely to be a gut coloniser. human faeces and enriched nitrifying community Yang2020 Proteobacteria Alphaproteobacteria Devosiaceae neg SAER Sessile Rod No spore
Devosia riboflavina Pseudomonas riboflavina 1 Unlikely Transient Non/unknown Pathogen Obligate aerobe; unlikely to be a gut coloniser. human faeces and soil Yang2020 Proteobacteria Alphaproteobacteria Devosiaceae neg SAER Swimming Rod No spore 61.4
Dialister hominis Positive Rare Known Commensal Non/unknown Pathogen human faeces (Sakamoto2020a) New2022 Firmicutes Negativicutes Veillonellaceae neg SANA Sessile Coccobacillus No spore 48.2 20(neg)
Dialister invisus 2 Moderate Known Commensal Opportunistic Infection human faeces, oral cavity and clinical sources (oral infections) Wang2005, McLaughlin2010, Walker2011, Zupancic2012, Nielsen2014, RajilicStojanovic2014, Lagier2016, Chung2019, Byrd2020, Chen2020, Dubinkina2017, Hu2019, Jie2017, Zeller2014, Wang2018, Vachida2019, Wang2020a, Minerbi2019, Karlsson2013 Firmicutes Negativicutes Veillonellaceae neg SANA Sessile Coccobacillus No spore 45.5 20(neg)
Dialister massiliensis Dialister sp. Marseille-P5638 Rare Possible Commensal Non/unknown Pathogen the faeces of a healthy volunteer, France New2022, Wang2020a Firmicutes Negativicutes Veillonellaceae neg ANA Sessile Rod No spore 48.4
Dialister micraerophilus 2 Rare Possible Commensal Non/unknown Pathogen clinical specimens Zeller2014, Vachida2019 Firmicutes Negativicutes Veillonellaceae neg Micr Sessile Coccus No spore 36.3
Dialister pneumosintes Bacteroides pneumosintes 2 Minor Transient Opportunistic Pathogen human faeces, oral cavity and clinical sources (abscesses, infections, blood) Finegold1974, McLaughlin2010, Walker2011, RajilicStojanovic2014, Lagier2016, Byrd2020, New2022 Firmicutes Negativicutes Veillonellaceae neg SANA Sessile Rod No spore 35 20(neg)
Dialister propionicifaciens 2 Rare Possible Commensal Opportunistic Pathogen clinical specimens (ulcer, semen, abscess, wound) Firmicutes Negativicutes Veillonellaceae neg ANA Sessile Coccobacillus No spore
Dialister succinatiphilus Positive Minor Known Commensal Non/unknown Pathogen human faeces Nielsen2014, RajilicStojanovic2014, Lagier2016, Rothschild2018, Zou2019, Forster2019, Byrd2020, De2020, Dubinkina2017, Hu2019, Jeong2021, Jie2017, Vachida2019, Minerbi2019 Firmicutes Negativicutes Veillonellaceae neg SANA Sessile Coccobacillus No spore 51.9
Dielma fastidiosa Positive Minor Known Commensal Non/unknown Pathogen In 44% of Europeans (unseenbio.com). Minor coloniser. human faeces RajilicStojanovic2014, Lagier2016, Zou2019, Forster2019, Byrd2020, Jeong2021 Firmicutes Erysipelotrichia Erysipelotrichaceae neg SANA Swimming Rod No spore 40.0
Dietzia cercidiphylli Unlikely Transient Non/unknown Pathogen Borderline cold mesophile, with optimum growth temp of 28C. Unlikely gut coloniser. surface-sterilised plant tissue, China Yang2020 Actinobacteria Actinomycetia Dietziaceae + AER Sessile Short Rod No spore 72.6
Dietzia cinnamea 1 Opportunistic in immunocompromised patients Rare Possible Commensal Opportunistic Pathogen clinical sources (blood, bone - CCUG) and human faeces RajilicStojanovic2014, Lagier2016 Actinobacteria Actinomycetia Dietziaceae + AER Rod 72.3
Dietzia kunjamensis 1 Unlikely Transient Non/unknown Pathogen Borderline cold mesophile, so unlikely to be a gut coloniser. mountain soil, Himalayas, India Yang2020 Actinobacteria Actinomycetia Dietziaceae + AER Sessile Pleiomorph rod No spore 67.0
Dietzia maris Rhodococcus maris 1 Opportunistic in immunocompromised patients Rare Possible Commensal Rare Opportunist carp gut, soil, clinical samples (articular fluid - CCUG) and human faeces RajilicStojanovic2014, Lagier2016, Byrd2020 Actinobacteria Actinomycetia Dietziaceae + AER Coccus No spore 73
Dietzia natronolimnaea 1 Rare Possible Commensal Non/unknown Pathogen an alkaline lake and human faeces RajilicStojanovic2014, Lagier2016 Actinobacteria Actinomycetia Dietziaceae + Sessile Rod No spore 66.1
Dolosigranulum pigrum 2 Unlikely Transient Non/unknown Pathogen human sources New2022, Vachida2019 Firmicutes Bacilli Carnobacteriaceae + FANA Sessile Oval-shaped No spore 40.5 40(neg)
Dorea faecis Minor Isolation and characterisation not yet published. In 57% of Europeans (unseenbio.com). A minor coloniser. Byrd2020 Firmicutes Clostridia Lachnospiraceae
Dorea formicigenerans Eubacterium formicgenerans Positive 1 Widespread Known Commensal Non/unknown Pathogen human faeces (Ludwig2009) Moore1974, McLaughlin2010, Walker2011, Zupancic2012, Tyakht2013, Nielsen2014, RajilicStojanovic2014, Salonen2014, Lagier2016, Rothschild2018, Zou2019, Forster2019, Byrd2020, De2020, Yang2020, Chen2020, Hu2019, Jeong2021, Jie2017, Zeller2014, Wang2018, Vachida2019, Wang2020a, Qin2012, Minerbi2019, Li2019b, LeChatelier2013, PerezBrocal2015 Firmicutes Clostridia Lachnospiraceae + SANA Sessile Rod No spore 40-44
Dorea hylemonae Rare Isolation and characterisation not yet published. Byrd2020 Firmicutes Clostridia Lachnospiraceae
Dorea longicatena Mixed 1 Widespread Known Commensal Non/unknown Pathogen human faeces (CCUG) McLaughlin2010, Walker2011, Tyakht2013, Nielsen2014, RajilicStojanovic2014, Browne2016, Lagier2016, Rothschild2018, Zou2019, Almeida2019, Forster2019, Byrd2020, De2020, Yang2020, Chen2020, Dubinkina2017, Hu2019, Jie2017, Zeller2014, Wang2018, Vachida2019, Wang2020a, Qin2012, Minerbi2019, LeChatelier2013, Karlsson2013 Firmicutes Clostridia Lachnospiraceae + SANA Sessile Rod No spore 43.8-45.6
Dorea phocaeensis Rare Possible Commensal Non/unknown Pathogen human faeces (CCUG) Firmicutes Clostridia Lachnospiraceae neg SANA Sessile Rod No spore
Dorea scindens Rare Isolation and characterisation not yet published. Byrd2020 Firmicutes Clostridia Lachnospiraceae
Drancourtella massiliensis Rare Possible Commensal Non/unknown Pathogen human faeces (Durand2016) Lagier2016 Firmicutes Clostridia Ruminococcaceae + SANA Sessile Rod Endospore 45.2
Dubosiella newyorkensis Rare Possible Commensal Non/unknown Pathogen murine intestinal contents De2020 Firmicutes Epsilonproteobacteria Erysipelotrichaceae + SANA Sessile Short Rod No spore 42.5
Duncaniella dubosii Unlikely Transient Non/unknown Pathogen the faeces of mice New2022 Bacteroidetes Bacteroidia Muribaculaceae neg SANA Short Rod No spore 47.9
Duncaniella muris Rare Possible Commensal Non/unknown Pathogen mouse gut Byrd2020 Bacteroidetes Bacteroidia Muribaculaceae neg SANA Sessile Short Rod No spore 50.8
Duodenibacillus massiliensis Minor Possible Commensal Non/unknown Pathogen In 25% of Europeans (unseenbio.com). Minor coloniser. human duodenum (Mailhe2016b) Byrd2020, De2020, Minerbi2019 Proteobacteria Betaproteobacteria Sutterellaceae + ANA Swimming Rod No spore
Dyadobacter beijingensis 1 Unlikely Transient Non/unknown Pathogen Borderline cold mesophile, with optimum growth temp of 28C. Unlikely gut coloniser. human faeces, and turf grass RajilicStojanovic2014 Bacteroidetes Cytophagia Cytophagaceae neg AER Sessile Rod No spore 52.1
Dyadobacter fermentans 1 Unlikely Transient Non/unknown Pathogen Borderline cold mesophile, with optimum growth temp of 28C. Unlikely gut coloniser. human faeces, and plants RajilicStojanovic2014, Zeller2014 Bacteroidetes Cytophagia Cytophagaceae neg AER Sessile Filamentous No spore 51.5
Dysgonomonas capnocytophagoides 2 Rare Possible Commensal Opportunistic Pathogen clinical specimens Forster2019, Byrd2020 Bacteroidetes Bacteroidia Dysgonomonadaceae neg FANA Sessile Coccobacillus No spore 38 +
Dysgonomonas gadei CDC Group DF-3 1 Opportunistic in immunocompromised patients Rare Possible Commensal Opportunistic Pathogen human faeces and gall bladder RajilicStojanovic2014, Lagier2016, Forster2019, Byrd2020, Vachida2019 Bacteroidetes Bacteroidia Dysgonomonadaceae neg FANA Sessile Coccobacillus No spore 39.6 +
Dysgonomonas massiliensis Rare Possible Commensal Non/unknown Pathogen human faeces (CCUG) Bacteroidetes Bacteroidia Dysgonomonadaceae neg FANA Sessile Coccobacillus No spore 37.3
Dysgonomonas mossii 1 Opportunistic in immunocompromised patients Rare Possible Commensal Opportunistic Pathogen human faeces and clinical samples (blood, abdominal drainage - CCUG) Tyakht2013, Lagier2016, Forster2019, Vachida2019, Qin2012 Bacteroidetes Bacteroidia Dysgonomonadaceae neg ANA Sessile Coccobacillus No spore 38.5 5(+)
Dysosmobacter welbionis Positive Moderate Known Commensal Non/unknown Pathogen Recently discovered but reported to be widespread ("up to 70% of the population"). human faeces (Roy2020) New2022 Firmicutes Clostridia Oscillospiraceae neg SANA Sessile Rod No spore 58.9 2(+)
Edwardsiella tarda Paracolobactrum anguillimortiferum 2 Human and animal pathogen Minor Possible Commensal Known Pathogen human faeces, disease of fish and atherosclerotic plaques Tyakht2013, RajilicStojanovic2014, Lagier2016, Forster2019, Byrd2020, Zeller2014, Vachida2019 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Swimming Rod No spore 55-58
Eggerthella guodeyinii Rare Possible Commensal Non/unknown Pathogen Acid is not formed from sugars. human faeces, China New2022 Actinobacteria Coriobacteriia Eggerthellaceae + ANA Sessile Rod No spore 61-65
Eggerthella lenta Eubacterium lentum 2 Human and animal pathogen Widespread Known Commensal Known Pathogen human faeces and clinical sources (blood - CCUG) Finegold1974, Finegold1977, Benno1984, Benno1986, Benno1989, Woodmansey2004, McLaughlin2010, Walker2011, Pfleiderer2013, Tyakht2013, Nielsen2014, RajilicStojanovic2014, Salonen2014, Cassir2015, Lagier2016, Rothschild2018, Zou2019, Forster2019, King2019, Byrd2020, Yang2020, New2022, Chen2020, Dubinkina2017, Hu2019, Jie2017, Zeller2014, Wang2018, Vachida2019, Wang2020a, Qin2012, Minerbi2019, Li2019b, LeChatelier2013, PerezBrocal2015 Actinobacteria Coriobacteriia Eggerthellaceae + SANA Sessile Rod No spore 62
Eggerthella sinensis 1 Opportunistic in immunocompromised patients Rare Possible Commensal Rare Opportunist human gut, and patient with proctitis (Alkhalil2017) Zou2019, Yang2020 Actinobacteria Coriobacteriia Eggerthellaceae + SANA Sessile Coccobacillus No spore 65
Eggerthella timonensis Rare Possible Commensal Non/unknown Pathogen human faeces (CCUG) Lagier2016, Byrd2020 Actinobacteria Coriobacteriia Eggerthellaceae + SANA Sessile Rod No spore 65.2
Eggerthia catenaformis Bacteroides catenaformis Minor Possible Commensal Opportunistic Infection human faeces, clinical sources (blood, infection - CCUG) and dental disease Finegold1977, Benno1989, Woodmansey2004, Walker2011, RajilicStojanovic2014, Salonen2014, Lagier2016, Byrd2020, De2020, Vachida2019 Firmicutes Erysipelotrichia Coprobacillaceae + SANA Sessile Rod No spore 34.8
Eikenella corrodens Bacteroides corrodens 2 Rare Possible Commensal Opportunistic Pathogen clinical sources (blood, abscess, infection, appendix) and human faeces RajilicStojanovic2014, Lagier2016, Yang2020, Zeller2014, Vachida2019 Proteobacteria Betaproteobacteria Neisseriaceae neg FANA Sessile Rod No spore 56-58
Eisenbergiella massiliensis Moderate Possible Commensal Non/unknown Pathogen In 74% of Europeans (unseenbio.com). human faeces (Togo2016a) Lagier2016, Byrd2020, Minerbi2019 Firmicutes Clostridia Lachnospiraceae neg SANA Sessile Rod No spore
Eisenbergiella tayi Moderate Known Commensal Opportunistic Infection In 97% of Europeans (unseenbio.com). human blood and human faeces Zou2019, Forster2019, Byrd2020, Yang2020, Minerbi2019 Firmicutes Clostridia Lachnospiraceae neg SANA Sessile Rod No spore 46.0
Elizabethkingia meningoseptica Flavobacterium meningosepticum 2 Pathogen of humans and vertebrates Unlikely Transient Opportunistic Pathogen Obligate aerobe; unlikely to be a gut coloniser. throat and clinical sources (blood, wound, respiratory tract - CCUG) Lagier2016 Bacteroidetes Flavobacteriia Weeksellaceae neg SAER Sessile Rod - curved No spore 37.2
Elizabethkingia miricola Chryseobacterium miricola 1 Non Transient Non/unknown Pathogen the Mir spacecraft Lagier2016 Bacteroidetes Flavobacteriia Weeksellaceae neg AER Sessile Rod No spore 35.3
Ellagibacter isourolithinifaciens Rare Possible Commensal Non/unknown Pathogen human faeces (CCUG) Actinobacteria Coriobacteriia Eggerthellaceae + SANA Sessile Rod No spore 59.6
Elusimicrobium minutum Unlikely Possible Commensal Non/unknown Pathogen Produces alanine as a metabolic endpoint. Doesn't grow at 37C so probably not a coloniser of the gut. termite gut De2020 Elusimicrobia Elusimicrobia Elusimicrobiaceae neg SANA Sessile Pleiomorph rod No spore
Emergencia timonensis Minor Possible Commensal Non/unknown Pathogen In 44% of Europeans (unseenbio.com). Minor coloniser. human faeces (Bessis2016a) Lagier2016, Byrd2020 Firmicutes Clostridia Eubacteriales Family XIII. Incertae Sedis + SANA Rod
Empedobacter brevis Flavobacterium breve 2 Human and animal pathogen Rare Possible Commensal Opportunistic Pathogen canal water, food, clinical specimens Lagier2016 Bacteroidetes Flavobacteriia Weeksellaceae neg AER Sessile Rod No spore 31-33
Empedobacter falsenii Wautersiella falsenii 2 Rare Possible Commensal Opportunistic Pathogen human faeces and clinical sources (blood, wound, rectum - CCUG) RajilicStojanovic2014, Yang2020 Bacteroidetes Flavobacteriia Weeksellaceae neg AER Sessile Rod No spore 33.8-34.4
Enhydrobacter aerosaccus 1 Rare Possible Commensal Non/unknown Pathogen human faeces and oxygen-depleted eutrophic lake Yang2020, Hu2019 Proteobacteria Alphaproteobacteria Hyphomicrobiales incertae sedis neg FANA Sessile Rod No spore 63.3
Enorma massiliensis Coriobacteriaceae bacterium phI Minor Known Commensal Non/unknown Pathogen human faeces RajilicStojanovic2014, Lagier2016, Forster2019, Byrd2020, Chen2020, Hu2019, Vachida2019 Actinobacteria Coriobacteriia Coriobacteriaceae + SANA Sessile Rod No spore 62.0
Enorma phocaeensis Rare Possible Commensal Non/unknown Pathogen human faeces (Bilen2018e) Byrd2020 Actinobacteria Coriobacteriia Coriobacteriaceae neg SANA Swimming Rod No spore
Enorma timonensis Rare Possible Commensal Non/unknown Pathogen human faeces (Ramasamy2014a) Lagier2016 Actinobacteria Coriobacteriia Coriobacteriaceae + SANA Sessile Rod No spore 65.8
Ensifer adhaerens Ensifer morelensis 1 Unlikely Transient Non/unknown Pathogen Borderline cold mesophile, with optimum growth temp of 27C. Unlikely gut coloniser. human faeces and soil Byrd2020, Yang2020 Proteobacteria Alphaproteobacteria Rhizobiaceae neg AER Swimming Rod No spore 67
Enterobacter asburiae 2 Minor Possible Commensal Possible Pathogen human faeces (Alkhalil2017 - including an ulcerative colitis patient) and clinical sources (blood, urine, wound - CCUG) Favier2002, McLaughlin2010, RajilicStojanovic2014, Cassir2015, Lagier2016, Forster2019, Byrd2020, Byrd2020, Yang2020, New2022, Dubinkina2017, Zeller2014, Vachida2019 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Sessile Rod No spore 55-57
Enterobacter cancerogenus Erwinia cancerogena 2 Minor Known Commensal Opportunistic Pathogen human faeces, clinical sources (blood, wound - CCUG) and cankers in poplars Tyakht2013, RajilicStojanovic2014, Lagier2016, Byrd2020, Yang2020, Dubinkina2017, Zeller2014 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Swimming Rod No spore
Enterobacter cloacae 2 Human and animal pathogen Moderate Known Commensal Known Pathogen human faeces (including ulcerative colitis patients - Alkhalil2017), clinical sources (cerebrospinal fluid, blood, wound, nosocomial infections - CCUG), sewage, animals and soil Finegold1977, Benno1984, McLaughlin2010, Pfleiderer2013, Tyakht2013, Aujoulat2014, RajilicStojanovic2014, Cassir2015, Lagier2016, Rothschild2018, Almeida2019, Forster2019, Byrd2020, De2020, Yang2020, New2022, Dubinkina2017, Hu2019, Jie2017, Zeller2014, Vachida2019, Wang2020a Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Swimming Rod No spore 52-54
Enterobacter cloacae subsp. dissolvens Enterobacter dissolvens 1 Rare Possible Commensal Opportunistic Pathogen maize and clinical sources (blood, abdomen, skin abscess) Zou2019 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Swimming Rod No spore 55
Enterobacter himalayensis Minor Isolation and characterisation not yet published. In 11% of Europeans (unseenbio.com). A minor coloniser. Byrd2020 Proteobacteria Gammaproteobacteria Enterobacteriaceae No spore
Enterobacter hormaechei subsp. hormaechei Enterobacter hormaechei 2 Human and animal pathogen Minor Possible Commensal Known Pathogen clinical sources and human faeces (including ulcerative colitis patients) McLaughlin2010, Nielsen2014, RajilicStojanovic2014, Lagier2016, Zou2019, Byrd2020, De2020, New2022, Wang2020a Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Swimming Rod No spore
Enterobacter hormaechei subsp. steigerwaltii Rare Possible Commensal Opportunistic Pathogen human faeces and clinical sources (urine, wound, genitals - CCUG) Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Swimming Rod No spore
Enterobacter hormaechei subsp. xiangfangensis Enterobacter xiangfangensis Rare Possible Commensal Non/unknown Pathogen human faeces, urine and sourdough Yang2020 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Swimming Rod No spore 55.2
Enterobacter kobei 2 Rare Possible Commensal Opportunistic Pathogen human faeces (Bilen2018e) and clinical sources (throat, sputum, blood and urine) Lagier2016, Byrd2020, New2022 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Swimming Rod No spore 52.7
Enterobacter ludwigii 2 Rare Known Commensal Possible Pathogen human faeces (Alkhalil2017 - ulcerative colitis patient) and blood RajilicStojanovic2014, Lagier2016, Zou2019, Byrd2020, PerezBrocal2015 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Swimming Rod No spore
Enterobacter massiliensis Positive Rare Known Commensal Non/unknown Pathogen human faeces RajilicStojanovic2014, Lagier2016, Forster2019 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg AER Swimming Rod No spore 55.1
Enterobacter mori Rare Transient Non/unknown Pathogen Optimum growth temperature is 28C. In 4% of healthy Europeans (unseenbio.com). diseased mulberry roots Byrd2020, Vachida2019 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Swimming Short Rod No spore 55.1
Enterobacter roggenkampii Rare Possible Commensal Non/unknown Pathogen human faeces (CCUG) and wound New2022, Wang2020a Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Rod No spore
Enterobacter soli Rare Possible Commensal Non/unknown Pathogen soil. Has been detected in human faeces (Alkhalil2017, CCUG) Byrd2020 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Swimming Rod No spore 52.8
Enterobacter timonensis Rare Possible Commensal Non/unknown Pathogen human faeces (Alou2017) Lagier2016, Byrd2020 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Rod No spore
Enterocloster aldenensis Clostridium aldenense 2 Minor Possible Commensal Opportunistic Pathogen clinical sources and human faeces McLaughlin2010, Walker2011, Nielsen2014, RajilicStojanovic2014, Lagier2016, Zou2019, Yang2020, Jeong2021 Firmicutes Clostridia Clostridiaceae + SANA Rod Endospore
Enterocloster asparagiformis Clostridium asparagiforme 1 Moderate Known Commensal Rare Opportunist In 51% of Europeans (unseenbio.com), but in 95% of subjects in study by Qin2010. Moderate coloniser. human faeces and atherosclerotic plaques Tyakht2013, RajilicStojanovic2014, Lagier2016, Zou2019, Byrd2020, Chen2020, Dubinkina2017, Hu2019, Jeong2021, Jie2017, Vachida2019, Qin2012, LeChatelier2013 Firmicutes Clostridia Clostridiaceae + SANA Rod Endospore 53
Enterocloster bolteae Clostridium bolteae 1 Opportunistic in immunocompromised patients Widespread Known Commensal Opportunistic Pathogen human faeces (Alkhalil2017) and clinical sources (abscess, blood) McLaughlin2010, Walker2011, Zupancic2012, deGoffau2013, Tyakht2013, Nielsen2014, RajilicStojanovic2014, Lagier2016, Rothschild2018, Zou2019, Almeida2019, King2019, Byrd2020, Yang2020, New2022, Chen2020, Dubinkina2017, Hu2019, Jeong2021, Jie2017, Zeller2014, Wang2018, Vachida2019, Wang2020a, Qin2012, LeChatelier2013 Firmicutes Clostridia Clostridiaceae + SANA Swimming Rod Endospore 50.5
Enterocloster citroniae Clostridium citroniae 2 Moderate Possible Commensal Opportunistic Pathogen human faeces and clinical sources (peritoneal fluid - CCUG) Walker2011, Pfleiderer2013, RajilicStojanovic2014, Lagier2016, Rothschild2018, Zou2019, Byrd2020, Yang2020, Chen2020, Dubinkina2017, Hu2019, Jeong2021, Vachida2019, Qin2012, PerezBrocal2015 Firmicutes Clostridia Clostridiaceae + SANA Rod Endospore
Enterocloster clostridioformis Clostridium clostridioforme Mixed 2 Widespread Known Commensal Opportunistic Pathogen human faeces and clinical sources (blood, liver abscess - CCUG) Moore1974, Finegold1974, Holdeman1976, Finegold1977, Benno1984, Taylor1985, Benno1986, MacFarlane2004, Woodmansey2004, McLaughlin2010, Walker2011, deGoffau2013, Nielsen2014, RajilicStojanovic2014, Browne2016, Lagier2016, Almeida2019, Byrd2020, New2022, Chen2020, Dubinkina2017, Hu2019, Jie2017, Vachida2019, Qin2012, LeChatelier2013, Karlsson2013 Firmicutes Clostridia Clostridiaceae + SANA Swimming Rod Endospore 49.0 20(+)
Enterocloster lavalensis Clostridium lavalense Minor Known Commensal Non/unknown Pathogen In 68% of Europeans (unseenbio.com). Minor coloniser. human faeces (Alkhalil2017) RajilicStojanovic2014, Lagier2016, Zou2019, Byrd2020, Yang2020 Firmicutes Clostridia Clostridiaceae + SANA Swimming Rod Endospore 51–52
Enterococcus asini 1 Rare Possible Commensal Non/unknown Pathogen human faeces, and donkey caecal contents RajilicStojanovic2014, Lagier2016, Zou2019, Vachida2019 Firmicutes Bacilli Enterococcaceae + FANA Sessile Coccus No spore 39.4 40(+)
Enterococcus avium 2 Minor Known Commensal Opportunistic Pathogen human faeces (especially children) and clinical sources (wound, abscess, blood, infection) Benno1984, Favier2002, Woodmansey2004, Pfleiderer2013, RajilicStojanovic2014, Lagier2016, Zou2019, Byrd2020, New2022, Hu2019, Vachida2019 Firmicutes Bacilli Enterococcaceae + FANA Sessile Oval-shaped No spore 39-40 40(+)
Enterococcus burkinafasonensis Rare Possible Commensal Non/unknown Pathogen human faeces (healthy) Firmicutes Bacilli Enterococcaceae + AER Sessile Coccus No spore 41.9
Enterococcus caccae Positive 1 Rare Known Commensal Non/unknown Pathogen human faeces RajilicStojanovic2014, Lagier2016 Firmicutes Bacilli Enterococcaceae + FANA Coccus No spore 32.5
Enterococcus canintestini 1 Rare Possible Commensal Non/unknown Pathogen dogs Lagier2016 Firmicutes Bacilli Enterococcaceae + FANA Sessile Coccus No spore 36.0-37.0
Enterococcus canis 1 Opportunistic in immunocompromised patients Rare Possible Commensal Opportunistic Infection dog faeces Lagier2016 Firmicutes Bacilli Enterococcaceae + FANA Sessile Oval-shaped No spore 41.7-43.0
Enterococcus casseliflavus Streptococcus casseliflavus 2 Moderate Known Commensal Opportunistic Pathogen human faeces and clinical sources (blood, urine, abscess) Pandey2012, Pfleiderer2013, Tyakht2013, RajilicStojanovic2014, Lagier2016, Zou2019, Almeida2019, Forster2019, Byrd2020, De2020, Yang2020, New2022, Dubinkina2017, Zeller2014, Vachida2019 Firmicutes Bacilli Enterococcaceae + FANA Swimming Coccus No spore 40.5-44.9 5(+)
Enterococcus cecorum Streptococcus cecorum 1 Opportunistic in immunocompromised patients Rare Possible Commensal Rare Opportunist animal and clinical sources (blood), water and human faeces McLaughlin2010, RajilicStojanovic2014, Lagier2016, Byrd2020, New2022, Li2019b Firmicutes Bacilli Enterococcaceae + FANA Sessile Oval-shaped No spore 37-38
Enterococcus columbae 1 Rare Possible Commensal Non/unknown Pathogen domestic pigeons Byrd2020 Firmicutes Bacilli Enterococcaceae + FANA vr Coccus No spore 38.2 40(+)
Enterococcus devriesei Moderate Possible Commensal Non/unknown Pathogen In 79% of Europeans (unseenbio.com). animal sources and human faeces (Bilen2018e) Lagier2016, Byrd2020 Firmicutes Bacilli Enterococcaceae + FANA Coccus No spore 40
Enterococcus diestrammenae Rare Possible Commensal Non/unknown Pathogen a cricket from Korea. Has been detected in human faeces (Bilen2018e) Lagier2016 Firmicutes Bacilli Enterococcaceae + FANA Sessile Coccus No spore 41.3
Enterococcus dispar 2 Rare Possible Commensal Rare Opportunist clinical sources (Synovial fluid, blood), dog faeces and human faeces RajilicStojanovic2014, Lagier2016, Byrd2020, Vachida2019 Firmicutes Bacilli Enterococcaceae + FANA Sessile Coccus No spore 39
Enterococcus durans Streptococcus durans 2 Human and animal pathogen Moderate Known Commensal Opportunistic Pathogen Found in human breast milk (Jeurink2013). human clinical sources (infection, blood), veterinary clinical materials, food, the environment, and human faeces Finegold1977, Benno1986, Benno1989, MacFarlane2004, Woodmansey2004, Aujoulat2014, RajilicStojanovic2014, Cassir2015, Lagier2016, Zou2019, Forster2019, Byrd2020, De2020, Yang2020, New2022 Firmicutes Bacilli Enterococcaceae + FANA Sessile Oval-shaped No spore 38-40
Enterococcus eurekensis Rare Possible Commensal Non/unknown Pathogen pig manure storage pit Lagier2016 Firmicutes Bacilli Enterococcaceae + FANA Sessile Coccus No spore 36.0
Enterococcus faecalis Streptococcus faecalis 2 Widespread Known Commensal Opportunistic Pathogen Huycke MM, Abrams V, Moore DR. Enterococcus faecalis produces extracellular superoxide and hydrogen peroxide that damages colonic epithelial cell DNA. Carcinogenesis 2002; 23: 529–36. This organism also produces D-lactate, which could be linked to cronic fatigue syndrome (Sheedy2009). Found in human breast milk (Jeurink2013). human faeces, clinical sources (blood, sputum, wound, urine), and animal sources Finegold1977, Benno1986, Benno1989, Mangin2004, MacFarlane2004, Woodmansey2004, Pfleiderer2013, Tyakht2013, Aujoulat2014, RajilicStojanovic2014, Cassir2015, Lagier2016, Zou2019, Almeida2019, Chung2019, Forster2019, King2019, Byrd2020, Yang2020, New2022, Chen2020, Dubinkina2017, Hu2019, Jie2017, Zeller2014, Vachida2019, Wang2020a, Urban2020, Karlsson2013 Firmicutes Bacilli Enterococcaceae + FANA vr Coccus No spore 37-40
Enterococcus faecium Streptococcus faecium 2 Widespread Known Commensal Opportunistic Pathogen Found in human breast milk (Jeurink2013). human clinical sources (blood, sputum, wound, urine), veterinary clinical materials, food, the environment, and human faeces Finegold1977, Benno1984, Benno1986, Benno1989, Woodmansey2004, McLaughlin2010, Hoyles2012, Dubourg2013, Pfleiderer2013, Tyakht2013, Nielsen2014, RajilicStojanovic2014, Cassir2015, Lagier2016, Rothschild2018, Zou2019, Almeida2019, Forster2019, King2019, Byrd2020, De2020, Yang2020, New2022, Dubinkina2017, Hu2019, Jie2017, Zeller2014, Vachida2019, Wang2020a, Moore1995 Firmicutes Bacilli Enterococcaceae + Micr Coccus No spore 37-40
Enterococcus gallinarum Streptococcus gallinarum 2 Human and animal pathogen Rare Known Commensal Opportunistic Pathogen In 1% of Europeans (unseenbio.com). human clinical sources (blood, infection, urine), veterinary clinical materials, food, the environment, and human faeces Tyakht2013, RajilicStojanovic2014, Cassir2015, Lagier2016, Zou2019, Almeida2019, Forster2019, Byrd2020, Hu2019, Zeller2014, Vachida2019, Wang2020a Firmicutes Bacilli Enterococcaceae + FANA Swimming Coccus No spore 39-40
Enterococcus gilvus 1 Opportunistic in immunocompromised patients Rare Possible Commensal Opportunistic Infection the bile of a patient with cholecystitis Lagier2016, Byrd2020, New2022, Vachida2019 Firmicutes Bacilli Enterococcaceae + FANA Sessile Coccus No spore 40(+)
Enterococcus haemoperoxidus 1 Rare Possible Commensal Non/unknown Pathogen surface waters Firmicutes Bacilli Enterococcaceae + FANA Sessile Oval-shaped No spore 35.3-35.5
Enterococcus hermanniensis 1 Rare Possible Commensal Non/unknown Pathogen chicken meat and dogs Lagier2016, De2020 Firmicutes Bacilli Enterococcaceae + FANA Oval-shaped No spore 36.6-37.4
Enterococcus hirae 2 Human and animal pathogen Minor Known Commensal Known Pathogen Found in human breast milk (Jeurink2013). human clinical sources (blood), veterinary clinical materials, food, the environment, and human faeces Woodmansey2004, Bik2006, RajilicStojanovic2014, Lagier2016, King2019, Byrd2020, Vachida2019 Firmicutes Bacilli Enterococcaceae + FANA Sessile Coccus No spore 37-38
Enterococcus italicus Enterococcus saccharominimus 1 Rare Possible Commensal Non/unknown Pathogen dairy products from Italy Lagier2016, Byrd2020, De2020, Zeller2014 Firmicutes Bacilli Enterococcaceae + FANA Sessile Coccus No spore 39.9-41.1
Enterococcus lactis Enterococcus xinjiangensis Rare Possible Commensal Non/unknown Pathogen raw milk cheese from Italy and yogurt from China De2020 Firmicutes Bacilli Enterococcaceae + FANA Sessile Coccus No spore 44.5
Enterococcus malodoratus 1 Rare Possible Commensal Opportunistic Pathogen animal sources, cheese, clinical sources (blood, abscess - CCUG) and has been detected in human faeces (Bilen2018e) Lagier2016, Byrd2020 Firmicutes Bacilli Enterococcaceae + FANA Sessile Coccus No spore 40-41
Enterococcus massiliensis Rare Possible Commensal Non/unknown Pathogen the faeces of a healthy volunteer Lagier2016 Firmicutes Bacilli Enterococcaceae + FANA Swimming Oval-shaped No spore 39.6
Enterococcus mediterraneensis Rare Possible Commensal Non/unknown Pathogen human faeces (Bilen2018e) Firmicutes Bacilli Enterococcaceae + ANA Sessile Coccus No spore 40.9
Enterococcus moraviensis 1 Rare Possible Commensal Non/unknown Pathogen spring water Firmicutes Bacilli Enterococcaceae + FANA Sessile Coccus No spore 36.3
Enterococcus mundtii 1 Opportunistic in immunocompromised patients Rare Known Commensal Rare Opportunist Found in human breast milk (Jeurink2013). human faeces (Svec2011Bergey), cow teat, soil and plants Lagier2016, Byrd2020 Firmicutes Bacilli Enterococcaceae + FANA Sessile Oval-shaped No spore 38-39
Enterococcus pallens 1 Opportunistic in immunocompromised patients Rare Possible Commensal Opportunistic Pathogen clinical sources Lagier2016 Firmicutes Bacilli Enterococcaceae + FANA Sessile Coccus No spore 40(+)
Enterococcus phoeniculicola 1 Rare Known Commensal Non/unknown Pathogen bird gland and human faeces RajilicStojanovic2014, Lagier2016 Firmicutes Bacilli Enterococcaceae + FANA Sessile Coccus No spore 40(neg)
Enterococcus pseudoavium 2 Animal pathogen Rare Possible Commensal Rare Opportunist human faeces, clinical sources (blood) and bovine mastitis Woodmansey2004, RajilicStojanovic2014, Lagier2016, Byrd2020 Firmicutes Bacilli Enterococcaceae + FANA Sessile Coccus No spore 40
Enterococcus raffinosus 2 Rare Possible Commensal Opportunistic Pathogen human faeces (Bilen2018e) and clinical sources (blood, cerebrospinal fluid, wound - CCUG) Favier2002, Lagier2016, Byrd2020, Vachida2019 Firmicutes Bacilli Enterococcaceae + FANA Sessile Oval-shaped No spore 39-40
Enterococcus saccharolyticus Streptococcus saccharolyticus 1 Opportunistic in immunocompromised patients Rare Transient Opportunistic Infection human faeces. Isolated from cows and straw bedding RajilicStojanovic2014, Lagier2016, Dubinkina2017 Firmicutes Bacilli Enterococcaceae + FANA Sessile Coccus No spore 37.6-38.3
Enterococcus saigonensis Unlikely Transient Non/unknown Pathogen retail chicken meat, Vietnam New2022 Firmicutes Bacilli Enterococcaceae + FANA Sessile Coccus No spore 36.8-37.5
Enterococcus sulfureus 1 Rare Possible Commensal Non/unknown Pathogen human faeces and plants Yang2020 Firmicutes Bacilli Enterococcaceae + FANA Sessile Oval-shaped No spore 38 +
Enterococcus thailandicus Enterococcus sanguinicola 1 Rare Possible Commensal Possible Pathogen fermented sausage, clinical sources (blood - CCUG) human faeces (Bilen2018e) Lagier2016, Byrd2020 Firmicutes Bacilli Enterococcaceae + FANA Sessile Oval-shaped No spore 37.9
Enterococcus timonensis Rare Possible Commensal Non/unknown Pathogen human faeces and sputum (healthy) Firmicutes Bacilli Enterococcaceae + FANA Swimming Coccus No spore 38.5
Enterococcus villorum 2 Animal pathogen Rare Possible Commensal Opportunistic Pathogen piglet diarrhoea Lagier2016, Byrd2020 Firmicutes Bacilli Enterococcaceae + FANA Sessile Coccus No spore 35.1-35.3
Enteroscipio rubneri Rare Possible Commensal Non/unknown Pathogen human faeces (Danylec2018) Byrd2020 Actinobacteria Coriobacteriia Eggerthellaceae + SANA Sessile Rod No spore 62.4
Enterovibrio nigricans Unlikely Possible Commensal Non/unknown Pathogen fish kidney, Spain Forster2019 Proteobacteria Gammaproteobacteria Vibrionaceae neg FANA Swimming Coccobacillus No spore 47.9
Ereboglobus luteus Unlikely Transient Non/unknown Pathogen Ferments sugars but not amino acids or organic acids the hindgut of a cockroach New2022 Verrucomicrobia Opitutae Opitutaceae neg FANA Swimming Coccus No spore 59.7
Erwinia billingiae 1 Plant pathogen Unlikely Transient Rare Opportunist Can't grow at 37C, so unlikely to be a gut coloniser. trees, a clinical specimen (nasopharynx - CCUG) and has been detected in human faeces (Alkhalil2017) Zeller2014 Proteobacteria Gammaproteobacteria Erwiniaceae neg FANA Swimming Rod No spore 54-55
Erwinia tasmaniensis 1 Unlikely Transient Non/unknown Pathogen Inability to grow at 36C suggests this not a gut coloniser. apple and pear trees, Australia Zeller2014 Proteobacteria Gammaproteobacteria Erwiniaceae neg FANA Swimming Rod No spore 50.5-52.4
Erwinia teleogrylli Rare Possible Commensal Non/unknown Pathogen crickets from China Byrd2020, De2020 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Short Rod No spore 55.3
Erysipelatoclostridium ramosum Clostridium ramosum 2 Widespread Known Commensal Opportunistic Infection human faeces and clinical sources (infections and blood) Moore1974, Holdeman1976, Finegold1977, Benno1984, Taylor1985, Benno1986, Benno1989, Mangin2004, MacFarlane2004, Woodmansey2004, McLaughlin2010, Walker2011, Zupancic2012, Pfleiderer2013, Tyakht2013, Nielsen2014, RajilicStojanovic2014, Salonen2014, Chung2016, Lagier2016, Zou2019, Forster2019, Byrd2020, Yang2020, New2022, Chen2020, Hu2019, Jeong2021, Jie2017, Zeller2014, Wang2018, Vachida2019, Wang2020a, Qin2012, Minerbi2019, Moore1995, LeChatelier2013, Karlsson2013 Firmicutes Erysipelotrichia Erysipelotrichaceae + SANA Sessile Rod Rare 26 20(+)
Erysipelatoclostridium saccharogumia Minor Isolation and characterisation not yet published. In 52% of Europeans (unseenbio.com). A minor coloniser. Byrd2020 Firmicutes Erysipelotrichia Erysipelotrichaceae
Erysipelatoclostridium spiroforme Minor Isolation and characterisation not yet published. In 41% of Europeans (unseenbio.com). A minor coloniser. Byrd2020 Firmicutes Erysipelotrichia Erysipelotrichaceae
Erysipelothrix larvae Rare Possible Commensal Non/unknown Pathogen the gut of the rhinoceros beetle De2020 Firmicutes Erysipelotrichia Erysipelotrichaceae + FANA Sessile Rod No spore 36.3
Escherichia albertii 2 Human and animal pathogen Minor Possible Commensal Opportunistic Pathogen human faeces RajilicStojanovic2014, Lagier2016, Byrd2020, De2020, New2022, Dubinkina2017, Zeller2014 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Sessile Rod No spore 50.5-50.7
Escherichia coli 2 Human and animal pathogen Widespread Known Commensal Opportunistic Pathogen human faeces (high load in several ulcerative colitis patients) and clinical sources Moore1974, Holdeman1976, Finegold1977, Benno1984, Benno1986, Benno1989, Favier2002, Mangin2004, MacFarlane2004, Woodmansey2004, Wang2005, Bik2006, Frank2007, McLaughlin2010, Walker2011, Pandey2012, Dubourg2013, Pfleiderer2013, Tyakht2013, Aujoulat2014, Nielsen2014, RajilicStojanovic2014, Salonen2014, Cassir2015, Lagier2016, Rothschild2018, Zou2019, Forster2019, King2019, Byrd2020, De2020, Yang2020, New2022, Chen2020, Dubinkina2017, Hu2019, Jie2017, Zeller2014, Wang2018, Vachida2019, Wang2020a, Urban2020, Qin2012, Moore1995 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Swimming Rod No spore 50
Escherichia dysenteriae Rare Isolation and characterisation not yet published. Byrd2020 Proteobacteria Gammaproteobacteria Enterobacteriaceae
Escherichia fergusonii 2 Human and animal pathogen Minor Possible Commensal Known Pathogen human faeces, clinical sources (including atherosclerotic plaques) and raptors Zupancic2012, RajilicStojanovic2014, Lagier2016, Zou2019, Almeida2019, Byrd2020, New2022, Dubinkina2017, Hu2019 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Swimming Rod No spore
Escherichia marmotae Unlikely Transient Non/unknown Pathogen the faeces of Marmota himalayana Byrd2020, New2022 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Sessile Short Rod No spore 53
Escherichia ruysiae Rare Possible Commensal Possible Pathogen The organism was lost from the patient's gut after less than one month a European with diarrhoea after travelling through Asia Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Sessile Rod No spore
Ethanoligenens harbinense 1 Rare Possible Commensal Non/unknown Pathogen wastewater. Has been detected in human faeces (New2022) Byrd2020, New2022, Zeller2014, Qin2012 Firmicutes Clostridia Oscillospiraceae + SANA Swimming Rod No spore 47.8
Eubacterium barkeri Clostridium barkeri 1 Rare Known Commensal Non/unknown Pathogen human faeces and river sediment Finegold1974, Finegold1977, RajilicStojanovic2014, Lagier2016 Firmicutes Clostridia Eubacteriaceae + SANA Sessile Rod Endospore 45 20(neg)
Eubacterium biforme 1 Moderate Known Commensal Non/unknown Pathogen human faeces Moore1974, Holdeman1976, Finegold1977, Benno1986, Heilig2002, McLaughlin2010, Walker2011, Zupancic2012, Tyakht2013, Nielsen2014, RajilicStojanovic2014, Lagier2016, Rothschild2018, Zou2019, Chen2020, Dubinkina2017, Hu2019, Jie2017, Moore1995, Karlsson2013 Firmicutes Clostridia Eubacteriaceae + SANA Sessile Coccobacillus No spore 32 20(neg)
Eubacterium brachy 2 Rare Transient Opportunistic Infection clinical sources (oral infections, lung abscess) and human faeces Woodmansey2004, RajilicStojanovic2014, Lagier2016, Byrd2020, De2020, Vachida2019 Firmicutes Clostridia Eubacteriaceae + SANA Sessile Rod No spore 20(d)
Eubacterium callanderi 1 Minor Possible Commensal Non/unknown Pathogen In 30% of Europeans (unseenbio.com). Minor coloniser. human faeces, and an anaerobic digester RajilicStojanovic2014, Lagier2016, Byrd2020, New2022 Firmicutes Clostridia Eubacteriaceae + SANA Sessile Rod No spore 47
Eubacterium cellulosolvens 1 Minor Possible Commensal Non/unknown Pathogen Cellulolytic. human faeces, and cow and sheep rumen Finegold1977, Zupancic2012, RajilicStojanovic2014, Lagier2016, Byrd2020, New2022, Zeller2014, Qin2012 Firmicutes Clostridia Eubacteriaceae + SANA Swimming Short Rod No spore 50
Eubacterium coprostanoligenes 1 Minor Transient Non/unknown Pathogen In 38% of Europeans (unseenbio.com). Minor coloniser. human faeces and pig sewage Byrd2020, De2020, New2022, Minerbi2019 Firmicutes Clostridia Eubacteriaceae + ANA Sessile Coccobacillus No spore 41
Eubacterium dolichum 1 Moderate Known Commensal Non/unknown Pathogen human faeces Finegold1974, Woodmansey2004, Wang2005, Walker2011, Zupancic2012, Tyakht2013, Nielsen2014, RajilicStojanovic2014, Lagier2016, Zou2019, Yang2020, Dubinkina2017, Hu2019, Jie2017, Li2019b, LeChatelier2013 Firmicutes Clostridia Eubacteriaceae + SANA Sessile Rod No spore
Eubacterium infirmum 2 Rare Transient Opportunistic Pathogen human faeces (Bilen2018e) and peridontal pockets Lagier2016, Byrd2020, Yang2020, Hu2019, Vachida2019, Qin2012 Firmicutes Clostridia Eubacteriaceae + SANA Sessile Rod No spore 38
Eubacterium limosum 2 Moderate Known Commensal Opportunistic Pathogen Homoacetogen. Able to use the following donors: CO, methanol, betaine, phenylmethylether. human faeces, rumen, sewage, mud, animals and clinical sources (rectal abscesses, blood and wounds) Moore1974, Finegold1974, Benno1989, MacFarlane2004, Woodmansey2004, Pfleiderer2013, RajilicStojanovic2014, Salonen2014, Lagier2016, Forster2019, King2019, Byrd2020, New2022, Dubinkina2017, Hu2019, Zeller2014, Vachida2019, Qin2012 Firmicutes Clostridia Eubacteriaceae + SANA Sessile Rod No spore 47
Eubacterium maltosivorans Rare Possible Commensal Non/unknown Pathogen human faeces (Feng2018) New2022 Firmicutes Clostridia Eubacteriaceae + SANA Sessile Rod No spore 47.8
Eubacterium multiforme 1 Opportunistic in immunocompromised patients Rare Transient Opportunistic Infection human faeces, and soil, and clinical sources (deep wound) RajilicStojanovic2014 Firmicutes Clostridia Eubacteriaceae + SANA Swimming Rod No spore 20(neg)
Eubacterium nodatum Negative 2 Rare Transient Opportunistic Pathogen human faeces and subgingival samples Byrd2020, Yang2020 Firmicutes Clostridia Eubacteriales Family XIII. Incertae Sedis + SANA Sessile Rod No spore 36-38
Eubacterium oxidoreducens 1 Rare Possible Commensal Non/unknown Pathogen rumen. Has also been detected in human faeces (probably transient) Byrd2020, Yang2020 Firmicutes Clostridia Eubacteriaceae + SANA Sessile Rod - curved No spore 35.7
Eubacterium plexicaudatum 1 Rare Possible Commensal Non/unknown Pathogen caecal contents of a mouse Byrd2020 Firmicutes Clostridia Eubacteriaceae + SANA Swimming Rod - curved No spore 44
Eubacterium pyruvativorans 1 Rare Possible Commensal Non/unknown Pathogen High G+C for Clostridium/Eubacteria species. Net producer of mainly caproate, plus valerate. Net consumer of acetate, propionate and butyrate. sheep rumen Byrd2020, De2020 Firmicutes Clostridia Eubacteriaceae + ANA Sessile Rod - curved No spore 56.8
Eubacterium ramulus Positive 1 Moderate Known Commensal Non/unknown Pathogen human faeces (Ludwig2009) Woodmansey2004, McLaughlin2010, Walker2011, RajilicStojanovic2014, Browne2016, Lagier2016, Rothschild2018, Zou2019, Forster2019, Byrd2020, Chen2020, Hu2019, Jeong2021, Vachida2019, Minerbi2019 Firmicutes Clostridia Eubacteriaceae + SANA Sessile Rod No spore 39 20(+)
Eubacterium rectale Agathobacter rectalis Positive 1 Widespread Known Commensal Non/unknown Pathogen human faeces Finegold1974, Holdeman1976, Finegold1977, Benno1984, Benno1986, Benno1989, Mangin2004, MacFarlane2004, Woodmansey2004, McLaughlin2010, Walker2011, Tyakht2013, Nielsen2014, RajilicStojanovic2014, Salonen2014, Browne2016, Chung2016, Lagier2016, Rothschild2018, Zou2019, Forster2019, King2019, Yang2020, Chen2020, Hu2019, Jeong2021, Jie2017, Zeller2014, Wang2018, Vachida2019, Wang2020a, Urban2020, Qin2012, Moore1995, LeChatelier2013, Karlsson2013 Firmicutes Clostridia Eubacteriaceae + SANA Swimming Rod - curved Endospore 41.5 20(neg)
Eubacterium ruminantium 1 Rare Possible Commensal Non/unknown Pathogen human faeces and cow rumen Moore1974, RajilicStojanovic2014, Lagier2016, Byrd2020 Firmicutes Clostridia Eubacteriaceae + SANA Sessile Rod No spore 20(+)
Eubacterium saphenum 2 Rare Transient Opportunistic Pathogen dental disease and human faeces Bik2006, RajilicStojanovic2014, Byrd2020, De2020, Zeller2014, Vachida2019 Firmicutes Clostridia Eubacteriaceae + SANA Sessile Rod No spore 44-48
Eubacterium siraeum Positive 1 Widespread Known Commensal Non/unknown Pathogen human faeces Walker2011, Tyakht2013, Nielsen2014, RajilicStojanovic2014, Salonen2014, Browne2016, Lagier2016, Rothschild2018, Zou2019, King2019, De2020, Yang2020, Chen2020, Dubinkina2017, Hu2019, Jeong2021, Jie2017, Zeller2014, Wang2018, Vachida2019, Wang2020a, Urban2020, Qin2012, LeChatelier2013, Karlsson2013 Firmicutes Clostridia Eubacteriaceae + SANA Swimming Rod No spore 45 20(neg)
Eubacterium sulci Fusobacterium sulci 2 Rare Transient Opportunistic Pathogen dental disease and human faeces McLaughlin2010, RajilicStojanovic2014, Byrd2020, Yang2020 Firmicutes Clostridia Eubacteriaceae + SANA Sessile Rod No spore 39
Eubacterium tenue 2 Minor Possible Commensal Opportunistic Pathogen clinical sources (abscess, knee synovial fluid, blood) and human faeces Finegold1974, Holdeman1976, Finegold1977, Nam2008a, Pfleiderer2013, RajilicStojanovic2014, Lagier2016 Firmicutes Clostridia Eubacteriaceae + SANA Sessile Rod No spore
Eubacterium uniforme 1 Rare Possible Commensal Non/unknown Pathogen rumen of a sheep Byrd2020 Firmicutes Clostridia Eubacteriaceae + SANA Sessile Short Rod No spore 35.2
Eubacterium ventriosum Bacteroides ventriosus 2 Widespread Known Commensal Opportunistic Pathogen human faeces and clinical sources (mouth abscess, various infections) Moore1974, Finegold1974, Holdeman1976, Finegold1977, Woodmansey2004, Walker2011, Tyakht2013, Nielsen2014, RajilicStojanovic2014, Salonen2014, Lagier2016, Rothschild2018, Zou2019, Byrd2020, Chen2020, Dubinkina2017, Hu2019, Jie2017, Zeller2014, Wang2018, Vachida2019, Wang2020a, Qin2012, Moore1995, Karlsson2013 Firmicutes Clostridia Eubacteriaceae + SANA Sessile Rod No spore 20(neg)
Eubacterium xylanophilum 1 Rare Transient Non/unknown Pathogen human faeces, and sheep rumen Byrd2020, Yang2020 Firmicutes Clostridia Eubacteriaceae + SANA Swimming Rod No spore 39
Eubacterium yurii Eubacterium yurii subsp. yurii 2 Rare Possible Commensal Opportunistic Pathogen subgingival dental plaque Lagier2016, Zeller2014 Firmicutes Clostridia Eubacteriaceae + SANA Swimming Rod No spore 32
Ewingella americana 2 Rare Possible Commensal Causes Illness human faeces (CCUG - diarrhoea), clinical sources (blood, wound throat - CCUG) and the environment Byrd2020 Proteobacteria Gammaproteobacteria Yersiniaceae neg FANA Swimming Rod No spore 54.4
Exiguobacterium aurantiacum 1 Rare Known Commensal Non/unknown Pathogen wastewater and human faeces RajilicStojanovic2014, Lagier2016, Yang2020 Firmicutes Bacilli Family XI Incertae Sedis + FANA Swimming Pleiomorphic No spore 53.2-55.8
Exiguobacterium marinum 1 Rare Possible Commensal Non/unknown Pathogen tidal flats and human faeces Forster2019 Firmicutes Bacilli Family XI Incertae Sedis vr FANA Swimming Rod 48
Exiguobacterium mexicanum 1 Rare Possible Commensal Non/unknown Pathogen brine shrimp Zou2019 Firmicutes Bacilli Family XI Incertae Sedis + FANA Swimming Rod No spore
Exiguobacterium undae 1 Rare Possible Commensal Non/unknown Pathogen pond water and human faeces Forster2019 Firmicutes Bacilli Family XI Incertae Sedis + FANA Swimming No spore
Ezakiella coagulans Bacteroides coagulans 2 Minor Possible Commensal Opportunistic Pathogen human faeces Finegold1974, Holdeman1976, Finegold1977, Woodmansey2004, RajilicStojanovic2014, Lagier2016, Byrd2020, Yang2020 Bacteroidetes Bacteroidia Bacteroidaceae neg SANA Sessile Coccus No spore 37
Ezakiella massiliensis Rare Transient Rare Opportunist In 1% of Europeans (unseenbio.com). Rare coloniser. a woman with bacterial vaginosis New2022 Bacteroidetes Bacteroidia Bacteroidaceae + SANA Coccus No spore
Ezakiella peruensis Rare Possible Commensal Non/unknown Pathogen human faeces (CCUG) Yang2020 Firmicutes Tissierellia Tissierellia incertae sedis + SANA Sessile Coccus No spore 38.4
Facklamia hominis 2 Rare Possible Commensal Opportunistic Infection an abscess on the buttocks of a patient, clinical sources (blood, vagina, boil) Lagier2016, Byrd2020 Firmicutes Bacilli Aerococcaceae + FANA Sessile Coccus No spore 41
Facklamia languida 2 Rare Possible Commensal Opportunistic Pathogen clinical sources Lagier2016 Firmicutes Bacilli Aerococcaceae + FANA Sessile Oval-shaped No spore
Faecalibacillus faecis Rare Possible Commensal Non/unknown Pathogen human faeces (Seo2019) Firmicutes Erysipelotrichia Erysipelotrichaceae + SANA Sessile Rod No spore 30.2
Faecalibacillus intestinalis Rare Possible Commensal Non/unknown Pathogen human faeces (Seo2019) New2022 Firmicutes Erysipelotrichia Erysipelotrichaceae + SANA Sessile Rod No spore 29.2
Faecalibacterium prausnitzii Fusobacterium prausnitzii Positive 2 Widespread Known Commensal Opportunistic Pathogen human faeces and animal faeces Benno1986, Benno1989, Woodmansey2004, Wang2005, Nam2008a, McLaughlin2010, PerisBondia2011, Walker2011, Zupancic2012, deGoffau2013, Tyakht2013, Nielsen2014, RajilicStojanovic2014, Salonen2014, Cassir2015, Browne2016, Chung2016, Lagier2016, Rothschild2018, Zou2019, Chung2019, Forster2019, King2019, Byrd2020, De2020, Yang2020, New2022, Chen2020, Dubinkina2017, Hu2019, Jeong2021, Jie2017, Zeller2014, Wang2018, Vachida2019, Wang2020a, Urban2020, Qin2012, Minerbi2019, Moore1995, LeChatelier2013, Karlsson2013, PerezBrocal2015 Firmicutes Clostridia Oscillospiraceae neg SANA Sessile Rod No spore 57
Faecalibaculum rodentium Rare Transient Non/unknown Pathogen a femal mouse Byrd2020, New2022 Firmicutes Erysipelotrichia Erysipelotrichaceae + SANA Sessile Short Rod No spore 52.3
Faecalicatena contorta Eubacterium contortum 2 Minor Known Commensal Causes Illness human faeces (high in Crohn's patients), clinical specimens (wounds, blood) and vagina Finegold1974, Finegold1977, Taylor1985, Benno1989, Browne2016, Zou2019, Byrd2020, Yang2020 Firmicutes Clostridia Lachnospiraceae + SANA Sessile Rod No spore 48.7 20(+)
Faecalicatena faecis Moderate Possible Mutualist Isolation and characterisation not yet published. In 99% of Europeans (unseenbio.com). A moderate coloniser. Byrd2020 Firmicutes Clostridia Lachnospiraceae
Faecalicatena fissicatena Eubacterium fissicatena 1 Minor Possible Commensal Non/unknown Pathogen In 50% of Europeans (unseenbio.com). Minor coloniser. the alimentary tract of a goat Lagier2016, Byrd2020 Firmicutes Clostridia Lachnospiraceae + SANA Sessile Coccobacillus No spore 50.5
Faecalicatena glycyrrhizinilyticum Minor Possible Mutualist Isolation and characterisation not yet published. In 69% of Europeans (unseenbio.com). A minor coloniser. Byrd2020, Jeong2021 Firmicutes Clostridia Lachnospiraceae
Faecalicatena gnavus Moderate Possible Mutualist Isolation and characterisation not yet published. In 85% of Europeans (unseenbio.com). A moderate coloniser. Byrd2020 Firmicutes Clostridia Lachnospiraceae
Faecalicatena lactaris Moderate Possible Mutualist Isolation and characterisation not yet published. In 98% of Europeans (unseenbio.com). A moderate coloniser. Byrd2020 Firmicutes Clostridia Lachnospiraceae
Faecalicatena orotica Clostridium oroticum 2 Minor Known Commensal Opportunistic Pathogen human faeces, black mud and clinical sources (rectal abscess, bladder) Finegold1974, Finegold1977, Benno1984, Benno1989, Pfleiderer2013, Lagier2016, Zou2019, Byrd2020 Firmicutes Clostridia Lachnospiraceae + SANA Sessile Rod Endospore 49.9 20(+)
Faecalicatena torques Moderate Possible Mutualist Isolation and characterisation not yet published. In 97% of Europeans (unseenbio.com). A moderate coloniser. Byrd2020 Firmicutes Clostridia Lachnospiraceae
Faecalicoccus pleomorphus Streptococcus pleomorphus Unknown 1 Minor Possible Commensal Non/unknown Pathogen In 13% of Europeans (unseenbio.com). Minor coloniser. human faeces, and animal sources RajilicStojanovic2014, Lagier2016, Zou2019, Byrd2020, Minerbi2019 Firmicutes Bacilli Streptococcaceae + SANA Sessile No spore 39
Faecalimonas umbilicata Rare Possible Commensal Non/unknown Pathogen human faeces (Sakamoto2017) Jeong2021, Minerbi2019 Firmicutes Clostridia Lachnospiraceae + SANA Sessile Coccobacillus No spore 46.9
Faecalitalea cylindroides Eubacterium cylindroides 1 Widespread Known Commensal Non/unknown Pathogen human faeces Finegold1974, Holdeman1976, Finegold1977, Benno1989, Woodmansey2004, Tyakht2013, RajilicStojanovic2014, Salonen2014, Lagier2016, Forster2019, King2019, Byrd2020, New2022, Chen2020, Dubinkina2017, Hu2019, Jie2017, Zeller2014, Wang2018, Vachida2019, Li2019b, LeChatelier2013, Karlsson2013 Firmicutes Erysipelotrichia Erysipelotrichaceae + SANA Sessile No spore
Fannyhessea vaginae Atopobium vaginae 2 Minor Possible Commensal Opportunistic Pathogen human vagina and faeces Lagier2016, Almeida2019, Byrd2020, New2022, Hu2019, Zeller2014, Vachida2019 Actinobacteria Actinomycetia Actinomycetaceae + FANA Sessile Coccus 44
Fastidiosipila sanguinis Rare Possible Commensal Opportunistic Pathogen human blood Lagier2016, Byrd2020, New2022 Firmicutes Clostridia Oscillospiraceae + Micr Sessile Coccus No spore 32.9
Fenollaria massiliensis Minor Possible Commensal Non/unknown Pathogen In 13% of Europeans (unseenbio.com). Minor coloniser. an osteoarticular sample of a patient, France Byrd2020 Firmicutes Clostridia neg SANA Sessile Rod No spore 34.5
Fenollaria timonensis Micromassilia timonensis Rare Possible Commensal Non/unknown Pathogen the faeces of a healthy volunteer Lagier2016, Byrd2020, De2020 Firmicutes Clostridia Eubacteriales incertae sedis neg ANA Swimming Rod No spore
Fermentimonas caenicola Rare Possible Commensal Non/unknown Pathogen a bioreactor and human faeces King2019 Bacteroidetes Bacteroidia Porphyromonadaceae neg FANA Sessile Rod No spore 38.2
Ferrimonas balearica 1 Rare Possible Commensal Non/unknown Pathogen Uses Fe(III) and Mn(IV) as electron acceptors. Requires sodium for growth. marine sediment, Spain Forster2019 Proteobacteria Gammaproteobacteria Ferrimonadaceae neg FANA Swimming Short Rod No spore 54
Fibrobacter succinogenes Bacteroides succinogenes 1 Unlikely Transient Non/unknown Pathogen Sensitive to low concentrations of methanol (Caldwell1989). cattle rumen New2022, Zeller2014 Fibrobacteres Fibrobacteria Fibrobacteraceae neg SANA Sessile Oval-shaped No spore 48-51
Fictibacillus arsenicus Bacillus arsenicus 1 Unlikely Transient Non/unknown Pathogen Resistant to 20mM arsenic(V) and 0.3mM arsenic(III). Significant differences between Shivaji2005 and Glaeser2013 reported assimilation data. Obligate aerobe so unlikely to be a gut coloniser. human faeces and arsenic soils Dubourg2013, RajilicStojanovic2014, Lagier2016 Firmicutes Bacilli Bacillaceae + SAER Swimming Rod Endospore 35
Filifactor alocis Fusobacterium alocis Negative 2 Minor Transient Opportunistic Pathogen dental disease (oral infections, blood) and human faeces Woodmansey2004, Bik2006, RajilicStojanovic2014, Lagier2016, Byrd2020, De2020, New2022, Zeller2014, Vachida2019 Firmicutes Clostridia Peptostreptococcaceae neg SANA Swimming Rod No spore 28–34
Filifactor villosus Clostridium villosum Negative 1 Unlikely Transient Opportunistic Pathogen a cat abscess and human faeces RajilicStojanovic2014, Lagier2016 Firmicutes Clostridia Peptostreptococcaceae + SANA Sessile Rod Rare
Finegoldia magna Peptostreptococcus magnus 2 Widespread Known Commensal Opportunistic Pathogen clinical sources (vagina, abscess, tissue - CCUG) and human faeces Finegold1974, Holdeman1976, Finegold1977, Benno1984, Benno1986, Benno1989, Walker2011, Dubourg2013, Pfleiderer2013, Tyakht2013, RajilicStojanovic2014, Cassir2015, Lagier2016, Rothschild2018, Almeida2019, Forster2019, Byrd2020, Yang2020, New2022, Dubinkina2017, Hu2019, Zeller2014, Vachida2019 Firmicutes Clostridia Peptoniphilaceae + SANA Coccus No spore 32–34
Flaviflexus massiliensis Rare Possible Commensal Non/unknown Pathogen the faeces of a young girl from Niger suffering from kwashiorkor Lagier2016 Actinobacteria Actinomycetia Actinomycetaceae + AER Coccobacillus
Flavobacterium banpakuense Unlikely Transient Non/unknown Pathogen Obligate aerobe; unlikely to be a gut coloniser. human faeces, and compost RajilicStojanovic2014 Bacteroidetes Flavobacteriia Flavobacteriaceae neg SAER Gliding Rod No spore 31.1
Flavobacterium caeni Non Transient Non/unknown Pathogen Strict aerobe and only grows at 30C, so likely to be a non-coloniser of the gut. Significant descrepancy between some data reported by Fujii2014 and that originally reported by Liu2010a. a waste treatment plant Byrd2020, De2020 Bacteroidetes Flavobacteriia Flavobacteriaceae neg SAER Sessile Rod No spore 52
Flavobacterium cheniae Rare Possible Commensal Non/unknown Pathogen human faeces, and polluted waters RajilicStojanovic2014 Bacteroidetes Flavobacteriia Flavobacteriaceae neg AER Gliding Rod No spore 40.6
Flavobacterium daejeonense 1 Unlikely Transient Non/unknown Pathogen Obligate aerobe; unlikely to be a gut coloniser. greenhouse soil, Korea Forster2019 Bacteroidetes Flavobacteriia Flavobacteriaceae neg SAER Sessile Rod No spore 35
Flavobacterium lindanitolerans 1 Rare Possible Commensal Opportunistic Pathogen contaminated soil, clinical sources (wound, peritoneal - CCUG) and human faeces RajilicStojanovic2014, Lagier2016 Bacteroidetes Flavobacteriia Flavobacteriaceae neg AER Gliding Rod No spore 31
Flavobacterium oncorhynchi Unlikely Transient Non/unknown Pathogen Can't grow at 37C, so unlikely to be a gut coloniser. human faeces, and rainbow trout RajilicStojanovic2014 Bacteroidetes Flavobacteriia Flavobacteriaceae neg AER Sessile Rod No spore 33.0
Flavobacterium sakaeratica Rare Possible Commensal Non/unknown Pathogen human faeces RajilicStojanovic2014 Bacteroidetes Flavobacteriia Flavobacteriaceae neg Rod No spore
Flavonifractor plautii Eubacterium plautii Mixed 1 Widespread Known Commensal Non/unknown Pathogen Prevalent in paediatric patients with onset UC, CD and IBD-U vs. controls (Malham2019). human faeces and blood Mangin2004, Woodmansey2004, Wang2005, McLaughlin2010, Walker2011, Zupancic2012, Pfleiderer2013, Nielsen2014, RajilicStojanovic2014, Salonen2014, Browne2016, Lagier2016, Rothschild2018, Chung2019, Forster2019, King2019, Byrd2020, De2020, New2022, Chen2020, Dubinkina2017, Hu2019, Jeong2021, Jie2017, Vachida2019, Wang2020a, Minerbi2019 Firmicutes Clostridia Oscillospiraceae vr SANA Swimming Rod Endospore 58-61.6
Flexispira rappini Rare Possible Commensal Non/unknown Pathogen human faeces and blood RajilicStojanovic2014 Proteobacteria Epsilonproteobacteria Helicobacteraceae neg Micr Swimming Helical No spore
Flintibacter butyricus Rare Possible Commensal Non/unknown Pathogen mouse intestines (miBC collection) Diamanti2020 Firmicutes Clostridia Eubacteriales incertae sedis neg SANA Sessile Rod No spore 58
Fournierella massiliensis Moderate Possible Commensal Non/unknown Pathogen In 90% of Europeans (unseenbio.com). human faeces Lagier2016, Byrd2020 Firmicutes Clostridia Oscillospiraceae neg SANA Sessile Rod No spore 56.8
Francisella tularensis Brucella tularensis 3 Can be passed from animals to humans Non Transient Dangerous Pathogen Facultative intracellular parasite. Causes tularemia in humans. Can reach epidemic levels and is transmitted by zoonotic means. many types of animals and insects Lagier2016 Proteobacteria Gammaproteobacteria Francisellaceae neg Micr Sessile Short Rod No spore 34
Franconibacter pulveris Cronobacter pulveris Rare Possible Commensal Non/unknown Pathogen infant formula Byrd2020, De2020 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Swimming Coccobacillus No spore 56.6
Fredinandcohnia humi Bacillus humi 1 Non Transient Non/unknown Pathogen soil Lagier2016 Firmicutes Bacilli Bacillaceae + FANA Swimming Rod Endospore 37.5
Fretibacterium fastidiosum Rare Possible Commensal Non/unknown Pathogen Asaccharolytic. Growth stimulated by the presence of Fusobacterium nucleatum subsp. nucleatum. the human oral cavity Vachida2019 Synergistetes Synergistia Synergistaceae neg SANA Swimming Rod - curved No spore 63
Fructilactobacillus florum Lactobacillus florum Unlikely Transient Non/unknown Pathogen from flowers, South Africa Firmicutes Bacilli Lactobacillaceae + FANA Sessile Rod No spore 42
Fructilactobacillus fructivorans Lactobacillus fructivorans 1 Unlikely Transient Non/unknown Pathogen Can grow in media with up to 15% ethanol. Firmicutes Bacilli Lactobacillaceae + Micr Sessile Rod No spore 38.9
Fructilactobacillus sanfranciscensis Lactobacillus sanfranciscensis 1 Rare Transient Non/unknown Pathogen human faeces, food (fermented and spoilt) and sourdough bread fermentation Byrd2020, Yang2020, Hu2019, Zeller2014, Vachida2019 Firmicutes Bacilli Lactobacillaceae + Micr Sessile Rod No spore 36-38
Fucophilus fucoidanolyticus Rare Possible Commensal Non/unknown Pathogen Digests algal-derived fucoidan compounds (sulfated fucosyl polysaccharides). a sea cucumber gut Verrucomicrobia Verrucomicrobiae Verrucomicrobiaceae neg AER Sessile Coccus No spore 52
Fundidesulfovibrio putealis Desulfovibrio putealis 1 Rare Possible Commensal Non/unknown Pathogen Uses sulfate, sulfite and thiosulfate as electron acceptors water-producing well in France De2020 Proteobacteria Deltaproteobacteria Desulfovibrionaceae neg SANA Swimming Vibrio No spore 57.8
Furfurilactobacillus rossiae Lactobacillus rossiae 1 Unlikely Transient Non/unknown Pathogen wheat sourdough Byrd2020 Firmicutes Bacilli Lactobacillaceae + Micr Sessile Rod No spore 44.6
Fusicatenibacter saccharivorans Moderate Known Commensal Non/unknown Pathogen In 100% of Europeans (unseenbio.com). human faeces RajilicStojanovic2014, Browne2016, Lagier2016, Zou2019, Chung2019, Forster2019, Byrd2020, Yang2020, Minerbi2019 Firmicutes Clostridia Lachnospiraceae + SANA Sessile Rod Endospore 46.9-47.2
Fusobacterium canifelinum 2 Zoonotic pathogen Rare Possible Commensal Opportunistic Pathogen cats and dogs, and bites from them in humans Lagier2016 Fusobacteria Fusobacteriia Fusobacteriaceae neg SANA Sessile Rod No spore 26-28 neg
Fusobacterium gonidiaformans Bacillus gonidiaformans 2 Minor Possible Commensal Opportunistic Pathogen human faeces Finegold1974, Benno1986, McLaughlin2010, Tyakht2013, Nielsen2014, RajilicStojanovic2014, Lagier2016, Forster2019, Byrd2020, Yang2020, New2022, Dubinkina2017, Zeller2014, Vachida2019 Fusobacteria Fusobacteriia Fusobacteriaceae neg SANA Sessile Rod No spore neg
Fusobacterium massiliense Rare Possible Commensal Non/unknown Pathogen duodenum of a patient with iron deficiency Lagier2016 Fusobacteria Fusobacteriia Fusobacteriaceae neg SANA Sessile Rod No spore 27
Fusobacterium mortiferum Clostridium rectum 2 Moderate Known Commensal Opportunistic Pathogen human faeces and abscess Moore1974, Benno1984, Benno1986, Benno1989, Tyakht2013, RajilicStojanovic2014, Lagier2016, Zou2019, Forster2019, Byrd2020, New2022, Dubinkina2017, Hu2019, Jie2017, Zeller2014, Vachida2019, Wang2020a, Minerbi2019 Fusobacteria Fusobacteriia Fusobacteriaceae neg SANA Sessile Rod No spore +
Fusobacterium naviforme 2 Human and animal pathogen Rare Possible Commensal Opportunistic Pathogen human faeces and lesion (exudate) Benno1986, Mangin2004, Dubourg2013, RajilicStojanovic2014, Lagier2016 Fusobacteria Fusobacteriia Fusobacteriaceae neg SANA Rod No spore neg
Fusobacterium necrogenes 2 Rare Known Commensal Opportunistic Pathogen human faeces Finegold1974, Benno1986, Benno1989, RajilicStojanovic2014, Lagier2016, Yang2020 Fusobacteria Fusobacteriia Fusobacteriaceae neg SANA Rod No spore +
Fusobacterium necrophorum 2 Human and animal pathogen Minor Possible Commensal Known Pathogen Strain F85 can grow in media containing 25% methanol, with only ~6% decrease in growth rate (Caldwell1989). human faeces and clinical sources (blood - CCUG) Finegold1974, Benno1984, RajilicStojanovic2014, Lagier2016, Forster2019, Byrd2020, New2022, Vachida2019 Fusobacteria Fusobacteriia Fusobacteriaceae neg SANA Rod No spore
Fusobacterium necrophorum subsp. funduliforme 2 Human and animal pathogen Rare Possible Commensal Opportunistic Pathogen pathogenic legions of animals Lagier2016 Fusobacteria Fusobacteriia Fusobacteriaceae neg SANA Sessile Rod No spore 27-31 20(neg)
Fusobacterium nucleatum Fusobacterium nucleatum subsp. nucleatum Negative 2 Minor Known Commensal Opportunistic Infection human faeces and clinical sources (blood, lesion - CCUG) Benno1986, Bik2006, Walker2011, Nielsen2014, RajilicStojanovic2014, Lagier2016, Almeida2019, Chung2019, Forster2019, Byrd2020, De2020, New2022, Urban2020 Fusobacteria Fusobacteriia Fusobacteriaceae neg SANA Rod No spore
Fusobacterium nucleatum subsp. animalis Fusobacterium animalis 2 Rare Possible Commensal Possible Pathogen human gut and amniotic fluid Tyakht2013, Byrd2020, Yang2020, Jie2017 Fusobacteria Fusobacteriia Fusobacteriaceae neg SANA Sessile Rod No spore 26-28 20(+)
Fusobacterium nucleatum subsp. nucleatum Fusobacterium nucleatum 2 Minor Possible Commensal Opportunistic Infection human gut and clinical sources (blood, lesion - CCUG) Benno1986, Tyakht2013, Yang2020, Dubinkina2017, Hu2019, Zeller2014, Vachida2019, Wang2020a Fusobacteria Fusobacteriia Fusobacteriaceae neg SANA Sessile Rod No spore 26-28 20(neg)
Fusobacterium nucleatum subsp. polymorphum 2 Rare Possible Commensal Opportunistic Pathogen human gut and clinical sources (blood, throat, gingiva - CCUG) Yang2020 Fusobacteria Fusobacteriia Fusobacteriaceae neg SANA Sessile Rod No spore 26-28 20(neg)
Fusobacterium nucleatum subsp. vincentii 2 Rare Possible Commensal Opportunistic Pathogen human gut and clinical sources (blood, periodontal pocket - CCUG) Yang2020 Fusobacteria Fusobacteriia Fusobacteriaceae neg SANA Sessile Rod No spore 26-28 20(neg)
Fusobacterium perfoetens 1 Opportunistic in immunocompromised patients Rare Possible Commensal Non/unknown Pathogen an infant with diarrhoea, and piglet faeces Fusobacteria Fusobacteriia Fusobacteriaceae neg SANA Sessile Oval-shaped No spore 28-30 S
Fusobacterium periodonticum Fusobacterium sp. 2_1_31 2 Minor Possible Commensal Opportunistic Pathogen dental disease and human faeces RajilicStojanovic2014, Lagier2016, Forster2019, Byrd2020, Hu2019, Zeller2014, Vachida2019 Fusobacteria Fusobacteriia Fusobacteriaceae neg SANA Sessile Rod No spore 28 neg
Fusobacterium pseudoperiodonticum Unlikely Transient Non/unknown Pathogen human tongue, Korea New2022 Fusobacteria Fusobacteriia Fusobacteriaceae neg ANA Sessile Fusobacterium No spore 28
Fusobacterium russii 2 Minor Known Commensal Opportunistic Pathogen human faeces Moore1974, Benno1986, Finegold1974, Benno1989, Woodmansey2004, RajilicStojanovic2014, Lagier2016, De2020 Fusobacteria Fusobacteriia Fusobacteriaceae neg SANA Rod No spore neg
Fusobacterium ulcerans 2 Rare Possible Commensal Opportunistic Pathogen Few Europeans have it (unseenbio.com). tropical ulcers and human faeces Tyakht2013, Lagier2016, Zou2019, Forster2019, Byrd2020, New2022, Dubinkina2017, Hu2019, Jeong2021, Jie2017, Zeller2014, Vachida2019, Wang2020a Fusobacteria Fusobacteriia Fusobacteriaceae neg SANA Sessile Rod No spore 29.2-29.5
Fusobacterium varium 2 Human and animal pathogen Moderate Known Commensal Opportunistic Pathogen human faeces Benno1986, Benno1989, Wang2005, Tyakht2013, RajilicStojanovic2014, Lagier2016, Zou2019, Forster2019, Byrd2020, Yang2020, New2022, Dubinkina2017, Hu2019, Jeong2021, Jie2017, Zeller2014, Vachida2019 Fusobacteria Fusobacteriia Fusobacteriaceae neg SANA Rod No spore +
Gabonia massiliensis Rare Possible Commensal Non/unknown Pathogen human faeces (Mourembou2016) Lagier2016 Bacteroidetes Bacteroidia Porphyromonadaceae neg ANA Sessile Rod No spore 37.9
Gabonibacter massiliensis Minor Possible Commensal Opportunistic Infection In 31% of Europeans (unseenbio.com). Minor coloniser. human faeces (Bilen2018e) and clinical specimens (blood - CCUG) Byrd2020 Bacteroidetes Bacteroidia Porphyromonadaceae neg SANA Swimming Coccobacillus No spore 42.1
Gabonibacter timonensis Rare Possible Commensal Non/unknown Pathogen human faeces (CCUG) Bacteroidetes Bacteroidia Porphyromonadaceae + Rod No spore
Gallibacterium anatis Pasteurella anatis 2 Animal pathogen Rare Possible Commensal Opportunistic Pathogen Description for G. anatis bv anatis, not the haemolytic biovar. duck intestines Forster2019, Zeller2014 Proteobacteria Gammaproteobacteria Pasteurellaceae neg FANA Sessile Rod No spore 39.9-42.6
Gardnerella leopoldii Unlikely Transient Non/unknown Pathogen human vagina, Belgium New2022 Actinobacteria Actinomycetia Bifidobacteriaceae neg FANA Coccobacillus No spore 41.9-43.2
Gardnerella vaginalis Haemophilus vaginalis 2 Minor Transient Opportunistic Pathogen human faeces, clinical sources (UTI, blood) and vagina Lagier2016, King2019, New2022, Hu2019, Jeong2021, Zeller2014, Vachida2019 Actinobacteria Actinomycetia Bifidobacteriaceae neg FANA Sessile Rod No spore 41.0-42.8
Gemella asaccharolytica Rare Possible Commensal Opportunistic Pathogen human faeces and clinical sources (abscess) Byrd2020, Yang2020 Firmicutes Bacilli Bacillales Family XI. Incertae Sedis vr FANA Sessile Coccus No spore
Gemella haemolysans Neisseria haemolysans 2 Minor Known Commensal Opportunistic Pathogen human faeces and clinical sources (blood, eye, abscess, cerebrospinal fluid) Wang2005, Bik2006, McLaughlin2010, Walker2011, RajilicStojanovic2014, Cassir2015, Lagier2016, Almeida2019, Byrd2020, Yang2020, New2022, Hu2019, Zeller2014, Vachida2019 Firmicutes Bacilli Family XI Incertae Sedis + FANA Sessile Oval-shaped No spore 30-34
Gemella morbillorum Streptococcus morbillorum 2 Minor Known Commensal Opportunistic Pathogen human faeces, and clinical sources (blood, abscess - CCUG) Benno1986, Walker2011, RajilicStojanovic2014, Lagier2016, Byrd2020, De2020, Yang2020, New2022, Dubinkina2017, Hu2019, Zeller2014, Vachida2019 Firmicutes Bacilli Family XI Incertae Sedis + FANA Sessile Coccus No spore 30
Gemella sanguinis 2 Minor Known Commensal Opportunistic Pathogen clinical sources (blood) and human faeces McLaughlin2010, RajilicStojanovic2014, Lagier2016, Byrd2020, De2020, Yang2020, New2022, Hu2019, Zeller2014, Vachida2019 Firmicutes Bacilli Family XI Incertae Sedis + FANA Sessile Coccus No spore 31
Gemmatimonas groenlandica Non Transient Non/unknown Pathogen Yeast extract used as a N source. Likely not a gut coloniser because maximum temperature for growth is 32C. surface water, Greenland New2022 Gemmatimonadetes Gemmatimonadetes Gemmatimonadaceae neg AER Rod 65.1
Gemmiger formicilis Positive 1 Moderate Known Commensal Non/unknown Pathogen In 97% of Europeans (unseenbio.com). human faeces MacFarlane2004, deGoffau2013, RajilicStojanovic2014, Lagier2016, Forster2019, Byrd2020, Minerbi2019, Moore1995 Firmicutes Clostridia Eubacteriales Family XIII. Incertae Sedis neg SANA Sessile Oval-shaped No spore 59
Gemmiger variabile Moderate Possible Mutualist No record in the NCBI database for this organism. In 77% of Europeans (unseenbio.com). A moderate coloniser. Byrd2020 Firmicutes Clostridia Ruminococcaceae
Geobacillus stearothermophilus Bacillus stearothermophilus Positive 1 Unlikely Transient Non/unknown Pathogen High optimum growth temperature so unlikely to be a gut coloniser. human faeces, hot springs, compost, food and soil RajilicStojanovic2014, Lagier2016 Firmicutes Bacilli Bacillaceae + AER Swimming Rod Endospore 51.9
Geobacillus vulcani Bacillus vulcani 1 Unlikely Possible Commensal Non/unknown Pathogen human faeces and marine thermal vent RajilicStojanovic2014, Lagier2016 Firmicutes Bacilli Bacillaceae + AER Swimming Rod Endospore 53.0
Geodermatophilus obscurus 1 Non Transient Non/unknown Pathogen Aerobic and poor growth at 37C suggests this not a gut coloniser. desert soil, USA Zeller2014 Actinobacteria Actinomycetia Geodermatophilaceae + AER Swimming Filamentous Exospore
Georgenia muralis 1 Rare Possible Commensal Non/unknown Pathogen old painting and human faeces RajilicStojanovic2014, Lagier2016 Actinobacteria Actinomycetia Bogoriellaceae + FANA Sessile No spore 70
Georgenia satyanarayanai Oceanitalea nanhaiensis Unlikely Transient Non/unknown Pathogen Obligate aerobe; unlikely to be a gut coloniser. Data for antibiotic activity from Oceanitalea nanhaiensis (Fu2012). soda lake sediment, India Yang2020 Actinobacteria Actinomycetia Bogoriellaceae + SAER Sessile Oval-shaped No spore 73.4
Geosporobacter ferrireducens Unlikely Transient Non/unknown Pathogen Fe(III) acts as an electron acceptor an oil-contaminated site, Korea New2022 Firmicutes Clostridia Clostridiaceae neg ANA Swimming Rod No spore 37.2
Gleimia europaea Actinomyces europaeus 2 Rare Possible Commensal Opportunistic Pathogen clinical sources (abscess, ulcer, cyst) Lagier2016, Byrd2020, Vachida2019 Actinobacteria Actinomycetia Actinomycetaceae + FANA Sessile Short Rod No spore 61-63
Globicatella sulfidifaciens 2 Animal pathogen Rare Possible Commensal Possible Pathogen animal wounds Lagier2016, Byrd2020 Firmicutes Bacilli Aerococcaceae vr FANA Sessile Coccus No spore 35-36 neg
Glutamicibacter arilaitensis Arthrobacter arilaitensis 1 Unlikely Transient Non/unknown Pathogen Aerobic and low growth temperatures of 10-30C suggests this is an unlikely gut coloniser. the surface of Reblochon cheese Zeller2014 Actinobacteria Actinomycetia Micrococcaceae + AER Sessile Rod-coccus cycle No spore
Glutamicibacter protophormiae Arthrobacter protophormiae 1 Rare Possible Commensal Non/unknown Pathogen human faeces, soil and flies Yang2020 Actinobacteria Actinomycetia Micrococcaceae + FANA Swimming Club rod No spore 63.2-65.9
Gorbachella massiliensis Rare Possible Commensal Non/unknown Pathogen human faeces (Bilen2018e) Lagier2016 Firmicutes Clostridia Oscillospiraceae neg SANA Sessile Rod No spore
Gordonia alkanivorans 1 Rare Possible Commensal Non/unknown Pathogen tar-contaminated soil Zeller2014 Actinobacteria Actinomycetia Gordoniaceae + FANA Sessile Rod-coccus cycle No spore 68
Gordonia rubripertincta Rhodococcus rubripertinctus 1 Unlikely Transient Non/unknown Pathogen Obligate aerobe; unlikely to be a gut coloniser. human faeces and soil RajilicStojanovic2014, Lagier2016 Actinobacteria Actinomycetia Gordoniaceae + SAER Sessile Coccus No spore 62-67
Gordonia terrae Rhodococcus terrae 2 Rare Possible Commensal Opportunistic Pathogen clinical sources (eye, blood, plural effusion - CCUG) and human faeces McLaughlin2010, RajilicStojanovic2014 Actinobacteria Actinomycetia Gordoniaceae + AER Sessile Rod No spore 64-69
Gordonibacter massiliensis Rare Possible Commensal Non/unknown Pathogen human faeces (Bilen2018e) Lagier2016, Byrd2020 Actinobacteria Coriobacteriia Eggerthellaceae + SANA Swimming Coccobacillus No spore 65.1
Gordonibacter pamelaeae Moderate Possible Commensal Possible Pathogen human faeces and clinical sources (inflammatory bowel disease) Pfleiderer2013, Tyakht2013, RajilicStojanovic2014, Lagier2016, Rothschild2018, Forster2019, King2019, Byrd2020, New2022, Chen2020, Dubinkina2017, Hu2019, Jeong2021, Vachida2019, Qin2012 Actinobacteria Coriobacteriia Eggerthellaceae + SANA Swimming Coccobacillus No spore 66.4
Gordonibacter urolithinfaciens Minor Possible Commensal Non/unknown Pathogen In 28% of Europeans (unseenbio.com). Minor coloniser. human faeces (Alkhalil2017, CCUG) Lagier2016, Byrd2020, New2022, Jeong2021 Actinobacteria Coriobacteriia Eggerthellaceae + SANA Sessile Coccobacillus No spore 66.4
Gorillibacterium timonense Rare Possible Commensal Non/unknown Pathogen human faeces (Ndongo2018) Lagier2016 Firmicutes Bacilli Paenibacillaceae neg FANA Swimming Rod Endospore
Gottschalkia acidurici Unlikely Transient Non/unknown Pathogen garden soil, USA New2022 Firmicutes Tissierellia Gottschalkiaceae + Swimming Rod Endospore 29.9
Gracilibacillus dipsosauri Bacillus dipsosauri 1 Rare Possible Commensal Non/unknown Pathogen nasal cavity of desert iguana Lagier2016 Firmicutes Bacilli Bacillaceae + FANA Swimming Rod Endospore 39.4
Gracilibacillus massiliensis Rare Possible Commensal Non/unknown Pathogen cooking salt specimens Lagier2016 Firmicutes Bacilli Bacillaceae + AER Swimming Rod No spore 36
Gracilibacillus phocaeensis Positive Rare Known Commensal Non/unknown Pathogen human faeces (Senghor2017a) that are salty Firmicutes Bacilli Bacillaceae + Swimming Rod
Gracilibacillus thailandensis Non Transient Non/unknown Pathogen Obligate aerobe and high salt required for optimum growth, so likely a gut non-coloniser. fermented fish Lagier2016 Firmicutes Bacilli Bacillaceae + SAER Swimming Rod Endospore 37.6
Gracilibacillus timonensis Positive Rare Known Commensal Non/unknown Pathogen human faeces (Senghor2017) that are salty Lagier2016 Firmicutes Bacilli Bacillaceae + Swimming Rod - curved Endospore
Granulicatella adiacens Streptococcus adjacens, Abiotrophia adiacens Negative 2 Minor Known Commensal Opportunistic Pathogen clinical sources (blood, sputum, wound) and human faeces McLaughlin2010, RajilicStojanovic2014, Lagier2016, Byrd2020, Yang2020, Dubinkina2017, Hu2019, Zeller2014, Vachida2019 Firmicutes Bacilli Carnobacteriaceae + FANA Sessile Coccus No spore 36.6-37.4
Granulicatella elegans Abiotrophia elegans Negative 2 Minor Known Commensal Opportunistic Pathogen clinical sources (blood, joint fluid) and human faeces Bik2006, Walker2011, RajilicStojanovic2014, Lagier2016, Byrd2020, Yang2020, Hu2019, Zeller2014, Vachida2019 Firmicutes Bacilli Carnobacteriaceae + FANA Sessile Coccus No spore 36-37.5
Granulicatella para-adiacens Abiotrophia para-adiacens Rare Possible Commensal Opportunistic Pathogen clinical sources (endocarditis, bacteremia, blood and endovascular infections - Senn2006) and human faeces McLaughlin2010, Lagier2016, Wang2005, Bik2006, Walker2011, RajilicStojanovic2014 Firmicutes Bacilli Carnobacteriaceae + FANA Sessile Coccus No spore 36-37.4
Grimontia hollisae Vibrio hollisae 2 Zoonotic pathogen Rare Possible Commensal Opportunistic Pathogen Requires Na+ for growth. human faeces and is a likely cause of diarrhoea RajilicStojanovic2014, Lagier2016 Proteobacteria Gammaproteobacteria Vibrionaceae neg FANA Swimming Rod No spore 49.3-51.0
Gulosibacter bifidus Zimmermannella bifida Unlikely Transient Opportunistic Infection Aerobic and low optimum growth temperature (30C) suggests this is unlikely to be a gut coloniser. soil and clinical specimens (blood, wounds) PerezBrocal2015 Actinobacteria Actinomycetia Microbacteriaceae + AER Sessile Short Rod No spore 62
Haemophilus ducreyi 2 Rare Possible Commensal Known Pathogen Produces many peptidases. patients with venereal disease (cause of soft chancre) Proteobacteria Gammaproteobacteria Pasteurellaceae neg AER Sessile Rod No spore 38
Haemophilus haemolyticus 1 Opportunistic in immunocompromised patients Minor Possible Commensal Opportunistic Infection human faeces, nasopharynx and oral cavity RajilicStojanovic2014, Lagier2016, Byrd2020, De2020, New2022, Hu2019, Zeller2014, Vachida2019 Proteobacteria Gammaproteobacteria Pasteurellaceae neg FANA Sessile Coccobacillus No spore 38.5
Haemophilus influenzae 2 Minor Possible Commensal Known Pathogen human faeces, oral cavity and clinical sources (sputum, blood, cerebrospinal fluid - CCUG) Bik2006, RajilicStojanovic2014, Lagier2016, Almeida2019, Byrd2020, De2020, New2022, Zeller2014, Vachida2019, PerezBrocal2015 Proteobacteria Gammaproteobacteria Pasteurellaceae neg FANA Sessile No spore 38.3-39.1
Haemophilus parahaemolyticus 2 Minor Possible Commensal Known Pathogen In 17% of Europeans (unseenbio.com). Minor coloniser. throat and clinical sources (oral infection, pharyngitis, endocarditis) Byrd2020, New2022, Vachida2019 Proteobacteria Gammaproteobacteria Pasteurellaceae neg FANA Sessile Pleiomorph rod No spore 40-41
Haemophilus parainfluenzae 2 Widespread Possible Commensal Opportunistic Pathogen human faeces, oral cavity and clinical sources (sputum, infection, wound - CCUG) Wang2005, McLaughlin2010, Zupancic2012, Nielsen2014, RajilicStojanovic2014, Cassir2015, Lagier2016, Rothschild2018, Almeida2019, King2019, Byrd2020, De2020, Yang2020, New2022, Chen2020, Dubinkina2017, Hu2019, Jeong2021, Jie2017, Zeller2014, Wang2018, Vachida2019, Qin2012, Minerbi2019, Li2019b, PerezBrocal2015 Proteobacteria Gammaproteobacteria Pasteurellaceae neg FANA Sessile Rod No spore 40.2
Haemophilus paraphrohaemolyticus 2 Rare Possible Commensal Opportunistic Pathogen human faeces, throat infections and sputum Byrd2020, Yang2020, Hu2019, Vachida2019 Proteobacteria Gammaproteobacteria Pasteurellaceae neg FANA Sessile Rod No spore 40-41
Haemophilus pittmaniae 2 Minor Possible Commensal Opportunistic Pathogen human saliva, human faeces and clinical sources (blood, urine, bile, other - CCUG) Lagier2016, Byrd2020, De2020, Yang2020, New2022, Zeller2014, Vachida2019 Proteobacteria Gammaproteobacteria Pasteurellaceae neg FANA Sessile No spore
Haemophilus quentini Rare Possible Commensal Rare Opportunist clinical sources and human faeces RajilicStojanovic2014, Byrd2020 Proteobacteria Gammaproteobacteria Pasteurellaceae neg FANA Rod No spore
Haemophilus sputorum Minor Possible Commensal Opportunistic Infection In 11% of Europeans (unseenbio.com). Minor coloniser. clinical sources (blood, oral cavity - CCUG) and human faeces RajilicStojanovic2014, Byrd2020, De2020, Yang2020, Hu2019, Vachida2019 Proteobacteria Gammaproteobacteria Pasteurellaceae neg FANA Sessile Rod No spore
Hafnia alvei 2 Human and animal pathogen Minor Known Commensal Opportunistic Pathogen human faeces, clinical sources (sputum, urine, blood - CCUG) animals, sewage, water and soil Finegold1977, McLaughlin2010, Walker2011, RajilicStojanovic2014, Cassir2015, Lagier2016, Forster2019, Byrd2020, Vachida2019 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA vr Rod No spore 48.0-48.7
Hafnia paralvei Hafnia alvei genomosp. 2 Rare Possible Commensal Opportunistic Pathogen human faeces and clinical sources (blood, urine - CCUG) Byrd2020, Yang2020 Proteobacteria Gammaproteobacteria Hafniaceae neg FANA Swimming Rod No spore 49.8
Hahella ganghwensis 1 Rare Possible Commensal Non/unknown Pathogen Sodium required for growth. tidal flats from Korea De2020 Proteobacteria Gammaproteobacteria Hahellaceae neg AER Swimming Rod No spore 44
Halanaerobaculum tunisiense Unlikely Transient Non/unknown Pathogen Very high salt concentration required for optimum growth, so unlikely gut coloniser. human faeces, and hypersaline lake RajilicStojanovic2014 Firmicutes Clostridia Halobacteroidaceae neg SANA Sessile Rod No spore 34.3
Halobacillus dabanensis 1 Unlikely Transient Non/unknown Pathogen Unlikely gut coloniser because its optimum growth is with high salt. salt lakes in China Lagier2016 Firmicutes Bacilli Bacillaceae + AER Swimming Rod Endospore 41.4
Halobacillus ihumii Rare Possible Commensal Non/unknown Pathogen Strictly halophilic. human faeces (healthy) Firmicutes Bacilli Bacillaceae + SAER Swimming Rod No spore 41.1
Halobacillus karajensis 1 Non Transient Non/unknown Pathogen Sodium required for growth. Likely a gut non-coloniser because its optimum growth is with high salt and is an obligate aerobe. saline soil from Iran Lagier2016 Firmicutes Bacilli Bacillaceae + SAER Sessile Rod Endospore 41.3
Halobacillus massiliensis Positive Unlikely Transient Non/unknown Pathogen High salt required for optimum growth, so unlikely gut coloniser. human faeces (Senghor2017) that are salty Firmicutes Bacilli Bacillaceae +
Halobacillus salinus 1 Rare Possible Commensal Non/unknown Pathogen Requires at least 2% salt concentration for optimal growth. salt lake in Korea Lagier2016 Firmicutes Bacilli Bacillaceae + FANA Swimming Rod Endospore 45
Halobacillus trueperi 1 Unlikely Transient Non/unknown Pathogen Obligate aerobe; unlikely to be a gut coloniser. salt lakes from the USA Lagier2016 Firmicutes Bacilli Bacillaceae + SAER Swimming Rod Endospore 43
Halobacteroides halobius 1 Unlikely Transient Non/unknown Pathogen Very high salt concentration requirement makes this an unlikely gut coloniser. Dead Sea sediment New2022 Firmicutes Clostridia Halobacteroidaceae neg SANA Swimming Rod No spore 30.7
Haloferax alexandrinus 1 Unlikely Transient Non/unknown Pathogen Lyses in water, so unlikely to be a coloniser of the gut. Requires high levels of Mg2+. extreme salt conditions, Egypt Lagier2016 Euryarchaeota Halobacteria Haloferacaceae neg SAER Sessile Pleiomorph rod No spore 59.3
Haloferax massiliensis Rare Possible Commensal Non/unknown Pathogen A halophilic archea the faeces of an obese Amazonian woman Lagier2016 Euryarchaeota Halobacteria Haloferacaceae neg AER Sessile Coccus No spore
Haloimpatiens massiliensis Rare Possible Commensal Non/unknown Pathogen human faeces (healthy) Firmicutes Clostridia Clostridiaceae + SANA Rod 29.8
Halomonas massiliensis Rare Possible Commensal Non/unknown Pathogen the faeces of a healthy man from Senegal Lagier2016 Proteobacteria Gammaproteobacteria Halomonadaceae neg FANA Swimming Rod - curved No spore
Halomonas muralis 1 Non Transient Non/unknown Pathogen Strictly aerobic and inability to grow at 37C suggests this not a gut coloniser. biofilm covering an old mural Cassir2015 Proteobacteria Gammaproteobacteria Halomonadaceae neg SAER Swimming Rod No spore 62.4
Halomonas salina Deleya salina 1 Non Transient Non/unknown Pathogen Requires both Na+ and Mg2+ along with chloride or sulfate counterions. salt lakes, sea and hypersaline soils Lagier2016 Proteobacteria Gammaproteobacteria Halomonadaceae neg Sessile Short Rod No spore 60.7-64
Halomonas utahensis Pseudomonas halophila 1 Unlikely Transient Non/unknown Pathogen Borderline cold mesophile, with optimum growth temp of 28C. Unlikely gut coloniser. salt lakes from the USA Lagier2016 Proteobacteria Gammaproteobacteria Halomonadaceae neg SAER Swimming Rod No spore 57 0.4(+)
Halopseudomonas bauzanensis Pseudomonas bauzanensis Unlikely Transient Non/unknown Pathogen Unlikely gut coloniser because this organism doesn't grow at 37C. soil Lagier2016 Proteobacteria Gammaproteobacteria Pseudomonadaceae neg AER Swimming Rod No spore 61.8
Halopseudomonas pelagia Pseudomonas pelagia Unlikely Transient Non/unknown Pathogen Low optimum temperatures (25C) and strictly aerobic requirements makes this a very unlikely gut coloniser. green alga, Antarctic New2022 Proteobacteria Gammaproteobacteria Pseudomonadaceae neg SAER Swimming Rod No spore 59.1
Haploplasma axanthum Acholeplasma axanthum 2 Animal pathogen Unlikely Transient Non/unknown Pathogen murine leukemia tissue culture Byrd2020, New2022 Tenericutes Mollicutes Acholeplasmataceae neg FANA Coccobacillus
Harryflintia acetispora Rare Possible Commensal Non/unknown Pathogen chicken caeca Zou2019 Firmicutes Clostridia Oscillospiraceae neg SANA Sessile Rod - curved Endospore 62.2
Hathewaya histolytica Clostridium histolyticum 2 Rare Known Commensal Opportunistic Pathogen human intestine (Rainey2011bBergey), estuary sediment, clinical sources (wounds, gas gangrene) and soil Lagier2016, New2022 Firmicutes Clostridia Clostridiaceae + SANA Swimming Rod Endospore
Hathewaya limosa Clostridium limosum 2 Rare Known Commensal Opportunistic Pathogen human faeces, clinical sources, and animal disease Finegold1977, RajilicStojanovic2014 Firmicutes Clostridia Clostridiaceae + SANA Swimming Rod Endospore 20(neg)
Hathewaya massiliensis Clostridium culturomicum Rare Possible Commensal Non/unknown Pathogen human faeces (Tall2020a) Firmicutes Clostridia Clostridiaceae + SANA Swimming Rod Endospore 29.4
Helcobacillus massiliensis Rare Possible Commensal Opportunistic Pathogen cutaneous discharge Lagier2016 Actinobacteria Actinomycetia Dermabacteraceae + AER Sessile Short Rod No spore 68.6
Helcococcus sueciensis 1 Opportunistic in immunocompromised patients Rare Possible Commensal Opportunistic Infection a wound De2020 Firmicutes Tissierellia Peptoniphilaceae + FANA Sessile Coccus No spore 29.5
Helicobacter bilis 2 Animal pathogen Unlikely Transient Opportunistic Pathogen human faeces and mice Tyakht2013, Lagier2016, Forster2019 Proteobacteria Epsilonproteobacteria Helicobacteraceae neg Micr Swimming Rod No spore 20(+)
Helicobacter canadensis Negative 2 Human and animal pathogen Unlikely Transient Opportunistic Pathogen human faeces (diarrhoea) Tyakht2013, RajilicStojanovic2014, Lagier2016, Forster2019, New2022 Proteobacteria Epsilonproteobacteria Helicobacteraceae neg Micr Swimming Helical No spore
Helicobacter canis 2 Human and animal pathogen Unlikely Transient Opportunistic Pathogen human faeces (diarrhoea), blood, and dogs Lagier2016, Forster2019 Proteobacteria Epsilonproteobacteria Helicobacteraceae neg Micr Swimming Helical No spore 48.2-48.8 1.5(+)
Helicobacter cinaedi Campylobacter cinaedi 2 Human and animal pathogen Rare Known Commensal Known Pathogen human faeces, clinical sources (blood - CCUG) and animals Tyakht2013, RajilicStojanovic2014, Lagier2016, Forster2019, Byrd2020, Vachida2019 Proteobacteria Epsilonproteobacteria Helicobacteraceae neg Micr Swimming Helical No spore 37-38
Helicobacter felis 2 Human and animal pathogen Non Possible Commensal Known Pathogen the gastic mucosa of a cat Lagier2016 Proteobacteria Epsilonproteobacteria Helicobacteraceae neg Micr Swimming Helical No spore 42.5
Helicobacter fennelliae Campylobacter fennelliae Negative 2 Rare Possible Commensal Rare Opportunist human faeces (CCUG) and clinical sources Lagier2016 Proteobacteria Epsilonproteobacteria Helicobacteraceae neg Micr Swimming Helical No spore 37-38
Helicobacter heilmannii Gastrospirillum hominis Non Possible Commensal Possible Pathogen the gastic mucosa of a cat Lagier2016, Byrd2020 Proteobacteria Epsilonproteobacteria Helicobacteraceae neg Micr Swimming Helical No spore 1(neg)
Helicobacter macacae Unlikely Transient Non/unknown Pathogen human faeces and Rhesus monkeys Lagier2016, Forster2019 Proteobacteria Epsilonproteobacteria Helicobacteraceae neg Micr Swimming Rod - curved No spore
Helicobacter pametensis 1 Rare Possible Commensal Possible Pathogen bird faeces Forster2019 Proteobacteria Epsilonproteobacteria Helicobacteraceae neg Micr Swimming Rod - curved No spore 38
Helicobacter pullorum 2 Human and animal pathogen Minor Possible Commensal Opportunistic Pathogen human faeces (diarrhoea), and animals Tyakht2013, RajilicStojanovic2014, Lagier2016, Forster2019, Byrd2020, Hu2019, Zeller2014, Vachida2019 Proteobacteria Epsilonproteobacteria Helicobacteraceae neg Micr Swimming Helical No spore 34-35 1(+)
Helicobacter pylori Negative 2 Non Transient Known Pathogen human faeces, clinical sources (ulcer) and stomach Bik2006, Tyakht2013, RajilicStojanovic2014, Lagier2016, Forster2019, De2020, Zeller2014, Vachida2019 Proteobacteria Epsilonproteobacteria Helicobacteraceae neg Micr Swimming Helical No spore 36–39
Helicobacter rodentium 2 Animal pathogen Rare Possible Commensal Opportunistic Pathogen mouse gastrointestinal tract Forster2019 Proteobacteria Epsilonproteobacteria Helicobacteraceae neg Micr Swimming Rod - curved No spore
Helicobacter winghamensis Rare Possible Commensal Non/unknown Pathogen human faeces Tyakht2013, RajilicStojanovic2014, Lagier2016, Forster2019 Proteobacteria Epsilonproteobacteria Helicobacteraceae neg Micr Swimming Helical No spore 1(+)
Heliomicrobium modesticaldum Heliobacterium modesticaldum 1 Unlikely Transient Non/unknown Pathogen Grows phototrophically by photoassimilating pyruvate, lactate and acetate. High optimum growth temperature so unlikely to be a gut coloniser. neutral or alkaline hot springs, Iceland New2022, Zeller2014 Firmicutes Clostridia Heliobacteriaceae neg SANA vr Rod - curved Endospore 54.6-55
Herbaspirillum autotrophicum Aquaspirillum autotrophicum 1 Unlikely Transient Non/unknown Pathogen Facultative autotroph. Can use nitrate as a source of N. Doesn't grow at 37C and under anaerobic conditions, so is unlikely to be a gut coloniser. eutrophic lake water, Switzerland Frank2007 Proteobacteria Betaproteobacteria Oxalobacteraceae neg AER Swimming Helical No spore 60-62 1(+)
Herbaspirillum huttiense Pseudomonas huttiensis 1 Rare Possible Commensal Non/unknown Pathogen human faeces and distilled water Yang2020 Proteobacteria Betaproteobacteria Oxalobacteraceae neg AER Swimming Rod No spore 62.5
Herbinix hemicellulosilytica Unlikely Transient Non/unknown Pathogen A high minimum growth temperature (45C) suggests this is an unlikely gut coloniser. a thermophilic biogas reactor Byrd2020 Firmicutes Clostridia Lachnospiraceae + SANA Sessile Pleiomorph rod No spore 36.6
Herbinix luporum Unlikely Transient Non/unknown Pathogen High minimum growth temperature (40C) so unlikely to be a gut coloniser. a thermophilic biogas plant, Germany New2022 Firmicutes Clostridia Lachnospiraceae + SANA Sessile Rod No spore 35.1
Herminiimonas contaminans Unlikely Possible Commensal Non/unknown Pathogen Can't grow at 37C, so unlikely to be a gut coloniser. human faeces and contaminated biopharmaceuticals Yang2020 Proteobacteria Betaproteobacteria Oxalobacteraceae neg FANA Swimming Rod No spore 55.4
Hespellia porcina 1 Rare Possible Commensal Non/unknown Pathogen human faeces, and pig faeces PerisBondia2011, RajilicStojanovic2014 Firmicutes Clostridia Lachnospiraceae + SANA Sessile Rod No spore 43.8
Hespellia stercorisuis 1 Rare Possible Commensal Non/unknown Pathogen human faeces, and pig faeces PerisBondia2011, RajilicStojanovic2014, Byrd2020 Firmicutes Clostridia Lachnospiraceae + SANA Sessile Rod No spore 43.7
Heyndrickxia oleronia Bacillus oleronius 1 Unlikely Transient Non/unknown Pathogen Obligate aerobe; unlikely to be a gut coloniser. the hindgut of termites, diary products and dairy equipment Lagier2016 Firmicutes Bacilli Bacillaceae neg SAER Sessile Short Rod Endospore 35
Heyndrickxia sporothermodurans Bacillus sporothermodurans 1 Unlikely Transient Non/unknown Pathogen Obligate aerobe; unlikely to be a gut coloniser. milk and has been detected in human faeces (Bilen2018e) Firmicutes Bacilli Bacillaceae + SAER Swimming Rod Endospore 36
Histophilus somni 2 Opportunistic in immunocompromised patients Rare Possible Commensal Possible Pathogen cattle and sheep infections Byrd2020, New2022, Zeller2014 Proteobacteria Gammaproteobacteria Pasteurellaceae neg FANA Sessile Rod No spore 37.5
Holdemanella biformis Eubacterium biforme 1 Moderate Known Commensal Non/unknown Pathogen human faeces (CCUG) Woodmansey2004, Salonen2014, Zou2019, Forster2019, Byrd2020, Yang2020, Dubinkina2017, Hu2019, Jeong2021, Zeller2014, Wang2018, Vachida2019, Wang2020a, Minerbi2019, PerezBrocal2015 Firmicutes Erysipelotrichia Erysipelotrichaceae + SANA Sessile Coccus No spore 32-34
Holdemania filiformis Positive 1 Moderate Known Commensal Non/unknown Pathogen human faeces Walker2011, Tyakht2013, RajilicStojanovic2014, Lagier2016, Rothschild2018, Zou2019, Forster2019, Byrd2020, Yang2020, Chen2020, Dubinkina2017, Hu2019, Zeller2014, Vachida2019, Wang2020a, Urban2020, Qin2012, Minerbi2019, LeChatelier2013 Firmicutes Erysipelotrichia Erysipelotrichaceae + SANA Sessile Rod No spore 38
Holdemania massiliensis Minor Known Commensal Non/unknown Pathogen human faeces (anorexia nervosa patient) Pfleiderer2013, RajilicStojanovic2014, Lagier2016, Forster2019, Byrd2020, Jeong2021, Vachida2019 Firmicutes Erysipelotrichia Erysipelotrichaceae + SANA Sessile Rod No spore 47.1
Holophaga foetida 1 Non Transient Non/unknown Pathogen Transforms methoxyaryl groups to methylsulfide. black anoxic freshwater mud De2020 Acidobacteria Holophagae Holophagaceae neg SANA Sessile Rod No spore 62.5
Howardella ureilytica 1 Rare Possible Commensal Non/unknown Pathogen human faeces, and Sheep rumen RajilicStojanovic2014, De2020, Yang2020 Firmicutes Clostridia Lachnospiraceae + SANA Sessile Coccus No spore 34
Hugonella massiliensis Rare Possible Commensal Non/unknown Pathogen human faeces (obese) Actinobacteria Coriobacteriia Eggerthellaceae + SANA Sessile Coccus No spore 63.5
Humisphaera borealis Unlikely Transient Non/unknown Pathogen Low optimum temperatures (20-25C) makes this an unlikely gut coloniser. a boreal eutrophic lake, Russia New2022 Planctomycetes Phycisphaerae Tepidisphaeraceae neg Micr Swimming Coccus No spore 63.1
Hungatella effluvii Minor Possible Commensal Non/unknown Pathogen In 65% of Europeans (unseenbio.com). Minor coloniser. human faeces (Alkhalil2017) and anaerobic digester Zou2019, Byrd2020, Yang2020 Firmicutes Clostridia Clostridiaceae + SANA Swimming Rod Endospore 51.4
Hungatella hathewayi Clostridium hathewayi 1 Widespread Known Commensal Rare Opportunist human faeces, blood and atherosclerotic plaques McLaughlin2010, Walker2011, Pfleiderer2013, Tyakht2013, Nielsen2014, RajilicStojanovic2014, Browne2016, Lagier2016, Rothschild2018, Zou2019, Forster2019, Byrd2020, Yang2020, New2022, Chen2020, Dubinkina2017, Hu2019, Jie2017, Vachida2019, Qin2012, Minerbi2019, LeChatelier2013, PerezBrocal2015 Firmicutes Clostridia Clostridiaceae + SANA Swimming Rod Endospore 50.9
Hungatella saccharolyticum Rare Isolation and characterisation not yet published. Byrd2020 Firmicutes Clostridia Clostridiaceae
Hungatella xylanolytica Bacteroides xylanolyticus 1 Rare Possible Commensal Rare Opportunist fermenting cattle manure, a clinical specimen (blood - CCUG) and human faeces (Bilen2018e) Lagier2016 Firmicutes Clostridia Clostridiaceae neg SANA Swimming Rod No spore 35
Hydrogenibacillus schlegelii Bacillus schlegelii 1 Unlikely Transient Non/unknown Pathogen Produces spores, but is an obligate aerobe and doesn't grow at 37C. Unlikely to be a gut coloniser. human faeces, lake, and soils RajilicStojanovic2014, Lagier2016 Firmicutes Bacilli Bacillaceae vr SAER Swimming Rod Endospore 62.3-65.4
Hydrogenoanaerobacterium saccharovorans Rare Possible Commensal Non/unknown Pathogen human faeces, and an anaerobic digester PerisBondia2011, RajilicStojanovic2014, Byrd2020 Firmicutes Clostridia Oscillospiraceae neg SANA Sessile Rod No spore 41.9-42.8
Hydrogenophaga pseudoflava Pseudomonas pseudoflava 1 Unlikely Transient Non/unknown Pathogen Autotrophic, using H2/CO2/O2 only. Also Heterotrophic using >42 different organic substrates. Obligate aerobe; unlikely to be a gut coloniser. soil, mud and water Yang2020 Proteobacteria Betaproteobacteria Comamonadaceae neg SAER Swimming Oval-shaped No spore 66.5-68.0
Hydrogenovibrio crunogenus Thiomicrospira crunogena 1 Unlikely Transient Non/unknown Pathogen Obligate aerobe and low optimum temperature suggest it is not a gut coloniser. a deep-sea hydrothermal vent Proteobacteria Gammaproteobacteria Piscirickettsiaceae neg SAER Swimming Vibrio No spore 41.8-42.6
Hymenobacter rigui 1 Rare Possible Commensal Non/unknown Pathogen human faeces, and freshwater RajilicStojanovic2014 Bacteroidetes Cytophagia Cytophagaceae neg AER Sessile Rod No spore 65
Hymenobacter russus Unlikely Transient Non/unknown Pathogen Radiation resistant. A low optimum growth temperature (25C) suggests this organism is unlikely to be a gut coloniser. soil, Korea New2022 Bacteroidetes Cytophagia Cytophagaceae neg AER Sessile Rod No spore
Hyphomicrobium facile 1 Rare Possible Commensal Non/unknown Pathogen human faeces and soil Yang2020 Proteobacteria Alphaproteobacteria Hyphomicrobiaceae neg AER Swimming Oval-shaped No spore 60
Ihubacter massiliensis Rare Possible Commensal Non/unknown Pathogen the faeces of a healthy volunteer Lagier2016, Jeong2021 Firmicutes Clostridia Eubacteriales Family XIII. Incertae Sedis neg SANA Sessile Rod No spore
Ihuprevotella massiliensis Rare Possible Commensal Non/unknown Pathogen human faeces Bacteroidetes Bacteroidia Prevotellaceae neg ANA Sessile Pleiomorph rod No spore
Ileibacterium valens Rare Possible Commensal Non/unknown Pathogen murine intestinal contents Byrd2020 Firmicutes Erysipelotrichia Erysipelotrichaceae + SANA Sessile Coccus No spore 41.1
Inediibacterium massiliense Rare Possible Commensal Non/unknown Pathogen human faeces (Alou2017a) Lagier2016 Firmicutes Clostridia Clostridiaceae + SANA Swimming Rod Endospore 30.5
Intestinibacillus massiliensis Rare Possible Commensal Non/unknown Pathogen human left colon (Ricaboni2016d) Byrd2020 Firmicutes Clostridia Eubacteriaceae neg SANA Swimming Rod No spore
Intestinibacter bartlettii Clostridium bartlettii Positive 1 Widespread Known Commensal Non/unknown Pathogen Higher than normal levels have been associated with neurodevelopmental disorders in children (see Bojovic2020). human faeces McLaughlin2010, Walker2011, Tyakht2013, Nielsen2014, RajilicStojanovic2014, Browne2016, Chung2016, Lagier2016, Rothschild2018, Forster2019, Byrd2020, Yang2020, Chen2020, Dubinkina2017, Hu2019, Jeong2021, Jie2017, Zeller2014, Wang2018, Vachida2019, Wang2020a, Qin2012, Minerbi2019, Karlsson2013 Firmicutes Clostridia Clostridiaceae + SANA Sessile Rod Endospore 29.8 20(+)
Intestinibaculum porci Unlikely Transient Non/unknown Pathogen pig small intestines New2022 Firmicutes Erysipelotrichia Erysipelotrichaceae + SANA Sessile Rod No spore 39.5
Intestinimonas butyriciproducens Clostridium anorexicus Moderate Known Commensal Non/unknown Pathogen In 94% of Europeans (unseenbio.com). human faeces , and mouse caeca Pfleiderer2013, RajilicStojanovic2014, Lagier2016, Zou2019, Forster2019, King2019, Byrd2020, New2022, Jeong2021, Wang2020a, Minerbi2019 Firmicutes Clostridia unclassified Clostridiales + SANA Sessile Rod Endospore 59.1
Intestinimonas gabonensis Rare Possible Commensal Non/unknown Pathogen human faeces (Bilen2018e) Lagier2016 Firmicutes Clostridia Eubacteriales incertae sedis neg SANA Sessile Rod Endospore
Intestinimonas massiliensis Moderate Possible Commensal Non/unknown Pathogen In 94% of Europeans (unseenbio.com). human faeces (Afouda2018) Lagier2016, Byrd2020, Minerbi2019 Firmicutes Clostridia Eubacteriales incertae sedi neg SANA Sessile Rod No spore 60.7
Intestinimonas timonensis Rare Possible Commensal Non/unknown Pathogen human faeces (Durand2017b) Lagier2016, Jeong2021 Firmicutes Clostridia Eubacteriales incertae sedis neg SANA Swimming Rod No spore
Isoptericola variabilis Cellulosimicrobium variabile 1 Rare Possible Commensal Non/unknown Pathogen Cellulolytic and xylanolytic termite gut Lagier2016, Zeller2014 Actinobacteria Actinomycetia Promicromonosporaceae + FANA Sessile Pleiomorph rod No spore 70-72
Janibacter anophelis 1 Rare Possible Commensal Non/unknown Pathogen human faeces and gut of Anophiles mosquito Yang2020 Actinobacteria Actinomycetia Intrasporangiaceae + AER Sessile Coccus No spore
Janibacter hoylei Non Transient Non/unknown Pathogen Resistant to UV light high altitude air samples Lagier2016 Actinobacteria Actinomycetia Intrasporangiaceae + AER Sessile Coccus No spore 72.8
Janibacter limosus 1 Unlikely Transient Opportunistic Pathogen Borderline cold mesophile, with optimum growth temp of 28C. Unlikely gut coloniser. human faeces (Hoyles2012), clinical sources (cerebrospinal fluid, blood - CCUG) and wastewater Hoyles2012, RajilicStojanovic2014, Lagier2016 Actinobacteria Actinomycetia Intrasporangiaceae + AER Sessile Coccus No spore 70
Janibacter terrae 1 Rare Possible Commensal Non/unknown Pathogen human faeces, blood and wastewater McLaughlin2010, RajilicStojanovic2014 Actinobacteria Actinomycetia Intrasporangiaceae + AER Sessile Coccus No spore 69
Jeotgalibaca arthritidis Unlikely Transient Non/unknown Pathogen a pig joint fluid New2022 Firmicutes Bacilli Carnobacteriaceae + FANA Sessile Coccus No spore
Jeotgalibaca porci Unlikely Transient Non/unknown Pathogen a pig joint fluid New2022 Firmicutes Bacilli Carnobacteriaceae + FANA Sessile Coccus No spore
Jeotgalicoccus halotolerans 1 Rare Possible Commensal Non/unknown Pathogen fermented fish (jeotgal), Korea Yang2020 Firmicutes Bacilli Staphylococcaceae + FANA Sessile Coccus No spore 42
Johnsonella ignava 2 Rare Possible Commensal Opportunistic Infection gingival crevices of humans with gingivitis and periodontitis Byrd2020, De2020 Firmicutes Clostridia Lachnospiraceae neg SANA Sessile Rod No spore 32 20(neg)
Jonquetella anthropi 2 Rare Possible Commensal Opportunistic Pathogen Carbohydrates are not fermented. clinical sources (wound, pelvis, cyst) Byrd2020, New2022, Zeller2014, Vachida2019 Synergistetes Synergistia Synergistaceae neg SANA Sessile Rod No spore 59.4
Kalamiella piersonii Unlikely Transient Non/unknown Pathogen human faeces (CCUG), and metal surfaces Proteobacteria Gammaproteobacteria Erwiniaceae neg AER Swimming No spore 57.1
Kallipyga gabonensis Rare Possible Commensal Non/unknown Pathogen the faces of a man from Gabon Lagier2016 Firmicutes Clostridia Family XI Incertae Sedis + SANA Sessile Coccus No spore 50
Kallipyga massiliensis Rare Known Commensal Non/unknown Pathogen human faeces RajilicStojanovic2014, Lagier2016, Byrd2020 Firmicutes Clostridia Family XI Incertae Sedis + SANA Sessile Coccus No spore 51.4
Kandleria vitulina Lactobacillus vitulinus 1 Rare Possible Commensal Non/unknown Pathogen human faeces, and bovine rumen RajilicStojanovic2014, Byrd2020 Firmicutes Erysipelotrichia Erysipelotrichaceae + FANA Sessile Rod No spore 35.7
Kerstersia gyiorum 2 Rare Possible Commensal Opportunistic Pathogen clinical sources (sputum, wound - CCUG) and human faeces (CCUG) RajilicStojanovic2014, Lagier2016 Proteobacteria Betaproteobacteria Alcaligenaceae neg vr Coccus No spore 62.7-62.9
Khelaifiella massiliensis Rare Possible Commensal Non/unknown Pathogen human faeces (Alou2017) Byrd2020 Firmicutes Clostridia Clostridiaceae + SANA Rod
Kineothrix alysoides Rare Possible Commensal Non/unknown Pathogen switchgrass microcosm seeded with forest soil Byrd2020 Firmicutes Clostridia Lachnospiraceae neg SANA Swimming Rod Endospore 42.7
Kingella denitrificans 2 Unlikely Transient Opportunistic Pathogen respiratory tract Lagier2016, Byrd2020, Zeller2014 Proteobacteria Betaproteobacteria Neisseriaceae neg FANA Sessile Short Rod No spore 54.1-54.8 10(d)
Kingella kingae Moraxella kingii 2 Rare Possible Commensal Opportunistic Infection nasopharynx and clinical sources (blood, joint, bone legion) Lagier2016 Proteobacteria Betaproteobacteria Neisseriaceae neg AER Sessile Coccobacillus No spore 44.5
Kingella oralis 2 Unlikely Transient Opportunistic Pathogen dental disease and human faeces RajilicStojanovic2014, Vachida2019 Proteobacteria Betaproteobacteria Neisseriaceae neg FANA Sessile Rod No spore 56-58
Kiritimatiella glycovorans Unlikely Transient Non/unknown Pathogen Strictly fermentative and moderately halophilic. Borderline cold mesophile, with optimum growth temp of 28C. Unlikely gut coloniser. the suboxic zone of a hypersaline microbial mat, Republic of Kiribati New2022 Kiritimatiellaeota Kiritimatiellae Kiritimatiellaceae neg SANA Sessile Coccus No spore 63.3
Klebsiella aerogenes Enterobacter aerogenes Negative 1 Moderate Known Commensal Opportunistic Pathogen human faeces (Salonen2014, Alkhalil2017 - high loads in several ulcerative colitis patients) and clinical sources (infections, blood, urine) Finegold1977, Favier2002, RajilicStojanovic2014, Salonen2014, Cassir2015, Lagier2016, Almeida2019, Forster2019, King2019, Byrd2020, De2020, Yang2020, New2022, Hu2019, Jie2017, Zeller2014, Vachida2019, Wang2020a Proteobacteria Gammaproteobacteria Enterobacteriaceae neg Micr Swimming Rod No spore 54.8
Klebsiella grimontii Minor Possible Commensal Opportunistic Pathogen In 11% of Europeans (unseenbio.com). Minor coloniser. bacteraemia, wounds, faeces, haemorrhagic colitis Byrd2020, New2022 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Sessile Rod No spore 55.4
Klebsiella michiganensis Minor Possible Commensal Opportunistic Pathogen In 12% of Europeans (unseenbio.com). Minor coloniser. human faeces, clinical sources (blood, urine - CCUG) and tooth brush holder King2019, Byrd2020, New2022, Wang2020a Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Sessile Rod No spore 54.6
Klebsiella oxytoca Mixed 2 Human and animal pathogen Moderate Possible Commensal Opportunistic Pathogen human faeces (2-4% in several ulcerative colitis patients) and clinical sources (blood, urine - CCUG) Aujoulat2014, RajilicStojanovic2014, Cassir2015, Lagier2016, Almeida2019, Forster2019, Byrd2020, Yang2020, New2022, Chen2020, Hu2019, Jie2017, Zeller2014, Vachida2019, Wang2020a Proteobacteria Gammaproteobacteria Enterobacteriaceae neg Micr Sessile Rod No spore 55-58
Klebsiella pneumoniae Negative 2 Human and animal pathogen Widespread Known Commensal Opportunistic Pathogen clinical sources (blood, urine, wound, nasopharynx - CCUG) and human faeces (including ulcerative colitis patients). Implicated in CVD progression Finegold1977, Benno1984, Taylor1985, Benno1986, Benno1989, Mangin2004, Woodmansey2004, McLaughlin2010, Pandey2012, Pfleiderer2013, Tyakht2013, Aujoulat2014, RajilicStojanovic2014, Salonen2014, Lagier2016, Rothschild2018, Zou2019, Almeida2019, Forster2019, King2019, Byrd2020, De2020, Yang2020, New2022, Dubinkina2017, Hu2019, Jie2017, Zeller2014, Vachida2019, Wang2020a, Minerbi2019 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg Micr Sessile Rod No spore 56-58
Klebsiella pneumoniae subsp. ozaenae Klebsiella ozaenae 2 Rare Possible Commensal Possible Pathogen clinical sources (blood, nasopharynx- CCUG) and has been detected in human faeces Finegold1974, Finegold1977, Zou2019 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Sessile Rod No spore
Klebsiella pneumoniae subsp. rhinoscleromatis 2 Rare Possible Commensal Known Pathogen nasopharynx and clinical sources (rhinoscleromatis) Zou2019 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Sessile Rod No spore
Klebsiella quasipneumoniae subsp. quasipneumoniae Minor Possible Commensal Opportunistic Pathogen In 10% of Europeans (unseenbio.com). Minor coloniser. clinical sources (blood) Zou2019, New2022 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Sessile Rod No spore 55.9
Klebsiella quasivariicola Minor Opportunistic Pathogen Characterisation not yet published. In 63% of Europeans (unseenbio.com). Byrd2020 Proteobacteria Gammaproteobacteria Enterobacteriaceae No spore
Klebsiella variicola 2 Human and animal pathogen Minor Possible Commensal Known Pathogen human faeces (infant - CCUG), clinical (wound, blood, urine - CCUG) and plant sources Nielsen2014, Lagier2016, King2019, Byrd2020, New2022, Jie2017, Vachida2019, Wang2020a, Minerbi2019 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Sessile Rod No spore
Kluyvera ascorbata 2 Minor Known Commensal Opportunistic Pathogen Kluyvera ascorbata in 8% of Europeans, Kluyvera ascorbata_B also with 8% (unseenbio.com). Minor coloniser. human faeces (Alkhalil2017), and clinical sources (urine - CCUG) Woodmansey2004, McLaughlin2010, RajilicStojanovic2014, Lagier2016, Byrd2020, Yang2020 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Swimming Rod No spore 56.1
Kluyvera cryocrescens Negative 2 Rare Possible Commensal Possible Pathogen sewage, soil, clinical sources (blood - CCUG) and human faeces (high load in several ulcerative colitis patients - Alkhalil2017) McLaughlin2010, Lagier2016, Byrd2020 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Swimming Rod No spore 55.1
Kluyvera georgiana Kluyvera species group 3 1 Rare Possible Commensal Non/unknown Pathogen human faeces, sputum and throat cultures Lagier2016, Byrd2020, Yang2020 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Swimming Rod No spore
Kluyvera intermedia Enterobacter intermedium 2 Rare Possible Commensal Opportunistic Pathogen molluscs, water, soil, clinical sources (blood, wounds, bile) and human faeces (Alkhalil2017- ulcerative colitis patient) Byrd2020 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Swimming Rod No spore
Kocuria carniphila 1 Unlikely Transient Non/unknown Pathogen Obligate aerobe; unlikely to be a gut coloniser. meat Yang2020 Actinobacteria Actinomycetia Micrococcaceae + SAER Sessile Coccus No spore 71
Kocuria marina 1 Rare Possible Commensal Non/unknown Pathogen marine sediment and human faeces RajilicStojanovic2014, Lagier2016 Actinobacteria Actinomycetia Micrococcaceae + AER Sessile Coccus No spore
Kocuria palustris 1 Unlikely Transient Non/unknown Pathogen roots of cattail plant and human faeces McLaughlin2010, RajilicStojanovic2014, Cassir2015, Lagier2016, Yang2020, PerezBrocal2015 Actinobacteria Actinomycetia Micrococcaceae + AER Sessile Coccus No spore 69.6
Kocuria polaris 1 Unlikely Transient Non/unknown Pathogen Probably transient because optimum growth temperature is low and unlikely to be a gut coloniser. a cyanobacterial mat Lagier2016, Yang2020 Actinobacteria Actinomycetia Micrococcaceae + AER Sessile Coccus No spore 72.5
Kocuria rhizophila 1 Unlikely Possible Commensal Non/unknown Pathogen Found in human breast milk (Jeurink2013). roots of cattail plant and human faeces McLaughlin2010, Dubourg2013, RajilicStojanovic2014, Lagier2016, Zeller2014, PerezBrocal2015 Actinobacteria Actinomycetia Micrococcaceae + AER Sessile Coccus No spore 69.4
Kocuria rosea Micrococcus roseus 1 Unlikely Possible Commensal Non/unknown Pathogen human faeces Dubourg2013, RajilicStojanovic2014, Lagier2016 Actinobacteria Actinomycetia Micrococcaceae + AER Sessile Coccus No spore 66-75
Kocuria salsicia Unlikely Possible Commensal Non/unknown Pathogen human faeces and Korean fermented seafood Yang2020 Actinobacteria Actinomycetia Micrococcaceae + AER Sessile Coccus No spore 60.6
Kocuria varians Micrococcus varians 1 Rare Possible Commensal Non/unknown Pathogen skin, soil and water Lagier2016 Actinobacteria Actinomycetia Micrococcaceae + AER Sessile Coccus No spore 66-72
Kosakonia cowanii Enterobacter cowanii 2 Minor Possible Commensal Opportunistic Infection In 10% of Europeans (unseenbio.com). Minor coloniser. clinical sources and the environment Lagier2016, Byrd2020 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Swimming Rod No spore 53
Krasilnikoviella flava Promicromonospora flava Rare Possible Commensal Non/unknown Pathogen marine sediment and human faeces RajilicStojanovic2014, Lagier2016 Actinobacteria Actinomycetia Promicromonosporaceae + AER Sessile No spore 71.9
Kurthia gibsonii Positive 1 Opportunistic in immunocompromised patients Rare Known Commensal Opportunistic Infection animal faeces and human faeces RajilicStojanovic2014, Lagier2016 Firmicutes Bacilli Planococcaceae + AER Swimming Rod No spore 36-38
Kurthia massiliensis Positive Rare Known Commensal Non/unknown Pathogen human faeces RajilicStojanovic2014, Lagier2016, Forster2019, Byrd2020 Firmicutes Bacilli Planococcaceae + SAER Swimming Coccobacillus No spore 39.3
Kurthia senegalensis Positive Rare Known Commensal Non/unknown Pathogen human faeces RajilicStojanovic2014, Lagier2016 Firmicutes Bacilli Planococcaceae + SAER Swimming Coccobacillus No spore 38.2
Kurthia sp. Dielmo Kurthia timonensis Positive Rare Known Commensal Non/unknown Pathogen human faeces RajilicStojanovic2014, Lagier2016 Firmicutes Bacilli Planococcaceae + AER Rod No spore
Kurthia zopfii 1 Opportunistic in immunocompromised patients Rare Possible Commensal Opportunistic Infection animal faeces, human faeces (Bilen2018e), fresh water and meat Firmicutes Bacilli Planococcaceae + AER Swimming Rod No spore 36-38
Kushneria sinocarnis Unlikely Transient Non/unknown Pathogen Unlikely gut coloniser because its optimum growth is with high salt. cured meat from China Lagier2016 Firmicutes Bacilli Planococcaceae neg AER Sessile Oval-shaped No spore 59.1
Kytococcus schroeteri 1 Opportunistic in immunocompromised patients Rare Possible Commensal Opportunistic Pathogen clinical sources (blood, wound, abdominal fluid - CCUG) and human faeces Pfleiderer2013, RajilicStojanovic2014, Lagier2016 Actinobacteria Actinomycetia Dermacoccaceae + AER Sessile Coccus No spore
Kytococcus sedentarius Micrococcus sedentarius 1 Opportunistic in immunocompromised patients Rare Possible Commensal Opportunistic Infection human faeces Pfleiderer2013, RajilicStojanovic2014, Lagier2016, Zeller2014 Actinobacteria Actinomycetia Dermacoccaceae + AER Sessile Coccus No spore 68-69
Labilithrix luteola Non Transient Non/unknown Pathogen Low maximum growth temperature (30C) and strictly aerobic requirements makes this likely a gut non-coloniser. soil, Japan New2022 Proteobacteria Deltaproteobacteria Sorangiineae neg SAER Sessile Rod No spore 66.3
Lachnoanaerobaculum orale Rare Possible Commensal Non/unknown Pathogen the saliva of a healthy man Lagier2016 Firmicutes Clostridia Lachnospiraceae + SANA Sessile Rod Endospore 38 20(neg)
Lachnoanaerobaculum saburreum Eubacterium saburreum 1 Opportunistic in immunocompromised patients Rare Transient Opportunistic Infection dental disease and human faeces RajilicStojanovic2014, Byrd2020, Zeller2014, Vachida2019, Qin2012 Firmicutes Clostridia Lachnospiraceae + SANA Rod Endospore 37.0
Lachnoanaerobaculum umeaense Rare Possible Commensal Non/unknown Pathogen human faeces, and human gut RajilicStojanovic2014, Lagier2016, Byrd2020, New2022 Firmicutes Clostridia Lachnospiraceae + SANA Rod Endospore 35.0
Lachnobacterium bovis 1 Rare Known Commensal Non/unknown Pathogen human faeces and bovine faeces Zupancic2012, RajilicStojanovic2014, Salonen2014, Byrd2020 Firmicutes Clostridia Lachnospiraceae + SANA vr Rod No spore 33.9
Lachnoclostridium bouchesdurhonense Rare Possible Commensal Non/unknown Pathogen human faeces (Amadou2016) Lagier2016 Firmicutes Clostridia Lachnospiraceae neg Rod
Lachnoclostridium edouardi Minor Possible Commensal Non/unknown Pathogen In 59% of Europeans (unseenbio.com). Minor coloniser. human faeces (CCUG) Byrd2020, Minerbi2019 Firmicutes Clostridia Lachnospiraceae + SANA Swimming Rod No spore
Lachnoclostridium massiliosenegalense Rare Possible Commensal Non/unknown Pathogen human faeces (Alou2016b) Firmicutes Clostridia Lachnospiraceae + ANA Rod
Lachnoclostridium pacaense Clostridium pacaense Rare Possible Commensal Non/unknown Pathogen human faeces (Pham2017a) Minerbi2019 Firmicutes Clostridia Lachnospiraceae vr ANA Sessile Rod Endospore 50
Lachnoclostridium phocaeense Rare Possible Commensal Opportunistic Infection UTI, France Diamanti2020, New2022, Wang2020a Firmicutes Clostridia Lachnospiraceae + SANA Swimming Rod Endospore 50.6
Lachnoclostridium phytofermentans Clostridium phytofermentans 1 Minor Possible Commensal Non/unknown Pathogen In 14% of Europeans (unseenbio.com). Minor coloniser. human faeces and from forest soil King2019, Byrd2020, New2022, Zeller2014, Qin2012 Firmicutes Clostridia Lachnospiraceae neg SANA Swimming Rod Endospore 35.9
Lachnoclostridium touaregense Unknown Rare Possible Commensal Non/unknown Pathogen human faeces (healthy) Firmicutes Clostridia Lachnospiraceae + ANA Rod
Lachnospira eligens Eubacterium eligens Positive 1 Widespread Known Commensal Non/unknown Pathogen human faeces Moore1974, Holdeman1976, Finegold1977, Mangin2004, Woodmansey2004, Nam2008a, McLaughlin2010, Walker2011, Hoyles2012, Tyakht2013, Nielsen2014, RajilicStojanovic2014, Browne2016, Chung2016, Lagier2016, Rothschild2018, Zou2019, King2019, Byrd2020, De2020, Yang2020, New2022, Chen2020, Dubinkina2017, Hu2019, Jeong2021, Jie2017, Zeller2014, Wang2018, Vachida2019, Wang2020a, Qin2012, Minerbi2019, Moore1995, LeChatelier2013, Karlsson2013 Firmicutes Clostridia Lachnospiraceae + SANA Swimming Rod Endospore 36
Lachnospira multipara 1 Rare Possible Commensal Non/unknown Pathogen the reticulo-rumen of cattle Byrd2020 Firmicutes Clostridia Lachnospiraceae + ANA Swimming Rod - curved No spore
Lachnospira pectinoschiza 1 Minor Known Commensal Non/unknown Pathogen human faeces (Ludwig2009), and pig intestine McLaughlin2010, Walker2011, Zupancic2012, RajilicStojanovic2014, Salonen2014, Browne2016, Forster2019, Byrd2020, Minerbi2019 Firmicutes Clostridia Lachnospiraceae + SANA Swimming Rod Endospore 42
Lachnospira rogosae Moderate Possible Mutualist No record in the NCBI database for this organism. In 99% of Europeans (unseenbio.com). A moderate coloniser. Byrd2020 Firmicutes Clostridia Lachnospiraceae
Lacrimispora aerotolerans Clostridium aerotolerans 1 Rare Possible Commensal Non/unknown Pathogen the rumina of sheep Lagier2016 Firmicutes Clostridia Lachnospiraceae neg SANA Swimming Rod Endospore 40
Lacrimispora amygdalina Clostridium amygdalinum 1 Rare Possible Commensal Non/unknown Pathogen anaerobic digestive sludge. HuCA19 - a closely related bacterium (S16 94%) - was detected in human faeces Lagier2016 Firmicutes Clostridia Lachnospiraceae + ANA Swimming Rod Endospore 32
Lacrimispora celerecrescens Clostridium celerecrescens 1 Rare Possible Commensal Possible Pathogen Cellulolytic. cow manure and clinical sources (eye, osteitis - CCUG). NE90 - a related bacterium (S16 94%) - was detected in human faeces Zupancic2012, Lagier2016 Firmicutes Clostridia Lachnospiraceae + SANA Swimming Rod - curved Endospore 38
Lacrimispora indolis Clostridium indolis 2 Minor Known Commensal Opportunistic Pathogen human faeces and clinical sources Finegold1974, Finegold1977, Benno1986, Benno1989, Mangin2004, Woodmansey2004, Walker2011, RajilicStojanovic2014, Lagier2016 Firmicutes Clostridia Lachnospiraceae neg ANA Swimming Rod Endospore 44 20(neg)
Lacrimispora saccharolytica Clostridium saccharolyticum 1 Moderate Transient Non/unknown Pathogen In 99% of Europeans (unseenbio.com). anaerobic sewage sludge. 8844 - a closely related bacterium (S16 95%) - was detected in human faeces (probably transient) Lagier2016, King2019, Byrd2020, New2022, Dubinkina2017, Zeller2014, Wang2020a, Qin2012, LeChatelier2013 Firmicutes Clostridia Lachnospiraceae neg SANA Sessile Rod Endospore 28
Lacrimispora sphenoides Clostridium sphenoides 2 Minor Known Commensal Opportunistic Pathogen human faeces, mud, sludge and clinical sources (infections, wounds, gas gangrene) Finegold1974, Finegold1977, Benno1984, Taylor1985, Benno1989, Woodmansey2004, Walker2011, RajilicStojanovic2014, Salonen2014, Lagier2016, New2022 Firmicutes Clostridia Lachnospiraceae + SANA Swimming Rod Endospore 41-43.8
Lacticaseibacillus casei Lactobacillus casei Positive 1 Opportunistic in immunocompromised patients Rare Transient Rare Opportunist An unlikely permanent inhabitant of the colon. Found in human breast milk (Jeurink2013). human faeces, blood and dairy products Finegold1977, Benno1989, Heilig2002, DalBello2006, Tyakht2013, RajilicStojanovic2014, Lagier2016, Forster2019, Byrd2020, Dubinkina2017, Jie2017, Zeller2014, Vachida2019 Firmicutes Bacilli Lactobacillaceae + FANA Sessile Rod No spore 45–47
Lacticaseibacillus paracasei Lactobacillus paracasei Positive 1 Minor Known Commensal Rare Opportunist In 17% of Europeans (unseenbio.com). Produces GABA (Sahad2020). human faeces (Sanz2007), dairy products, sewage, silage, humans, and clinical sources Benno1984, Heilig2002, MacFarlane2004, Woodmansey2004, Pfleiderer2013, Tyakht2013, RajilicStojanovic2014, Lagier2016, Forster2019, King2019, Byrd2020, New2022, Chen2020, Hu2019, Wang2020a Firmicutes Bacilli Lactobacillaceae + FANA Sessile Rod No spore 45-47
Lacticaseibacillus paracasei subsp. tolerans Lactobacillus paracasei subsp. tolerans 1 Unlikely Transient Non/unknown Pathogen dairy products Woodmansey2004, Zou2019 Firmicutes Bacilli Lactobacillaceae + FANA Sessile Rod No spore 45-47
Lacticaseibacillus paragasseri Lactobacillus paragasseri Unlikely Transient Non/unknown Pathogen human faeces (Tanizawa2018) New2022 Firmicutes Bacilli Lactobacillaceae + FANA Sessile Rod No spore 34.9
Lacticaseibacillus rhamnosus Lactobacillus rhamnosus Positive 2 Moderate Transient Rare Opportunist Found in human breast milk (Jeurink2013). human faeces, dairy, sewage, and clinical sources (blood, cervix, abscess, other - CCUG) Heilig2002, Woodmansey2004, DalBello2006, Pfleiderer2013, Tyakht2013, RajilicStojanovic2014, Lagier2016, Almeida2019, Forster2019, King2019, Byrd2020, New2022, Dubinkina2017, Hu2019, Zeller2014, Vachida2019, Wang2020a, Urban2020 Firmicutes Bacilli Lactobacillaceae + FANA Sessile Rod No spore 45–47
Lacticaseibacillus saniviri Lactobacillus saniviri Unlikely Transient Non/unknown Pathogen human faeces RajilicStojanovic2014, Lagier2016 Firmicutes Bacilli Lactobacillaceae + FANA Sessile Rod No spore 48.1
Lacticaseibacillus sharpeae Lactobacillus sharpeae 1 Unlikely Transient Non/unknown Pathogen human faeces, and sewage Woodmansey2004, RajilicStojanovic2014, Lagier2016 Firmicutes Bacilli Lactobacillaceae + FANA Sessile Rod No spore 53
Lacticaseibacillus zeae Lactobacillus zeae 1 Unlikely Transient Non/unknown Pathogen corn steep liquor Lagier2016, Li2019b, PerezBrocal2015 Firmicutes Bacilli Lactobacillaceae + FANA Sessile Rod No spore 47.6-47.9
Lacticigenium naphtae Non Transient Non/unknown Pathogen Likely not a gut coloniser since it doesn't grow at body temperature crude oil-water De2020 Firmicutes Bacilli Carnobacteriaceae vr FANA Swimming Oval-shaped No spore 38
Lactiplantibacillus paraplantarum Lactobacillus paraplantarum 1 Rare Possible Commensal Non/unknown Pathogen human faeces (Hammes2011Bergey) Lagier2016, Byrd2020 Firmicutes Bacilli Lactobacillaceae + FANA Sessile Rod No spore 44–45
Lactiplantibacillus pentosus Lactobacillus pentosus 1 Rare Possible Commensal Non/unknown Pathogen human faeces, blood, corn silage, fermenting olives, and sewage DalBello2006, RajilicStojanovic2014, Lagier2016, Zou2019, Vachida2019 Firmicutes Bacilli Lactobacillaceae + FANA Sessile Rod No spore 46–47
Lactiplantibacillus plantarum Lactobacillus plantarum 1 Moderate Known Commensal Rare Opportunist Reduces quinate to dihydroshikimate. Able to reduce alpha-keto acids (pyruvate, a-ketobutyrate, a-ketovalerate, a-ketocaprylate) when fermenting mannitol with lactate dehydrogenase. Produces GABA (Sahad2020). Found in human breast milk (Jeurink2013).. human faeces and clinical sources (blood, gall, urine, trachea - CCUG) Finegold1974, Finegold1977, Benno1989, Woodmansey2004, Tyakht2013, RajilicStojanovic2014, Salonen2014, Lagier2016, Zou2019, Forster2019, Byrd2020, Yang2020, New2022, Dubinkina2017, Hu2019, Zeller2014, Vachida2019, Wang2020a, Karlsson2013 Firmicutes Bacilli Lactobacillaceae + FANA Sessile Rod No spore 45
Lactiplantibacillus xiangfangensis Lactobacillus xiangfangensis Rare Possible Commensal Non/unknown Pathogen human faeces and traditional Chinese fermented pickle Yang2020 Firmicutes Bacilli Lactobacillaceae + FANA Rod No spore 46.6
Lactobacillus acidophilus Positive 1 Opportunistic in immunocompromised patients Widespread Known Commensal Rare Opportunist human faeces and clinical sources (blood, urine - CCUG) Moore1974, Finegold1974, Finegold1977, Benno1984, Heilig2002, Woodmansey2004, Zupancic2012, deGoffau2013, Tyakht2013, RajilicStojanovic2014, Lagier2016, Rothschild2018, Almeida2019, Forster2019, King2019, Byrd2020, Yang2020, New2022, Chen2020, Dubinkina2017, Zeller2014, Vachida2019, Moore1995 Firmicutes Bacilli Lactobacillaceae + FANA Sessile Rod No spore 34–37
Lactobacillus amylolyticus 1 Unlikely Transient Non/unknown Pathogen High optimum growth temperature so unlikely to be a gut coloniser. malt-mash, malt and human faeces Tyakht2013, Lagier2016, Forster2019, Byrd2020, Dubinkina2017 Firmicutes Bacilli Lactobacillaceae + Micr Sessile Rod No spore 39
Lactobacillus amylovorus 1 Minor Transient Non/unknown Pathogen human faeces, and cattle waste fermentation Nielsen2014, RajilicStojanovic2014, Zou2019, Almeida2019, Byrd2020, Jie2017, Zeller2014, Vachida2019, Wang2020a Firmicutes Bacilli Lactobacillaceae + FANA Sessile Rod No spore 37.8
Lactobacillus crispatus Positive 1 Moderate Known Commensal Rare Opportunist Found in human breast milk (Jeurink2013). human faeces and clinical sources (UTI, pleurisy, abscess) Finegold1977, Heilig2002, DalBello2006, Tyakht2013, RajilicStojanovic2014, Cassir2015, Lagier2016, Almeida2019, Byrd2020, Yang2020, New2022, Dubinkina2017, Hu2019, Jie2017, Zeller2014, Vachida2019, Wang2020a Firmicutes Bacilli Lactobacillaceae + FANA Rod No spore 35–38
Lactobacillus delbrueckii subsp. bulgaricus Lactobacillus bulgaricus Positive 1 Rare Transient Non/unknown Pathogen yoghurt and cheese; human faeces (Sanz2007 - healthy and coeliac children) and clinical sources (bile, vagina - CCUG) Tyakht2013, Lagier2016, Dubinkina2017, Jie2017 Firmicutes Bacilli Lactobacillaceae + Micr Sessile Rod No spore 50
Lactobacillus delbrueckii subsp. delbrueckii Lactobacillus delbrueckii Positive 1 Minor Transient Rare Opportunist In 12% of Europeans (unseenbio.com). Minor coloniser. human faeces and clinical sources (blood, urine) Heilig2002, MacFarlane2004, Bik2006, DalBello2006, Zupancic2012, RajilicStojanovic2014, Lagier2016, Rothschild2018, Almeida2019, Forster2019, Byrd2020, Yang2020, New2022, Zeller2014, Vachida2019, PerezBrocal2015 Firmicutes Bacilli Lactobacillaceae + FANA Sessile Rod No spore 49-51
Lactobacillus delbrueckii subsp. lactis Lactobacillus lactis 1 Unlikely Transient Non/unknown Pathogen milk, cheese, compressed yeast and grain mash Finegold1977, Woodmansey2004, Tyakht2013, Lagier2016 Firmicutes Bacilli Lactobacillaceae + FANA Sessile Rod No spore 49-51
Lactobacillus equicursoris Rare Possible Commensal Non/unknown Pathogen the faeces of a thoroughbred racehorse Vachida2019 Firmicutes Bacilli Lactobacillaceae + SANA Sessile Rod - curved No spore 48.3
Lactobacillus gasseri 1 Opportunistic in immunocompromised patients Moderate Known Commensal Rare Opportunist Found in human breast milk (Jeurink2013). human faeces (CCUG, Sanz2007), vagina, oral cavity and clinical sources (wounds, blood, urine) Benno1986, Benno1989, Heilig2002, DalBello2006, RajilicStojanovic2014, Salonen2014, Lagier2016, Zou2019, Almeida2019, Forster2019, Byrd2020, Yang2020, New2022, Chen2020, Dubinkina2017, Hu2019, Jie2017, Zeller2014, Vachida2019, Wang2020a, Karlsson2013 Firmicutes Bacilli Lactobacillaceae + FANA Rod No spore 33–35
Lactobacillus gigeriorum Unlikely Transient Non/unknown Pathogen a chicken crop Byrd2020 Firmicutes Bacilli Lactobacillaceae + FANA Sessile Short Rod No spore 41.9
Lactobacillus hamsteri 1 Rare Transient Non/unknown Pathogen hamster faeces Zupancic2012 Firmicutes Bacilli Lactobacillaceae + SANA Sessile Rod No spore 34.1
Lactobacillus helveticus Positive 1 Rare Transient Non/unknown Pathogen A probiotic, but only present in the faeces of 3% of Europeans (unseenbio.com). Found in human breast milk (Jeurink2013). human faeces, and Isolated from sour milk, and cheese starter cultures Finegold1977, Woodmansey2004, Tyakht2013, RajilicStojanovic2014, Lagier2016, Forster2019, Byrd2020, New2022, Dubinkina2017, Hu2019, Zeller2014 Firmicutes Bacilli Lactobacillaceae + FANA Sessile Rod No spore 37-40 2(neg)
Lactobacillus hominis Unlikely Transient Non/unknown Pathogen human intestine Firmicutes Bacilli Lactobacillaceae + FANA Sessile Short Rod No spore 42.8
Lactobacillus iners 1 Opportunistic in immunocompromised patients Rare Transient Rare Opportunist Rare coloniser. clinical sources (urine, vagina, wound) and human faeces McLaughlin2010, RajilicStojanovic2014, Lagier2016, Forster2019, Byrd2020, Yang2020, New2022, Jeong2021, Zeller2014, Vachida2019, PerezBrocal2015 Firmicutes Bacilli Lactobacillaceae + FANA Sessile Rod No spore 34.4
Lactobacillus intestinalis 1 Unlikely Transient Non/unknown Pathogen rat and mice intestines. Detected in human faeces Lagier2016, Forster2019, Byrd2020 Firmicutes Bacilli Lactobacillaceae + FANA Sessile Rod No spore 32.5-35.4
Lactobacillus jensenii 1 Opportunistic in immunocompromised patients Unlikely Transient Rare Opportunist clinical sources (vagina, kidney, cervix, urine) and human faeces RajilicStojanovic2014, Lagier2016, Dubinkina2017, Zeller2014 Firmicutes Bacilli Lactobacillaceae + FANA Rod No spore 35–37
Lactobacillus johnsonii 1 Minor Known Commensal Rare Opportunist human faeces, clinical sources (blood) and other animal faeces Tyakht2013, RajilicStojanovic2014, Lagier2016, Almeida2019, Forster2019, Byrd2020, New2022, Dubinkina2017, Zeller2014, Vachida2019 Firmicutes Bacilli Lactobacillaceae + FANA Rod No spore 33–35
Lactobacillus kalixensis Positive 1 Minor Possible Commensal Non/unknown Pathogen In 24% of Europeans (unseenbio.com). Minor coloniser. human faeces and human stomach (gastric mucosa) RajilicStojanovic2014, Lagier2016, Byrd2020 Firmicutes Bacilli Lactobacillaceae + FANA Sessile Rod No spore 35.5
Lactobacillus kefiranofaciens 1 Rare Possible Commensal Non/unknown Pathogen kefir grains Zeller2014 Firmicutes Bacilli Lactobacillaceae + FANA Sessile Rod No spore 37.3-38.2
Lactobacillus leichmannii Positive 1 Rare Transient Non/unknown Pathogen human faeces Moore1974, Holdeman1976, Finegold1977, RajilicStojanovic2014, Lagier2016 Firmicutes Bacilli Lactobacillaceae + FANA Sessile Rod No spore
Lactobacillus pasteurii Unlikely Transient Non/unknown Pathogen unknown origin Firmicutes Bacilli Lactobacillaceae + FANA Sessile Rod No spore 45.4
Lactobacillus psittaci 1 Opportunistic in immunocompromised patients Unlikely Transient Non/unknown Pathogen lungs of a dead hyacinth macaw Firmicutes Bacilli Lactobacillaceae + FANA Coccobacillus No spore
Lactobacillus rogosae 1 Rare Transient Non/unknown Pathogen human faeces Moore1974, RajilicStojanovic2014, Lagier2016, Yang2020, Minerbi2019 Firmicutes Bacilli Lactobacillaceae + SANA Swimming Rod No spore 59
Lactobacillus timonensis Unlikely Transient Non/unknown Pathogen human faeces (CCUG) Byrd2020 Firmicutes Bacilli Lactobacillaceae + Micr Sessile Rod No spore
Lactobacillus ultunensis 1 Minor Transient Non/unknown Pathogen human faeces and human stomach (gastric mucosa) Tyakht2013, RajilicStojanovic2014, Lagier2016, Forster2019, Byrd2020, Dubinkina2017, Zeller2014 Firmicutes Bacilli Lactobacillaceae + FANA Sessile Rod No spore 35.7
Lactococcus cremoris Streptococcus cremoris 1 Rare Possible Commensal Opportunistic Infection cheese and dairy products, clinical sources (blood -CCUG) and human faeces Finegold1974, Finegold1977, Lagier2016, New2022, Dubinkina2017, Jie2017 Firmicutes Bacilli Streptococcaceae + FANA Sessile Coccus No spore 35.0-36.1
Lactococcus garvieae Streptococcus garvieae Negative 2 Human and animal pathogen Minor Possible Commensal Opportunistic Pathogen clinical sources (blood, perfusion fluid - CCUG), waste whey, wastewater, farm animals and human faeces RajilicStojanovic2014, Lagier2016, Zou2019, Almeida2019, Byrd2020, Yang2020, New2022, Hu2019, Zeller2014, Vachida2019, Wang2020a, Li2019b Firmicutes Bacilli Streptococcaceae + FANA Sessile Oval-shaped No spore 38.3-38.7
Lactococcus lactis subsp. lactis Lactococcus lactis 1 Opportunistic in immunocompromised patients Widespread Known Commensal Opportunistic Infection Found in human breast milk (Jeurink2013). clinical sources (blood, wound - CCUG), sour milk, cheese starter cultures and human faeces Finegold1974, Finegold1977, Taylor1985, Mangin2004, Woodmansey2004, Zupancic2012, Pfleiderer2013, RajilicStojanovic2014, Lagier2016, Rothschild2018, Zou2019, Almeida2019, King2019, Byrd2020, Yang2020, New2022, Chen2020, Hu2019, Jie2017, Zeller2014, Vachida2019, Urban2020, Karlsson2013 Firmicutes Bacilli Streptococcaceae + FANA Sessile Oval-shaped No spore 33.4-36.3 40(+)
Lactococcus petauri Rare Possible Commensal Non/unknown Pathogen an abscess of a sugar glider Byrd2020 Firmicutes Bacilli Streptococcaceae + FANA Sessile Coccus No spore 37.7
Lactococcus plantarum Streptococcus plantarum Positive 1 Rare Known Commensal Non/unknown Pathogen In 5% of Europeans (unseenbio.com). Rare coloniser. Probiotic. human faeces, and frozen peas Woodmansey2004, RajilicStojanovic2014, Lagier2016 Firmicutes Bacilli Streptococcaceae + FANA Sessile Coccus No spore 36.9-38.1
Lactococcus raffinolactis Streptococcus raffinolactis 1 Minor Possible Commensal Non/unknown Pathogen In 13% of Europeans (unseenbio.com). Minor coloniser. human faeces, wastewater, and raw milk Dubourg2013, RajilicStojanovic2014, Byrd2020, Byrd2020, New2022 Firmicutes Bacilli Streptococcaceae + FANA Sessile Coccus No spore 40-43
Lactonifactor longoviformis 1 Minor Possible Commensal Non/unknown Pathogen In 56% of Europeans (unseenbio.com). Minor coloniser. human faeces RajilicStojanovic2014, Lagier2016, Zou2019, Byrd2020, Yang2020, Jeong2021 Firmicutes Clostridia Lachnospiraceae neg SANA Sessile Rod No spore 48.0
Lacunisphaera limnophila Unlikely Transient Non/unknown Pathogen a freshwater lake New2022 Verrucomicrobia Opitutae Opitutaceae neg AER Swimming Coccus No spore 66.5
Lagierella massiliensis Rare Possible Commensal Non/unknown Pathogen the faeces of a healthy child from Senegal Lagier2016 Firmicutes Tissierellia Peptoniphilaceae + SANA Sessile Coccus No spore 32
Lancefieldella parvula Atopobium parvulum Minor Possible Commensal Opportunistic Infection Also known as Anaerostipes sp 3 2 56FAA and Peptostreptococcus parvulus dental disease, clinical sources (wound, blood, abscess - CCUG) and human faeces Finegold1974, Benno1986, Benno1989, Bik2006, Walker2011, RajilicStojanovic2014, Lagier2016, Byrd2020, Yang2020, New2022, Hu2019, Jie2017, Zeller2014, Vachida2019 Actinobacteria Coriobacteriia Atopobiaceae + SANA Sessile Coccus No spore 35-41
Lancefieldella rimae Lactobacillus rimae Minor Possible Commensal Opportunistic Pathogen In 11% of Europeans (unseenbio.com). Minor coloniser. dental disease, clinical sources (blood, abscess - CCUG) and human faeces RajilicStojanovic2014, Byrd2020, Hu2019, Zeller2014, Vachida2019 Actinobacteria Coriobacteriia Atopobiaceae + SANA Sessile Rod No spore 45-46
Lapidilactobacillus dextrinicus Lactobacillus dextrinicus Non Transient Non/unknown Pathogen a brewery (silage) and has been detected in human faeces (Bilen2018e) Lagier2016 Firmicutes Bacilli Lactobacillaceae + FANA Sessile Coccus No spore 40.6
Laribacter hongkongensis Negative 2 Rare Possible Commensal Opportunistic Pathogen clinical sources (blood) and human faeces RajilicStojanovic2014, Lagier2016, Zeller2014 Proteobacteria Betaproteobacteria Neisseriaceae neg FANA Sessile Spirochete No spore 68
Lascolabacillus massiliensis Rare Possible Commensal Non/unknown Pathogen the faeces of a healthy child from Senegal Lagier2016 Bacteroidetes Bacteroidia Porphyromonadaceae neg FANA Rod No spore
Latilactobacillus curvatus Lactobacillus curvatus Positive 1 Minor Transient Non/unknown Pathogen human faeces (Sanz2007), clinical sources (cerebrospinal fluid, joint, blood - CCUG), cow dung, fermented food and silage Woodmansey2004, RajilicStojanovic2014, Lagier2016, Forster2019, Byrd2020, Yang2020, Vachida2019 Firmicutes Bacilli Lactobacillaceae + FANA vr Rod - curved No spore 42–44
Latilactobacillus sakei Lactobacillus sakei Positive 1 Minor Known Commensal Non/unknown Pathogen human faeces, blood and fermented foods Heilig2002, DalBello2006, Tyakht2013, RajilicStojanovic2014, Lagier2016, Byrd2020, Dubinkina2017, Jeong2021, Zeller2014, Vachida2019 Firmicutes Bacilli Lactobacillaceae + Micr Sessile Rod No spore 42-44
Latilactobacillus sakei subsp. carnosus Lactobacillus sake subsp. carnosus 1 Rare Possible Commensal Non/unknown Pathogen fermented meat products, sauerkraut and other fermented plant material Firmicutes Bacilli Lactobacillaceae + FANA Sessile Rod - curved No spore 42-44
Lautropia mirabilis 1 Minor Possible Commensal Non/unknown Pathogen human faeces, and human mouth (including sputum, abscess, gingiva - CCUG) Bik2006, RajilicStojanovic2014, Byrd2020, De2020, New2022, Zeller2014, Vachida2019 Proteobacteria Betaproteobacteria Burkholderiaceae neg FANA Swimming Coccus No spore 64.6-65.4
Lawsonella clevelandensis Rare Possible Commensal Possible Pathogen a spinal abscess Byrd2020, De2020, New2022 Actinobacteria Actinomycetia Lawsonellaceae vr SANA Sessile Pleiomorph rod No spore 58.6
Lawsonia intracellularis 2 Opportunistic in immunocompromised patients Unlikely Transient Possible Pathogen Intracellular pathogen of pigs. epithelial cells in the ilea of pigs New2022 Proteobacteria Deltaproteobacteria Desulfovibrionaceae neg Micr Sessile Rod - curved No spore
Lawsonibacter asaccharolyticus Moderate Possible Commensal Non/unknown Pathogen In 97% of Europeans (unseenbio.com). human faeces (Sakamoto2018a) Byrd2020 Firmicutes Clostridia Eubacteriales incertae sedis + SANA Sessile Rod No spore 61.2 20(neg)
Leclercia adecarboxylata Escherichia adecarboxylata 2 Rare Possible Commensal Possible Pathogen clinical sources (throat, blood, cerebrospinal fluid - CCUG) and human faeces (CCUG; including ulcerative colitis patients - Alkhalil2017) Lagier2016, Byrd2020, New2022 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Swimming Rod No spore 52.4-54.8
Lederbergia galactosidilyticus Bacillus galactosidilyticus 1 Rare Possible Commensal Non/unknown Pathogen raw milk Lagier2016 Firmicutes Bacilli Bacillaceae + FANA Swimming Short Rod Endospore 35.7-38.2
Lederbergia lentus Bacillus lentus 1 Unlikely Transient Non/unknown Pathogen Obligate aerobe; unlikely to be a gut coloniser. soil Lagier2016 Firmicutes Bacilli Bacillaceae + SAER Swimming Rod Endospore 36.3
Legionella bozemanae Fluoribacter bozemanae 2 Non Transient Known Pathogen potable water and lungs. Causes pneumonia Lagier2016 Proteobacteria Gammaproteobacteria Legionellaceae neg AER Swimming Rod No spore 43
Legionella pneumophila 2 Non Transient Known Pathogen lungs. Cause of legionellosis Lagier2016 Proteobacteria Gammaproteobacteria Legionellaceae neg AER Swimming Rod No spore 39-41
Lelliottia amnigena Enterobacter amnigenus 2 Rare Possible Commensal Opportunistic Pathogen trees (wetwood disease), soil, clinical sources (wound, infection - CCUG) and human faeces (Alkhalil2017 - including ulcerative colitis patients) Lagier2016, Byrd2020 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Swimming Rod No spore 54.2
Lelliottia nimipressuralis Enterobacter nimipressuralis 1 Plant pathogen Rare Possible Commensal Non/unknown Pathogen elm trees with a disease called wetwood Byrd2020 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Swimming Rod No spore 59
Leminorella grimontii 1 Opportunistic in immunocompromised patients Rare Possible Commensal Possible Pathogen human faeces, and clinical sources RajilicStojanovic2014, Lagier2016 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Sessile Rod No spore
Leminorella richardii 1 Opportunistic in immunocompromised patients Rare Possible Commensal Opportunistic Infection human faeces RajilicStojanovic2014, Lagier2016 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Sessile Rod No spore
Lentibacillus massiliensis Positive Rare Known Commensal Non/unknown Pathogen human faeces (Senghor2017) that are salty Lagier2016 Firmicutes Bacilli Bacillaceae + Swimming Rod Endospore
Lentibacillus timonensis Unknown Rare Possible Commensal Non/unknown Pathogen human faeces (healthy) Firmicutes Bacilli Bacillaceae + SAER Swimming Rod Endospore 38.4
Lentilactobacillus buchneri subsp. buchneri Lactobacillus buchneri Positive 1 Minor Transient Non/unknown Pathogen silage, dairy products, the oral cavity and human faeces Benno1986, Woodmansey2004, Tyakht2013, RajilicStojanovic2014, Lagier2016, Hu2019, Zeller2014 Firmicutes Bacilli Lactobacillaceae + FANA Sessile Rod No spore 44–46
Lentilactobacillus diolivorans Lactobacillus diolivorans 1 Unlikely Transient Non/unknown Pathogen maize silage, The Netherlands Lagier2016 Firmicutes Bacilli Lactobacillaceae + FANA Sessile Rod No spore 40
Lentilactobacillus farraginis Lactobacillus farraginis Unknown 1 Unlikely Transient Non/unknown Pathogen compost of distilled shochu residue Firmicutes Bacilli Lactobacillaceae + FANA Sessile Rod 41
Lentilactobacillus hilgardii Lactobacillus hilgardii 1 Rare Transient Non/unknown Pathogen In 1% of Europeans (unseenbio.com). Rare coloniser. wines and human faeces Tyakht2013, Forster2019 Firmicutes Bacilli Lactobacillaceae + FANA Sessile Rod No spore 39-41
Lentilactobacillus kefiri Lactobacillus kefiri Positive 1 Non Transient Non/unknown Pathogen Probiotic. kefir (sour milk) Lagier2016, Byrd2020 Firmicutes Bacilli Lactobacillaceae + Micr Sessile Rod No spore 41.5
Lentilactobacillus kisonensis Lactobacillus kisonensis Unlikely Transient Non/unknown Pathogen non-salted pickle solution Firmicutes Bacilli Lactobacillaceae + FANA Sessile Rod No spore 38.8
Lentilactobacillus otakiensis Lactobacillus otakiensis Unlikely Transient Non/unknown Pathogen non-salted pickle solution from Japan Lagier2016, Byrd2020 Firmicutes Bacilli Lactobacillaceae + FANA Sessile Rod No spore 39.6
Lentilactobacillus parabuchneri Lactobacillus parabuchneri 1 Rare Possible Commensal Non/unknown Pathogen In 1% of Europeans (unseenbio.com). Rare coloniser. human faeces DalBello2006, RajilicStojanovic2014, Lagier2016, Byrd2020 Firmicutes Bacilli Lactobacillaceae + FANA Rod No spore 43-44
Lentilactobacillus parafarraginis Lactobacillus parafarraginis 1 Unlikely Transient Non/unknown Pathogen compost of distilled shochu residue Firmicutes Bacilli Lactobacillaceae + FANA Sessile Rod No spore 40-41
Lentilactobacillus senioris Lactobacillus senioris Unlikely Transient Non/unknown Pathogen human faeces RajilicStojanovic2014, Lagier2016 Firmicutes Bacilli Lactobacillaceae + FANA Sessile Rod No spore 39.8
Leptospira interrogans 2 Zoonotic pathogen Non Transient Known Pathogen Consumes no carbohydrates or amino acids, just lipids. kidneys Lagier2016 Spirochaetes Spirochaetia Leptospiralaceae neg Micr Swimming Helical No spore 35
Leptotrichia amnionii Rare Possible Commensal Non/unknown Pathogen human faeces, and human amniotic fluid Bik2006, Walker2011, RajilicStojanovic2014 Fusobacteria Fusobacteriia Leptotrichiaceae neg ANA Sessile Coccobacillus No spore
Leptotrichia buccalis 2 Human and animal pathogen Rare Possible Commensal Known Pathogen human faeces, human mouth, and clinical sources (blood - CCUG) Walker2011, RajilicStojanovic2014, Lagier2016, De2020, Zeller2014 Fusobacteria Fusobacteriia Leptotrichiaceae neg SANA Sessile Rod No spore 25 20(+)
Leptotrichia hofstadii 1 Rare Possible Commensal Non/unknown Pathogen the saliva of a healthy volunteer Zeller2014, Vachida2019 Fusobacteria Fusobacteriia Leptotrichiaceae neg ANA Sessile Rod - curved No spore
Leptotrichia hongkongensis Rare Possible Commensal Opportunistic Pathogen a blood culture of cancer patient and oral specimens Fusobacteria Fusobacteriia Leptotrichiaceae vr FANA Sessile Rod No spore
Leptotrichia massiliensis Rare Possible Commensal Non/unknown Pathogen the respiratory tract Lagier2016 Fusobacteria Fusobacteriia Leptotrichiaceae + FANA Sessile Rod Endospore
Leptotrichia shahii Leptotrichia sp. LB37 1 Opportunistic in immunocompromised patients Rare Possible Commensal Opportunistic Infection a patient with gingivitis Vachida2019 Fusobacteria Fusobacteriia Leptotrichiaceae neg FANA Sessile Filamentous No spore
Leptotrichia wadei 1 Rare Transient Non/unknown Pathogen In 3% of Europeans (unseenbio.com). Rare coloniser. the saliva of a healthy volunteer Byrd2020, New2022, Vachida2019 Fusobacteria Fusobacteriia Leptotrichiaceae neg ANA Sessile Rod No spore
Leucobacter aridicollis 1 Unlikely Transient Non/unknown Pathogen Borderline cold mesophile, with optimum growth temp of 28C. Unlikely gut coloniser. activated sludge containing chromium waste and human faeces Yang2020 Actinobacteria Actinomycetia Microbacteriaceae + AER Sessile No spore 67.3
Leuconostoc carnosum 1 Unlikely Transient Non/unknown Pathogen Can't grow at 37C, so unlikely to be a gut coloniser. human faeces (Sanz2007 -coeliac children) and vacuum-packaged meat Byrd2020, Vachida2019 Firmicutes Bacilli Lactobacillaceae + FANA Sessile Coccus No spore 39
Leuconostoc citreum Holdemania sp AP2 1 Opportunistic in immunocompromised patients Minor Transient Rare Opportunist Found in human breast milk (Jeurink2013). human faeces, food, and clinical sources (blood) Almeida2019, King2019, Byrd2020, Yang2020, Hu2019, Jeong2021, Zeller2014, Vachida2019 Firmicutes Bacilli Leuconostocaceae + FANA Sessile Oval-shaped No spore 38.0-40.3
Leuconostoc gelidum 1 Rare Transient Non/unknown Pathogen human faeces, and packed meat RajilicStojanovic2014, Byrd2020, New2022, Zeller2014, Vachida2019 Firmicutes Bacilli Leuconostocaceae + FANA Sessile Coccus No spore 37
Leuconostoc gelidum subsp. gasicomitatum 1 Non Transient Non/unknown Pathogen Inability to grow at 37C suggests this not a gut coloniser. spoiled marinated broiler meat strips Zeller2014, Vachida2019 Firmicutes Bacilli Leuconostocaceae + ANA Sessile Coccus No spore 37
Leuconostoc holzapfelii 1 Rare Possible Commensal Non/unknown Pathogen Slime is produced from sucrose fermented coffee, Ethiopia Firmicutes Bacilli Lactobacillaceae + FANA Sessile Oval-shaped No spore 43.5
Leuconostoc inhae 1 Unlikely Transient Non/unknown Pathogen Can't grow at 37C, so unlikely to be a gut coloniser. human faeces (Sanz2007 - healthy children) and Korean kimchi Byrd2020 Firmicutes Bacilli Lactobacillaceae + FANA Sessile Coccus No spore 39.9
Leuconostoc kimchii 1 Rare Possible Commensal Non/unknown Pathogen kimchii, Korea Zeller2014 Firmicutes Bacilli Leuconostocaceae + FANA Sessile Coccobacillus No spore 37
Leuconostoc lactis 1 Opportunistic in immunocompromised patients Minor Transient Rare Opportunist human faeces, clinical sources (blood, wound, urine) and dairy fermentation Heilig2002, RajilicStojanovic2014, Lagier2016, Byrd2020, Yang2020, Hu2019, Zeller2014, Vachida2019 Firmicutes Bacilli Leuconostocaceae + FANA Sessile Coccus No spore 43-45
Leuconostoc mesenteroides subsp. cremoris Leuconostoc cremoris 1 Rare Known Commensal Non/unknown Pathogen dairy and other fermenting food Tyakht2013, Lagier2016 Firmicutes Bacilli Leuconostocaceae + FANA Sessile Oval-shaped No spore 37-39
Leuconostoc mesenteroides subsp. mesenteroides Leuconostoc mesenteroides 2 Minor Possible Commensal Rare Opportunist Found in human breast milk (Jeurink2013). human faeces (Sanz2007 - healthy and coeliac children) and clinical sources (CCUG - blood, wound, abscess, bile) Heilig2002, DalBello2006, Tyakht2013, RajilicStojanovic2014, Lagier2016, Almeida2019, Forster2019, Byrd2020, New2022, Dubinkina2017, Zeller2014, Vachida2019 Firmicutes Bacilli Leuconostocaceae + FANA Sessile Oval-shaped No spore 37-41
Leuconostoc pseudomesenteroides 1 Opportunistic in immunocompromised patients Unlikely Transient Rare Opportunist human faeces (Bilen2018e), clinical sources (blood, human joint) and a starter Lagier2016, Forster2019, Byrd2020 Firmicutes Bacilli Lactobacillaceae + FANA Sessile Coccus No spore 38.1-40.8
Levilactobacillus brevis Lactobacillus brevis 1 Minor Known Commensal Rare Opportunist Produces GABA (Sahab2020). Found in human breast milk (Jeurink2013). human faeces, clinical sources (infection, blood), fermented food and rats Finegold1977, Benno1989, Woodmansey2004, Tyakht2013, RajilicStojanovic2014, Lagier2016, Forster2019, Byrd2020, Hu2019, Zeller2014, Vachida2019, PerezBrocal2015 Firmicutes Bacilli Lactobacillaceae + FANA Rod No spore 44–47
Levilactobacillus brevis subsp. gravesensis Lactobacillus brevis subsp. gravesensis Unlikely Transient Non/unknown Pathogen dairy and other fermenting food Tyakht2013, Lagier2016 Firmicutes Bacilli Lactobacillaceae + FANA Sessile Rod No spore 44-47
Levilactobacillus namurensis Lactobacillus namurensis 1 Unlikely Transient Non/unknown Pathogen an artisanal sourdough manufactured with wheat, rye and spelt flour, Belgium Firmicutes Bacilli Lactobacillaceae + FANA Sessile Rod No spore 52
Levilactobacillus parabrevis Lactobacillus parabrevis 1 Unlikely Transient Non/unknown Pathogen wheat and cheese Firmicutes Bacilli Lactobacillaceae + FANA Sessile Rod No spore 49
Levyella massiliensis Rare Possible Commensal Non/unknown Pathogen Byrd2020 Firmicutes Clostridia + Coccus
Ligilactobacillus acidipiscis Lactobacillus acidipiscis 1 Unlikely Transient Non/unknown Pathogen fermented fish from Thailand and halloumi cheese Lagier2016 Firmicutes Bacilli Lactobacillaceae + Micr Sessile Rod No spore 38.6-41.5
Ligilactobacillus agilis Lactobacillus agilis 1 Rare Known Commensal Non/unknown Pathogen animal faeces, sewage Lagier2016, Byrd2020, Yang2020, New2022, PerezBrocal2015 Firmicutes Bacilli Lactobacillaceae + FANA Swimming Rod No spore 43–44
Ligilactobacillus animalis Lactobacillus animalis 1 Minor Transient Non/unknown Pathogen Found in human breast milk (Jeurink2013). human faeces, clinical sources ( blood, abscess, wound - CCUG), human dental plaque, animal faeces MacFarlane2004, Woodmansey2004, RajilicStojanovic2014, Lagier2016, Forster2019, Byrd2020, Zeller2014 Firmicutes Bacilli Lactobacillaceae + FANA Sessile Rod No spore 41–44
Ligilactobacillus ceti Lactobacillus ceti Unlikely Transient Non/unknown Pathogen the lungs of a beaked whale Firmicutes Bacilli Lactobacillaceae + FANA Sessile Rod No spore
Ligilactobacillus equi Lactobacillus equi 1 Unlikely Transient Non/unknown Pathogen horse faecal specimens Firmicutes Bacilli Lactobacillaceae + FANA Sessile Rod No spore 38.9
Ligilactobacillus murinus Lactobacillus murinus 1 Rare Transient Opportunistic Pathogen In 1% of Europeans (unseenbio.com). Rare coloniser. human faeces, sourdough, clinical sources (blood, drainage fluid, skin infection - CCUG) and animal intestines Lagier2016, Forster2019, Byrd2020 Firmicutes Bacilli Lactobacillaceae + FANA Sessile Rod No spore 43-44
Ligilactobacillus pobuzihii Lactobacillus pobuzihii Unlikely Transient Non/unknown Pathogen pobuzihi (fermented cummingcordia), Taiwan Firmicutes Bacilli Lactobacillaceae + FANA Sessile Rod No spore 37.2
Ligilactobacillus ruminis Lactobacillus ruminis Positive 1 Widespread Known Commensal Non/unknown Pathogen human faeces, rumen, and sewage Heilig2002, Walker2011, Pandey2012, Zupancic2012, Tyakht2013, Nielsen2014, RajilicStojanovic2014, Lagier2016, Rothschild2018, Zou2019, Almeida2019, Forster2019, King2019, Byrd2020, Yang2020, New2022, Dubinkina2017, Hu2019, Jie2017, Zeller2014, Vachida2019, Minerbi2019, Li2019b Firmicutes Bacilli Lactobacillaceae + ANA Pili Rod No spore 44–47
Ligilactobacillus salivarius Lactobacillus salivarius Positive 1 Widespread Known Commensal Opportunistic Pathogen Found in human breast milk (Jeurink2013). human faeces, clinical sources (blood, vagina, gall, abscess - CCUG), oral cavity and other animal intestines Benno1984, Benno1986, Benno1989, Heilig2002, Zupancic2012, Tyakht2013, Nielsen2014, RajilicStojanovic2014, Salonen2014, Lagier2016, Zou2019, Almeida2019, Forster2019, Byrd2020, Yang2020, New2022, Dubinkina2017, Hu2019, Zeller2014, Vachida2019, Wang2020a, Urban2020, Qin2012, Moore1995, PerezBrocal2015 Firmicutes Bacilli Lactobacillaceae + FANA Rod No spore 34-36
Limnobacter thiooxidans 1 Unlikely Transient Non/unknown Pathogen Obligate aerobe; unlikely to be a gut coloniser. human faeces, and freshwater sediment McLaughlin2010, Walker2011, RajilicStojanovic2014 Proteobacteria Betaproteobacteria Burkholderiaceae neg SAER Swimming Rod - curved No spore 55
Limnochorda pilosa Unlikely Transient Non/unknown Pathogen High optimum growth temperature so unlikely to be a gut coloniser. meromictic lake sediment, Japan New2022 Firmicutes Limnochordia Limnochordaceae neg FANA Pleiomorph rod Endospore 71
Limosilactobacillus antri Lactobacillus antri Rare Transient Non/unknown Pathogen human faeces, and human gastric mucosa Tyakht2013, RajilicStojanovic2014, Lagier2016, Forster2019, Dubinkina2017, Zeller2014 Firmicutes Bacilli Lactobacillaceae + FANA Sessile Rod No spore 44.9
Limosilactobacillus caccae Lactobacillus caccae Unknown Rare Possible Commensal Non/unknown Pathogen human faeces (healthy) Firmicutes Bacilli Lactobacillaceae + SANA Sessile Rod No spore 45.4
Limosilactobacillus coleohominis Lactobacillus coleohominis 1 Unlikely Transient Non/unknown Pathogen human faeces, and human sources (vagina, urinary tract) RajilicStojanovic2014, PerezBrocal2015 Firmicutes Bacilli Lactobacillaceae + FANA Rod No spore
Limosilactobacillus fermentum Lactobacillus fermentum 1 Opportunistic in immunocompromised patients Widespread Known Commensal Opportunistic Pathogen Found in human breast milk (Jeurink2013). human faeces, clinical sources (wound, blood, respiratory tract - CCUG), sewage, and mouth Moore1974, Finegold1974, Finegold1977, Benno1984, Heilig2002, Bik2006, McLaughlin2010, Zupancic2012, Tyakht2013, RajilicStojanovic2014, Lagier2016, Zou2019, Almeida2019, Forster2019, Byrd2020, New2022, Dubinkina2017, Hu2019, Jie2017, Zeller2014, Vachida2019, Wang2020a, Urban2020 Firmicutes Bacilli Lactobacillaceae + FANA Rod No spore 52–54
Limosilactobacillus frumenti Lactobacillus frumenti 1 Non Transient Non/unknown Pathogen rye-bran fermentation Lagier2016 Firmicutes Bacilli Lactobacillaceae + FANA Sessile Rod No spore 43.3-44.4
Limosilactobacillus gastricus Lactobacillus gastricus Positive 1 Unlikely Transient Non/unknown Pathogen Found in human breast milk (Jeurink2013). human faeces, and human gastric mucosa RajilicStojanovic2014, Lagier2016, Byrd2020, Vachida2019 Firmicutes Bacilli Lactobacillaceae + FANA Sessile Rod No spore 41.3
Limosilactobacillus ingluviei Lactobacillus ingluviei 1 Non Transient Non/unknown Pathogen pigeon crops and intestines Lagier2016, Hu2019 Firmicutes Bacilli Lactobacillaceae + FANA Sessile Short Rod No spore 49
Limosilactobacillus mucosae Lactobacillus mucosae 1 Rare Transient Non/unknown Pathogen In 4% of Europeans (unseenbio.com), i.e., a rare coloniser. pig intestine, sourdough and human faeces RajilicStojanovic2014, Lagier2016, Zou2019, Byrd2020, Yang2020, New2022, Hu2019, Jie2017, Vachida2019, Wang2020a, Qin2012, Li2019b, PerezBrocal2015 Firmicutes Bacilli Lactobacillaceae + FANA Sessile Rod No spore 46.5
Limosilactobacillus oris Lactobacillus oris 1 Minor Transient Non/unknown Pathogen Found in human breast milk (Jeurink2013). human faeces, and saliva MacFarlane2004, Woodmansey2004, RajilicStojanovic2014, Lagier2016, Byrd2020, Dubinkina2017, Hu2019, Zeller2014, Vachida2019 Firmicutes Bacilli Lactobacillaceae + FANA Sessile Rod No spore 49–51
Limosilactobacillus reuteri Lactobacillus reuteri Positive 1 Minor Known Commensal Rare Opportunist Found in human breast milk (Jeurink2013). human faeces, clinical sources (vagina, blood - CCUG), sourdough and meat products Benno1986, Benno1989, Woodmansey2004, Tyakht2013, RajilicStojanovic2014, Lagier2016, Almeida2019, Forster2019, Byrd2020, New2022, Dubinkina2017, Zeller2014, Vachida2019 Firmicutes Bacilli Lactobacillaceae + FANA Sessile Rod - curved No spore 40–42
Limosilactobacillus vaginalis Lactobacillus vaginalis 1 Rare Transient Opportunistic Pathogen In 3% of Europeans, so a rare coloniser. Found in human breast milk (Jeurink2013). human faeces, vagina and clinical sources (vaginosis, blood, drainage fluid) Heilig2002, DalBello2006, RajilicStojanovic2014, Lagier2016, Forster2019, Byrd2020, Yang2020, New2022, Dubinkina2017, Zeller2014, Vachida2019, Wang2020a, PerezBrocal2015 Firmicutes Bacilli Lactobacillaceae + FANA Sessile Rod No spore 38-41
Limosilactobacillus walteri Rare Possible Commensal Non/unknown Pathogen human faeces and used as a probiotic Firmicutes Bacilli Lactobacillaceae + FANA Sessile No spore 38.8
Liquorilactobacillus mali Lactobacillus mali 1 Unlikely Transient Non/unknown Pathogen fermenting wine, cider and molasses Lagier2016 Firmicutes Bacilli Lactobacillaceae + FANA Swimming Rod No spore 32.5
Liquorilactobacillus satsumensis Lactobacillus satsumensis 1 Non Transient Non/unknown Pathogen shochu mash from Japan Lagier2016, De2020 Firmicutes Bacilli Lactobacillaceae + FANA Swimming Rod No spore 39-41
Liquorilactobacillus vini Lactobacillus vini 1 Unlikely Transient Non/unknown Pathogen wine Firmicutes Bacilli Lactobacillaceae + FANA Swimming Rod No spore 39.4
Listeria floridensis Rare Possible Commensal Non/unknown Pathogen running water from the USA De2020 Firmicutes Bacilli Listeriaceae + FANA Sessile Rod No spore 41.8
Listeria grayi 1 Rare Possible Commensal Non/unknown Pathogen human faeces (CCUG), clinical sources, food and vegetation Tyakht2013, Lagier2016, Forster2019, Zeller2014 Firmicutes Bacilli Listeriaceae + FANA Swimming Rod No spore 41-42.5
Listeria innocua 1 Rare Possible Commensal Non/unknown Pathogen human faeces (McLauchlin2011Bergey), clinical sources, food and the environment Tyakht2013, Lagier2016, Forster2019, Qin2012 Firmicutes Bacilli Listeriaceae + FANA Swimming Rod No spore 36-38
Listeria ivanovii 2 Rare Known Commensal Possible Pathogen human faeces (McLauchlin2011Bergey), clinical sources and is pathogenic to animals Lagier2016 Firmicutes Bacilli Listeriaceae + FANA Swimming Rod No spore 36–38
Listeria marthii Rare Possible Commensal Non/unknown Pathogen soil and water, United States Yang2020 Firmicutes Bacilli Listeriaceae + FANA Swimming Short Rod No spore
Listeria monocytogenes Negative 2 Zoonotic pathogen Rare Known Commensal Known Pathogen human faeces (McLauchlin2011Bergey), clinical sources (blood, cerebrospinal fluid, fetus - CCUG) and the environment Lagier2016, New2022 Firmicutes Bacilli Listeriaceae + FANA Swimming Rod No spore 37–39
Listeria seeligeri Positive 1 Opportunistic in immunocompromised patients Rare Known Commensal Opportunistic Infection human faeces (McLauchlin2011Bergey), soil and environment Lagier2016 Firmicutes Bacilli Listeriaceae + FANA Swimming Rod No spore 36
Listeria welshimeri Positive 1 Rare Known Commensal Non/unknown Pathogen human faeces (McLauchlin2011Bergey), soil and environment Lagier2016, Byrd2020, Qin2012 Firmicutes Bacilli Listeriaceae + FANA Swimming Rod No spore 36
Litchfieldia alkalitelluris Bacillus alkalitelluris Rare Possible Commensal Non/unknown Pathogen sandy soil, Korea Cassir2015 Firmicutes Bacilli Bacillaceae + FANA Swimming Rod Endospore 37.9
Loigolactobacillus bifermentans Lactobacillus bifermentans 1 Unlikely Transient Non/unknown Pathogen in Edam and Gouda cheeses New2022 Firmicutes Bacilli Lactobacillaceae + FANA Sessile Short Rod No spore 45
Loigolactobacillus coryniformis Lactobacillus coryniformis 1 Minor Transient Non/unknown Pathogen human faeces, silage, bovine faeces and sewage Woodmansey2004, RajilicStojanovic2014, Cassir2015, Lagier2016, Byrd2020, De2020, Zeller2014 Firmicutes Bacilli Lactobacillaceae + FANA Coccus No spore 45
Loigolactobacillus coryniformis subsp. torquens Unlikely Transient Non/unknown Pathogen silage, cow faeces, sewage Woodmansey2004 Firmicutes Bacilli Lactobacillaceae + FANA Sessile Short Rod No spore 45
Longicatena caecimuris Rare Possible Commensal Non/unknown Pathogen mouse caeca Zou2019 Firmicutes Erysipelotrichia Erysipelotrichaceae + Sessile Rod No spore
Lutispora thermophila 1 Unlikely Transient Non/unknown Pathogen A high optimum growth temperature (55-58C) suggests this is an unlikely gut coloniser. a thermophilic methanogenic bioreactor digesting municipal solid wastes, Japan Byrd2020 Firmicutes Clostridia Clostridiaceae neg SANA Swimming Rod Endospore 36.2
Luxibacter massiliensis Rare Possible Commensal Non/unknown Pathogen human faeces (non-small cell lung cancer patient) Firmicutes Clostridia Lachnospiraceae + FANA Sessile Rod Endospore 44.4
Lysinibacillus boronitolerans 1 Rare Possible Commensal Non/unknown Pathogen Tolerates 100 mM boron, with some strains able to grow with 150 mM boron. contaminated soil from Japan Lagier2016 Firmicutes Bacilli Caryophanaceae + AER Swimming Rod Endospore 36.5
Lysinibacillus fusiformis Bacillus fusiformis Positive 1 Rare Known Commensal Non/unknown Pathogen human faeces (Hoyles2012), and soil Hoyles2012, Pfleiderer2013, RajilicStojanovic2014, Cassir2015, Lagier2016, Zeller2014 Firmicutes Bacilli Caryophanaceae vr SAER Swimming Rod Endospore 35-36
Lysinibacillus macroides Bacillus macroides Unlikely Transient Non/unknown Pathogen Obligate aerobe; unlikely to be a gut coloniser. cow faeces Lagier2016 Firmicutes Bacilli Caryophanaceae vr SAER Swimming Rod Endospore 38.2
Lysinibacillus meyeri Unlikely Transient Non/unknown Pathogen Obligate aerobe; unlikely to be a gut coloniser. a medical practise Lagier2016 Firmicutes Bacilli Caryophanaceae + SAER Swimming Rod Endospore 37.1
Lysinibacillus sphaericus Bacillus sphaericus 1 Opportunistic in immunocompromised patients, invertebrate pathogen Rare Known Commensal Opportunistic Pathogen soil, environment, food, clinical sources (blood - CCUG) and human faeces Taylor1985, Walker2011, RajilicStojanovic2014, Lagier2016, Zeller2014 Firmicutes Bacilli Caryophanaceae + AER Swimming Rod Endospore 37-38.3
Lysinibacillus varians Rare Possible Commensal Non/unknown Pathogen Can grow in the presence of 150 mM borate waste-contaminated sediment in China Lagier2016 Firmicutes Bacilli Caryophanaceae + AER Swimming Filamentous Endospore 43.2
Lysinibacillus xylanilyticus Rare Possible Commensal Non/unknown Pathogen forest humus in Korea Lagier2016 Firmicutes Bacilli Caryophanaceae + AER Swimming Rod Endospore 37.2
Lysobacter soli Rare Possible Commensal Non/unknown Pathogen human faeces, and soil RajilicStojanovic2014, Lagier2016 Proteobacteria Gammaproteobacteria Lysobacteraceae neg AER Gliding Rod No spore 65.4
Macellibacteroides fermentans Rare Possible Commensal Non/unknown Pathogen an abattoir waste treatment filter Cassir2015, Lagier2016 Bacteroidetes Bacteroidia Porphyromonadaceae + SANA Sessile Rod No spore 41.4
Macrococcus caseolyticus Staphylococcus caseolyticus 2 Animal pathogen Unlikely Known Commensal Rare Opportunist human faeces (CCUG) and clinical sources (newborn infection) Yang2020, Zeller2014 Firmicutes Bacilli Staphylococcaceae + FANA Sessile Coccus No spore 38-39
Mageeibacillus indolicus Rare Possible Commensal Possible Pathogen human faeces, vagina, and clinical sources King2019, Byrd2020, New2022, Qin2012, LeChatelier2013 Firmicutes Clostridia Hungateiclostridiaceae vr SANA Sessile Rod No spore 44.2
Mahella australiensis 1 Unlikely Transient Non/unknown Pathogen High optimum growth temperature so unlikely to be a gut coloniser. an oil well, Australia New2022, Qin2012 Firmicutes Clostridia Thermoanaerobacterales Family IV. Incertae Sedis + SANA Swimming Rod Endospore 55.5
Mailhella massiliensis Rare Possible Commensal Non/unknown Pathogen human faeces (Bilen2018e) Byrd2020, De2020 Proteobacteria Deltaproteobacteria Desulfovibrionaceae neg SANA Swimming Rod No spore
Mameliella alba Unlikely Transient Non/unknown Pathogen surface sea water, China New2022 Proteobacteria Alphaproteobacteria Roseobacteraceae neg FANA Sessile Rod No spore 63.7
Mammaliicoccus fleurettii Staphylococcus fleurettii 1 Rare Possible Commensal Non/unknown Pathogen goat’s milk cheeses Byrd2020 Firmicutes Bacilli Staphylococcaceae + FANA Sessile Coccus No spore 31-32
Mammaliicoccus lentus Staphylococcus lentus 1 Rare Possible Commensal Non/unknown Pathogen the skin and udders of goats and sheep Lagier2016, Forster2019, Byrd2020, Yang2020 Firmicutes Bacilli Staphylococcaceae + FANA Sessile Coccus No spore 29.8-34.2
Mammaliicoccus sciuri Staphylococcus sciuri Rare Known Commensal Non/unknown Pathogen animal, soil, water sources and human faeces RajilicStojanovic2014, Lagier2016, Yang2020, Li2019b Firmicutes Bacilli Staphylococcaceae + FANA Sessile Coccus No spore 32.7
Mammaliicoccus vitulinus Staphylococcus vitulinus 1 Opportunistic in immunocompromised patients Unlikely Possible Commensal Opportunistic Infection human faeces, meat, and animals Dubourg2013, RajilicStojanovic2014, Lagier2016, Byrd2020 Firmicutes Bacilli Staphylococcaceae + AER Sessile Coccus No spore 32.5
Mannheimia granulomatis Pasteurella granulomatis 2 Animal pathogen Rare Possible Commensal Opportunistic Pathogen diseased cattle Forster2019 Proteobacteria Gammaproteobacteria Pasteurellaceae neg FANA Sessile Coccobacillus No spore 39.2
Mannheimia haemolytica Pasteurella haemolytica 2 Human and animal pathogen Rare Possible Commensal Known Pathogen cattle and sheep with pneumonia and septicaemia De2020 Proteobacteria Gammaproteobacteria Pasteurellaceae neg FANA Sessile Coccobacillus No spore 43.6
Mannheimia succiniciproducens Rare Possible Commensal Non/unknown Pathogen bovine rumen Tyakht2013 Proteobacteria Gammaproteobacteria Pasteurellaceae neg FANA Sessile Coccobacillus No spore
Marasmitruncus massiliensis Rare Possible Commensal Non/unknown Pathogen human faeces (CCUG) Firmicutes Clostridia Oscillospiraceae + ANA Rod
Marseilla massiliensis Rare Possible Commensal Non/unknown Pathogen the right colon of a patient Lagier2016 Bacteroidetes Bacteroidia Prevotellaceae neg ANA Sessile Rod No spore
Marseillibacter massiliensis Rare Possible Commensal Non/unknown Pathogen human faeces (Ndongo2016b) Lagier2016, De2020, Minerbi2019 Firmicutes Clostridia Oscillospiraceae neg SANA Sessile Rod
Marvinbryantia formatexigens Bryantella formatexigens 1 Moderate Known Commensal Non/unknown Pathogen human faeces Zupancic2012, Tyakht2013, RajilicStojanovic2014, Salonen2014, Lagier2016, Chung2019, Forster2019, Byrd2020, De2020, Dubinkina2017, Jie2017, Zeller2014, Vachida2019, Qin2012, LeChatelier2013, Karlsson2013 Firmicutes Clostridia Lachnospiraceae + SANA Sessile Rod No spore 50.3
Massilia aurea 1 Unlikely Transient Non/unknown Pathogen Borderline cold mesophile, with optimum growth temp of 28C. Unlikely gut coloniser. human faeces, and drinking water McLaughlin2010, Walker2011, RajilicStojanovic2014 Proteobacteria Betaproteobacteria Oxalobacteraceae neg SAER Swimming Rod No spore 66.0
Massilia brevitalea 1 Non Transient Non/unknown Pathogen Grows best at 15C, so likely a gut non-coloniser. botanical garden soil, Germany McLaughlin2010 Proteobacteria Betaproteobacteria Oxalobacteraceae neg SAER Swimming Short Rod No spore 65.3
Massilia haematophila Naxibacter haematophilus 1 Opportunistic in immunocompromised patients Rare Possible Commensal Rare Opportunist human faeces and clinical sources (blood - CCUG) Yang2020 Proteobacteria Betaproteobacteria Oxalobacteraceae neg FANA Sessile Rod No spore
Massilia norwichensis Unlikely Transient Non/unknown Pathogen human faeces and air sample Yang2020 Proteobacteria Betaproteobacteria Oxalobacteraceae neg Micr Swimming Rod No spore
Massilia timonae 1 Opportunistic in immunocompromised patients Non Transient Opportunistic Pathogen Significant variation reported for assimilation of some substrates between references. Kampfer2011 used to override discrepancies. Likely a gut non-coloniser. clinical sources (blood) Lagier2016 Proteobacteria Betaproteobacteria Oxalobacteraceae neg SAER Swimming Rod No spore 64.6
Massilia varians Naxibacter varians 1 Opportunistic in immunocompromised patients Unlikely Transient Rare Opportunist Obligate aerobe; unlikely to be a gut coloniser. human faeces and clinical sources (eye - CCUG) Yang2020 Proteobacteria Betaproteobacteria Oxalobacteraceae neg SAER Sessile Rod No spore
Massilibacillus massiliensis Rare Possible Commensal Non/unknown Pathogen human faeces (Alou2017) Lagier2016 Firmicutes Negativicutes Veillonellaceae + ANA Rod No spore
Massilibacterium senegalense Rare Possible Commensal Non/unknown Pathogen human faeces (Alou2016c) Lagier2016 Firmicutes Bacilli Bacillaceae neg FANA Swimming Rod Endospore 35.7
Massilicoli timonensis Unknown Rare Possible Commensal Non/unknown Pathogen human faeces Firmicutes Erysipelotrichales Erysipelotrichaceae neg SANA Sessile Rod No spore 53.0
Massiliimalia massiliensis Rare Possible Commensal Non/unknown Pathogen human faeces (Bilen2018e) Lagier2016 Firmicutes Clostridia Oscillospiraceae neg SANA Sessile Rod No spore 47.2
Massiliimalia timonensis Massilimalia timonensis Minor Possible Commensal Non/unknown Pathogen In 67% of Europeans (unseenbio.com). Minor coloniser. human faeces (Afouda2018a) Firmicutes Clostridia Oscillospiraceae + Micr Sessile Rod No spore 46.9
Massilimicrobiota timonensis Moderate Possible Commensal Non/unknown Pathogen In 98% of Europeans (unseenbio.com). human faeces (Tall2019) Lagier2016, Jeong2021 Firmicutes Erysipelotrichia Erysipelotrichaceae neg SANA Sessile Rod No spore 31.8
Massilioclostridium coli Moderate Possible Commensal Non/unknown Pathogen In 98% of Europeans (unseenbio.com). human left colon (Lo2017) Lagier2016, Byrd2020 Firmicutes Clostridia Clostridiaceae neg ANA Sessile Rod No spore 40.0
Massiliprevotella massiliensis Rare Possible Commensal Non/unknown Pathogen human faeces (Bilen2018e) Lagier2016, De2020, Minerbi2019 Bacteroidetes Bacteroidia Prevotellaceae neg ANA Swimming Rod No spore
Massilistercora timonensis Mordavella sp. Marseille-P3756 Rare Possible Commensal Non/unknown Pathogen human faeces New2022, Wang2020a Firmicutes Clostridia Eubacteriales incertae sedis neg SANA Swimming Rod No spore 51.2
Mediterranea massiliensis Rare Possible Commensal Non/unknown Pathogen the colon of a patient Lagier2016 Bacteroidetes Bacteroidia Bacteroidaceae neg SANA Swimming Rod No spore 51.7
Mediterraneibacter faecis Ruminococcus faecis Minor Known Commensal Non/unknown Pathogen human faeces RajilicStojanovic2014, Lagier2016, Zou2019, Forster2019, Yang2020, Jeong2021, Minerbi2019 Firmicutes Clostridia Clostridiaceae + SANA Sessile Coccus No spore 43.4
Mediterraneibacter glycyrrhizinilyticus Clostridium glycyrrhizinilyticum Positive 1 Minor Known Commensal Non/unknown Pathogen human faeces McLaughlin2010, Walker2011, Nielsen2014, RajilicStojanovic2014, Lagier2016, Zou2019, Yang2020 Firmicutes Clostridia Clostridiaceae + SANA Sessile Rod No spore 45.7-46.2
Mediterraneibacter massiliensis Rare Possible Commensal Non/unknown Pathogen human faeces (Togo2018a) Firmicutes Clostridia Clostridiaceae + ANA Sessile Coccobacillus No spore 42.4
Megalodesulfovibrio gigas Desulfovibrio gigas 1 Unlikely Transient Non/unknown Pathogen saltwater, sewage New2022 Proteobacteria Deltaproteobacteria Desulfovibrionaceae neg SANA Swimming Vibrio No spore 60.2
Megamonas funiformis 1 Minor Possible Commensal Non/unknown Pathogen human faeces Nielsen2014, RajilicStojanovic2014, Lagier2016, Rothschild2018, Zou2019, Forster2019, Byrd2020, New2022, Hu2019, Jie2017, Vachida2019, Minerbi2019 Firmicutes Negativicutes Selenomonadaceae neg SANA Sessile Rod No spore 32.9
Megamonas hypermegale Bacteroides hypermegas 1 Moderate Known Commensal Non/unknown Pathogen human faeces, and turkey intestines Moore1974, Benno1986, Benno1989, Tyakht2013, RajilicStojanovic2014, Salonen2014, Lagier2016, Rothschild2018, King2019, Byrd2020, Dubinkina2017, Hu2019, Vachida2019, Wang2020a, Li2019b Firmicutes Negativicutes Selenomonadaceae neg SANA Sessile Rod No spore 32-34
Megamonas rupellensis Rare Possible Commensal Non/unknown Pathogen human faeces and duck caecum Rothschild2018, Hu2019, Vachida2019 Firmicutes Negativicutes Selenomonadaceae neg SANA Sessile Rod No spore 33
Megasphaera cerevisiae 1 Rare Possible Commensal Non/unknown Pathogen spoiled bottled beer Byrd2020 Firmicutes Negativicutes Veillonellaceae neg SANA Sessile Coccus No spore 42.4-44.8
Megasphaera elsdenii Peptostreptococcus elsdenii 2 Human and animal pathogen Moderate Known Commensal Opportunistic Pathogen human faeces, and Sheep rumen and other animal faeces Finegold1974, Benno1984, Benno1986, Benno1989, Mangin2004, Walker2011, Zupancic2012, Nielsen2014, RajilicStojanovic2014, Salonen2014, Lagier2016, Almeida2019, Byrd2020, Byrd2020, New2022, Hu2019, Jie2017, Zeller2014, Vachida2019, Wang2020a, Minerbi2019 Firmicutes Negativicutes Veillonellaceae neg SANA Sessile Diplococci No spore 53.1-54.1
Megasphaera indica Positive Rare Known Commensal Non/unknown Pathogen human faeces (Lanjekar2014) Lagier2016, Zou2019, Minerbi2019 Firmicutes Negativicutes Veillonellaceae neg SANA Sessile Coccus No spore 54.9-57.7
Megasphaera massiliensis Rare Possible Mutualist Non/unknown Pathogen human faeces (HIV patient - Padmanabhan2013) Lagier2016, Byrd2020, Urban2020, Minerbi2019 Firmicutes Negativicutes Veillonellaceae neg SANA Sessile Coccobacillus No spore 50.2
Megasphaera micronuciformis 1 Opportunistic in immunocompromised patients Minor Possible Commensal Opportunistic Infection clinical specimens Lagier2016, Zou2019, De2020, Hu2019, Jeong2021, Jie2017, Zeller2014, Vachida2019 Firmicutes Negativicutes Veillonellaceae neg SANA Sessile Coccus No spore 46.4
Megasphaera stantonii Rare Transient Non/unknown Pathogen chicken caeca New2022 Firmicutes Negativicutes Veillonellaceae neg SANA Sessile Coccus No spore 52.1 neg
Meiothermus silvanus Thermus silvanus 1 Unlikely Transient Non/unknown Pathogen A high minimum growth temperature (40C) suggests this is an unlikely gut coloniser. hot springs, Portugal Cassir2015, Vachida2019 Deinococcus-Thermus Deinococci Thermaceae neg AER Sessile Rod No spore 63.6
Merdibacter massiliensis Rare Possible Commensal Non/unknown Pathogen human faeces and ileum (Ricaboni2016a) Byrd2020 Firmicutes Erysipelotrichia Erysipelotrichaceae neg ANA Sessile Rod No spore
Merdimonas faecis Rare Possible Commensal Non/unknown Pathogen human faeces (Seo2017) Firmicutes Clostridia Lachnospiraceae + SANA Sessile Rod No spore 47.0
Mesobacillus jeotgali Bacillus jeotgali 1 Rare Possible Commensal Non/unknown Pathogen traditional Korean fermented seafood (jeotgal) Lagier2016 Firmicutes Bacilli Bacillaceae vr FANA Swimming Rod Endospore 41
Mesobacillus subterraneus Bacillus subterraneus 1 Rare Possible Commensal Non/unknown Pathogen Is able to reduce Fe(III) and Mn(IV) in addition to Nitrate an Australian subsurface thermal aquifer Lagier2016 Firmicutes Bacilli Bacillaceae neg FANA Swimming Rod - curved No spore 43
Mesorhizobium australicum Unlikely Transient Non/unknown Pathogen Aerobic and probable low optimum growth temperature suggests this is an unlikely gut coloniser. legume pasture species, Australia Byrd2020 Proteobacteria Alphaproteobacteria Phyllobacteriaceae neg AER Swimming Rod No spore 63.0
Mesorhizobium jarvisii Unlikely Transient Non/unknown Pathogen Borderline cold mesophile, with optimum growth temp of 28C. Unlikely gut coloniser. root nodules Yang2020 Proteobacteria Alphaproteobacteria Phyllobacteriaceae neg AER Swimming Rod No spore 62.7
Mesorhizobium loti Rhizobium loti 1 Rare Possible Commensal Non/unknown Pathogen human faeces, and plant symbiosis RajilicStojanovic2014, Zeller2014 Proteobacteria Alphaproteobacteria Phyllobacteriaceae neg AER Swimming Rod No spore 59–64
Mesorhizobium muleiense Unlikely Transient Non/unknown Pathogen Aerobic and optimum growth temperature of 28C suggests this is an unlikely gut coloniser. chickpea rhizobia, China Byrd2020 Proteobacteria Alphaproteobacteria Phyllobacteriaceae neg AER Swimming Rod No spore 61.2
Mesosutterella multiformis Rare Possible Commensal Non/unknown Pathogen human faeces (Sakamoto2018b) Proteobacteria Betaproteobacteria Sutterellaceae neg SANA Sessile Rod No spore 56.9 20(w)
Metabacillus galliciensis Bacillus galliciensis Unlikely Transient Non/unknown Pathogen Optimum growth temp is low (20C), so unlikely to be a gut coloniser. human faeces and seahorse faeces Yang2020 Firmicutes Bacilli Bacillaceae + AER Swimming Rod Endospore 48.1
Metabacillus idriensis Bacillus idriensis Rare Possible Commensal Opportunistic Pathogen a newborn child with sepsis McLaughlin2010 Firmicutes Bacilli Bacillaceae + AER Rod 41.2
Metabacillus litoralis Bacillus litoralis 1 Rare Possible Commensal Non/unknown Pathogen Korean tidal flats Lagier2016 Firmicutes Bacilli Bacillaceae vr AER Swimming Rod Endospore 35.2
Metabacillus niabensis Bacillus niabensis 1 Rare Possible Commensal Non/unknown Pathogen mushroom compost Lagier2016 Firmicutes Bacilli Bacillaceae + FANA Swimming Rod Endospore 37.7-40.8
Metakosakonia massiliensis Enterobacter massiliensis Rare Possible Commensal Non/unknown Pathogen human faeces (CCUG, Lagier2013) Byrd2020 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg AER Swimming No spore 55.1
Metamycoplasma anseris Mycoplasma anseris 1 Unlikely Transient Non/unknown Pathogen geese phallus and cloaca, Hungary New2022 Tenericutes Mollicutes Mycoplasmataceae unk FANA Sessile Coccus No spore 24.7-26.0
Metaprevotella massiliensis Rare Possible Commensal Non/unknown Pathogen the ileum of a patient Lagier2016 Bacteroidetes Bacteroidia Prevotellaceae neg SANA Rod No spore
Methanobrevibacter arboriphilus Methanobacterium arbophilicum 1 Rare Possible Commensal Non/unknown Pathogen Autotrophic, converting H2/CO2 to methane. wetwood enrichment cultures and paddy field soils Lagier2016 Euryarchaeota Methanobacteria Methanobacteriaceae + SANA Sessile Rod No spore 27.5
Methanobrevibacter millerae 1 Rare Possible Commensal Non/unknown Pathogen Uses H2/CO2 or formate to produce methane. Requires acetate and yeast extract components for growth. ovine and bovine rumen Lagier2016 Euryarchaeota Methanobacteria Methanobacteriaceae + SANA Sessile Coccobacillus No spore 31-32 S
Methanobrevibacter oralis 1 Rare Possible Commensal Non/unknown Pathogen Requires H2/CO2 and produces methane. Fecal extract (with VFA) was required for growth. subgingival dental plaque Lagier2016, De2020 Euryarchaeota Methanobacteria Methanobacteriaceae + SANA Sessile Coccobacillus No spore 28
Methanobrevibacter ruminantium Methanobacterium ruminantium 1 Rare Possible Commensal Non/unknown Pathogen Uses H2 and formate to produce methane. Widely distributed in the rumen of various animals. rumen contents Lagier2016, Zeller2014 Euryarchaeota Methanobacteria Methanobacteriaceae + SANA Sessile Rod No spore
Methanobrevibacter smithii 1 Moderate Possible Commensal Non/unknown Pathogen human faeces (gut) and sludge Nam2008a, Tyakht2013, Nielsen2014, Lagier2016, Rothschild2018, King2019, Chen2020, Dubinkina2017, Jie2017, Zeller2014, Wang2018, Vachida2019, Wang2020a, Urban2020, Minerbi2019, LeChatelier2013, Karlsson2013 Euryarchaeota Methanobacteria Methanobacteriaceae + SANA Sessile Oval-shaped No spore 30.6
Methanococcus voltae 1 Rare Possible Commensal Non/unknown Pathogen Uses only H2 and/or formate with CO2 as an electron acceptor, producing methane in the process. anaerobic sediments and water Qin2012 Euryarchaeota Methanococci Methanococcaceae neg SANA Swimming Coccus No spore 30.7
Methanomassiliicoccus intestinalis Rare Possible Commensal Non/unknown Pathogen human faeces (Borrel2013) King2019 Euryarchaeota Thermoplasmata Methanomassiliicoccaceae + SANA Coccus No spore 41.3
Methanomassiliicoccus luminyensis Rare Possible Commensal Non/unknown Pathogen human faeces (Dridi2012) Lagier2016 Candidatus Thermoplasmatota Thermoplasmata Methanomassiliicoccaceae + SANA Sessile Coccus No spore 59.9
Methanomethylophilus alvus Rare Known Commensal Non/unknown Pathogen A methanogen consuming methanol. human faeces Candidatus Thermoplasmatota Thermoplasmata Candidatus Methanomethylophilaceae 55.6
Methanosphaera stadtmanae Methanosphaera stadtmaniae 1 Minor Possible Commensal Non/unknown Pathogen human large intestine (Miller1985) Nam2008a, Tyakht2013, Lagier2016, Rothschild2018, De2020, Dubinkina2017, Jie2017, Zeller2014, Vachida2019, Karlsson2013 Euryarchaeota Methanobacteria Methanobacteriaceae + SANA Sessile Coccus No spore 25.8 20(+)
Methylibium petroleiphilum 1 Unlikely Transient Non/unknown Pathogen Unable to grow at 37C so unlikely to be a gut coloniser. Degrades methyl t-butylether. a compost biofilter, USA. Possible animal faecal material origin Zeller2014 Proteobacteria Betaproteobacteria Sphaerotilaceae neg AER Swimming Rod No spore 69
Methylobacterium adhaesivum 1 Unlikely Transient Non/unknown Pathogen Borderline cold mesophile, with optimum growth temp of 28C. Unlikely gut coloniser. human faeces, and drinking water McLaughlin2010, RajilicStojanovic2014, Yang2020 Proteobacteria Alphaproteobacteria Methylobacteriaceae neg AER Swimming Rod No spore 63.6
Methylobacterium brachiatum 1 Unlikely Transient Non/unknown Pathogen Obligate aerobe; unlikely to be a gut coloniser. water samples, Japan Byrd2020, Yang2020 Proteobacteria Alphaproteobacteria Methylobacteriaceae neg SAER Swimming Rod - curved No spore 69.2-69.7
Methylobacterium jeotgali 1 Non Transient Non/unknown Pathogen Obligate aerobe, no spore formation and doesn't grow at 37C, so probably a gut non-coloniser. human faeces, and fermented seafood McLaughlin2010, RajilicStojanovic2014 Proteobacteria Alphaproteobacteria Methylobacteriaceae neg SAER Swimming Rod No spore 64.9
Methylobacterium mesophilicum Pseudomonas mesophilica 1 Opportunistic in immunocompromised patients Non Transient Opportunistic Infection Obligate aerobe, no spore formation and doesn't grow at 37C, so probably a gut non-coloniser. human faeces, and plant leaves Walker2011, RajilicStojanovic2014 Proteobacteria Alphaproteobacteria Methylobacteriaceae neg SAER Swimming Rod No spore 65.8
Methylobacterium organophilum 1 Unlikely Transient Non/unknown Pathogen Aerobic and low growth temperatures of 25-31C suggests this is an unlikely gut coloniser. sediment of a lake, USA Li2019b Proteobacteria Alphaproteobacteria Methylobacteriaceae neg AER Swimming Short Rod No spore 66
Methylobacterium oryzae 1 Unlikely Transient Non/unknown Pathogen Borderline cold mesophile, with optimum growth temp of 28C. Unlikely gut coloniser. rice and human faeces Yang2020 Proteobacteria Alphaproteobacteria Methylobacteriaceae neg SAER Swimming Rod No spore 70.6
Methylobacterium phyllosphaerae Unlikely Transient Non/unknown Pathogen Borderline cold mesophile, with optimum growth temp of 28C. Unlikely gut coloniser. rice and human faeces Yang2020 Proteobacteria Alphaproteobacteria Methylobacteriaceae neg SAER Swimming Rod No spore 66.8
Methylobacterium radiotolerans Pseudomonas radiora 1 Non Transient Non/unknown Pathogen Obligate aerobe, no spore formation and doesn't grow at 37C, so probably a gut non-coloniser. rice grains and human faeces RajilicStojanovic2014, Lagier2016, Zeller2014 Proteobacteria Alphaproteobacteria Methylobacteriaceae neg SAER Swimming Rod No spore 72.3
Methylomusa anaerophila Unlikely Transient Non/unknown Pathogen Carbohydrates are not used for growth. sludge, Japan New2022 Firmicutes Negativicutes Sporomusaceae neg ANA Swimming Rod - curved Endospore 46.6
Methylorubrum aminovorans Methylobacterium aminovorans 1 Rare Possible Commensal Non/unknown Pathogen soil, Japan Yang2020 Proteobacteria Alphaproteobacteria Methylobacteriaceae neg AER Swimming Rod No spore 68.0
Methylorubrum extorquens Methylobacterium extorquens 1 Non Transient Non/unknown Pathogen Obligate aerobe, no spore formation and doesn't grow at 37C, so probably a gut non-coloniser. human faeces McLaughlin2010, Walker2011, Zeller2014 Proteobacteria Alphaproteobacteria Methylobacteriaceae neg SAER Swimming Rod No spore 69.4
Methylorubrum populi Methylobacterium populi 1 Unlikely Transient Non/unknown Pathogen Obligate aerobe; unlikely to be a gut coloniser. human faeces, and poplar tree rhizosphere RajilicStojanovic2014 Proteobacteria Alphaproteobacteria Methylobacteriaceae neg SAER Swimming Rod No spore 70.4
Methylorubrum thiocyanatum Methylobacterium thiocyanatum 1 Unlikely Transient Non/unknown Pathogen Can utilise potassium thiocyanate as a nitrogen source and this compound as well as thiosulfate or tetrathionate as chemolithotrophic energy sources. Obligate aerobe so unlikely to be a gut coloniser. soil from around tree roots McLaughlin2010 Proteobacteria Alphaproteobacteria Methylobacteriaceae neg SAER Sessile Short Rod No spore 68.5
Methylorubrum zatmanii Methylobacterium zatmanii 1 Unlikely Transient Non/unknown Pathogen Obligate aerobe; unlikely to be a gut coloniser. human faeces, and fermentor Dubourg2013, RajilicStojanovic2014, Cassir2015 Proteobacteria Alphaproteobacteria Methylobacteriaceae neg SAER Swimming Rod No spore 69.4-70.3
Methyloversatilis discipulorum Rare Possible Commensal Non/unknown Pathogen Can fix nitrogen. freshwater lake sediment, United States Yang2020 Proteobacteria Alphaproteobacteria Rhodocyclaceae neg AER Sessile Rod No spore 66.6
Methyloversatilis universalis 1 Rare Possible Commensal Non/unknown Pathogen human faeces, and contaminated soil McLaughlin2010, RajilicStojanovic2014, Byrd2020 Proteobacteria Betaproteobacteria Rhodocyclaceae neg AER Sessile Rod No spore 64-65
Microbacterium aurum 1 Rare Possible Commensal Rare Opportunist human faeces, clinical sources (blood - CCUG) and corn steep liquor Pfleiderer2013, RajilicStojanovic2014, Lagier2016 Actinobacteria Actinomycetia Microbacteriaceae + AER Sessile Rod No spore 69.2
Microbacterium chocolatum 1 Unlikely Transient Non/unknown Pathogen Borderline cold mesophile, with optimum growth temp of 28C. Unlikely gut coloniser. human faeces, and culture contamination McLaughlin2010, RajilicStojanovic2014 Actinobacteria Actinomycetia Microbacteriaceae + AER Sessile Rod No spore 69.5
Microbacterium deminutum 1 Unlikely Possible Commensal Non/unknown Pathogen Unlikely gut coloniser because this organism doesn't grow at 37C. soil, Japan Yang2020 Actinobacteria Actinomycetia Microbacteriaceae + AER Sessile Rod No spore 69
Microbacterium esteraromaticum Aureobacterium esteraromaticum 1 Unlikely Transient Non/unknown Pathogen Poor growth at 37C, so unlikely to be a gut coloniser. soil Yang2020 Actinobacteria Actinomycetia Microbacteriaceae + SAER Swimming Rod No spore 68.8
Microbacterium foliorum 1 Unlikely Transient Non/unknown Pathogen Borderline cold mesophile, so unlikely to be a gut coloniser. phyllosphere of grasses, mulch and human faeces RajilicStojanovic2014, Lagier2016 Actinobacteria Actinomycetia Microbacteriaceae + SAER Swimming Rod No spore 67
Microbacterium ginsengisoli 1 Non Transient Non/unknown Pathogen Obligate aerobe, no spore formation and doesn't grow at 37C, so probably a gut non-coloniser. human faeces and soil from Korea Yang2020 Actinobacteria Actinomycetia Microbacteriaceae + SAER Sessile Rod No spore 69.4
Microbacterium gubbeenense 1 Unlikely Transient Non/unknown Pathogen smear-ripened cheese and human faeces RajilicStojanovic2014, Lagier2016, Byrd2020, PerezBrocal2015 Actinobacteria Actinomycetia Microbacteriaceae + FANA Sessile Rod No spore 69-72
Microbacterium hydrocarbonoxydans 1 Unlikely Transient Non/unknown Pathogen Obligate aerobe; unlikely to be a gut coloniser. human faeces, and oil-contaminated soil Dubourg2013, RajilicStojanovic2014, Lagier2016 Actinobacteria Actinomycetia Microbacteriaceae + SAER Swimming Rod No spore
Microbacterium kitamiense 1 Unlikely Transient Non/unknown Pathogen Obligate aerobe; unlikely to be a gut coloniser. wastewater, Japan Lagier2016 Actinobacteria Actinomycetia Microbacteriaceae + SAER Sessile Rod No spore 69.2
Microbacterium lacticum 1 Unlikely Transient Non/unknown Pathogen Obligate aerobe; unlikely to be a gut coloniser. human faeces and blood RajilicStojanovic2014, Lagier2016, Yang2020 Actinobacteria Actinomycetia Microbacteriaceae + SAER Rod No spore
Microbacterium liquefaciens Aureobacterium liquefaciens 1 Unlikely Transient Non/unknown Pathogen Obligate aerobe; unlikely to be a gut coloniser. milk, cheese and other dairy products Lagier2016 Actinobacteria Actinomycetia Microbacteriaceae + SAER Sessile Rod No spore 68.6
Microbacterium luteolum Aureobacterium luteolum 1 Non Transient Possible Pathogen Obligate aerobe, no spore formation and doesn't grow at 37C, so probably a gut non-coloniser. human faeces, and soil, and clinical sources RajilicStojanovic2014 Actinobacteria Actinomycetia Microbacteriaceae + SAER Sessile Rod No spore 66-72
Microbacterium maritypicum Flavobacterium marinotypicum 1 Unlikely Transient Non/unknown Pathogen Borderline cold mesophile, with optimum growth temp of 28C. Unlikely gut coloniser. seawater and marine mud Lagier2016 Actinobacteria Actinomycetia Microbacteriaceae + SAER Swimming Rod No spore 71.6
Microbacterium mitrae Unlikely Possible Commensal Non/unknown Pathogen Korean salted Turbin shell and human faeces Yang2020 Actinobacteria Actinomycetia Microbacteriaceae + AER Sessile Rod No spore 73.1
Microbacterium natoriense 1 Unlikely Transient Non/unknown Pathogen Obligate aerobe; unlikely to be a gut coloniser. soil, Japan Lagier2016 Actinobacteria Actinomycetia Microbacteriaceae + SAER Sessile Rod No spore 69.1
Microbacterium oleivorans 1 Unlikely Transient Non/unknown Pathogen Obligate aerobe; unlikely to be a gut coloniser. oil storage, blood and human faeces RajilicStojanovic2014, Lagier2016 Actinobacteria Actinomycetia Microbacteriaceae + SAER Sessile Rod No spore
Microbacterium oxydans Brevibacterium oxydans 1 Unlikely Transient Non/unknown Pathogen Obligate aerobe; unlikely to be a gut coloniser. contaminated hospital material Lagier2016 Actinobacteria Actinomycetia Microbacteriaceae + SAER Swimming Rod No spore 70-71
Microbacterium paraoxydans 1 Opportunistic in immunocompromised patients Rare Possible Commensal Rare Opportunist clinical sources (blood - CCUG) and human faeces RajilicStojanovic2014, Lagier2016, Yang2020 Actinobacteria Actinomycetia Microbacteriaceae + FANA Swimming Rod No spore 69.9
Microbacterium phyllosphaerae 1 Unlikely Transient Non/unknown Pathogen Obligate aerobe; unlikely to be a gut coloniser. phyllosphere of grasses, mulch and human faeces RajilicStojanovic2014, Lagier2016 Actinobacteria Actinomycetia Microbacteriaceae + SAER Swimming Rod No spore 64
Microbacterium saccharophilum Unlikely Transient Non/unknown Pathogen Obligate aerobe; unlikely to be a gut coloniser. a sugar-refining factory Lagier2016 Actinobacteria Actinomycetia Microbacteriaceae + SAER Sessile Rod No spore 73
Microbacterium schleiferi Aureobacterium schleiferi 1 Unlikely Transient Rare Opportunist Borderline cold mesophile, with optimum growth temp of 28C. Unlikely gut coloniser. human faeces, clinical samples (blood - CCUG) and soil RajilicStojanovic2014, Lagier2016 Actinobacteria Actinomycetia Microbacteriaceae + SAER Sessile Rod No spore 66.9
Microbacterium sediminicola 1 Unlikely Possible Commensal Non/unknown Pathogen human faeces and river sediment Yang2020 Actinobacteria Actinomycetia Microbacteriaceae + AER Rod No spore 67.8
Microbacterium testaceum Brevibacterium testaceum 1 Non Transient Non/unknown Pathogen Obligate aerobe, no spore formation and doesn't grow at 37C, so probably a gut non-coloniser. human faeces and Chinese paddies Yang2020, Zeller2014 Actinobacteria Actinomycetia Microbacteriaceae + SAER Swimming Rod No spore 65.4-72.7
Microbispora rosea 1 Rare Possible Commensal Non/unknown Pathogen soil samples, Japan PerezBrocal2015 Actinobacteria Actinomycetia Streptosporangiaceae + AER Sessile Filamentous Exospore 69.9
Micrococcus cohnii Unlikely Possible Commensal Non/unknown Pathogen human faeces and air sample Yang2020 Actinobacteria Actinomycetia Micrococcaceae + AER Sessile Coccus No spore 70.4
Micrococcus endophyticus Unlikely Transient Non/unknown Pathogen Borderline cold mesophile, with optimum growth temp of 28C. Unlikely gut coloniser. human faeces and plant roots Cassir2015, Lagier2016, Yang2020 Actinobacteria Actinomycetia Micrococcaceae + AER Sessile Coccus No spore 72.9
Micrococcus luteus 1 Minor Possible Commensal Non/unknown Pathogen Data combined for biovars I, II and III sludge, painting, clinical samples (blood - CCUG) and human faeces Finegold1974, Taylor1985, MacFarlane2004, McLaughlin2010, Hoyles2012, Dubourg2013, Pfleiderer2013, RajilicStojanovic2014, Lagier2016, Forster2019, Zeller2014, PerezBrocal2015 Actinobacteria Actinomycetia Micrococcaceae + AER Sessile Coccus No spore 70-71
Micrococcus lylae 1 Rare Possible Commensal Non/unknown Pathogen human faeces (Hoyles2012), and old painting Hoyles2012, Pfleiderer2013, RajilicStojanovic2014, Lagier2016 Actinobacteria Actinomycetia Micrococcaceae + AER Sessile Coccus No spore
Micrococcus terreus Rare Possible Commensal Non/unknown Pathogen forest soil, China De2020 Actinobacteria Actinomycetia Micrococcaceae + AER Sessile Coccus No spore 67.2
Microlunatus phosphovorus 1 Unlikely Transient Non/unknown Pathogen Borderline cold mesophile, so unlikely to be a gut coloniser. human faeces and activated sludge Yang2020 Actinobacteria Actinomycetia Propionibacteriaceae + AER Sessile Coccus No spore 67.9
Micromonospora aurantiaca 1 Rare Possible Commensal Non/unknown Pathogen human faeces, and soil RajilicStojanovic2014, Lagier2016 Actinobacteria Actinomycetia Micromonosporaceae + AER Sessile Filamentous Exospore 72.8
Micropruina glycogenica 1 Rare Possible Commensal Non/unknown Pathogen Able to accumulate large amounts of glycogen; grows slowly an activated sludge reactor Cassir2015 Actinobacteria Actinomycetia Nocardioidaceae + AER Sessile Coccus No spore 70.5
Microvirga aerophila Unlikely Transient Non/unknown Pathogen Obligate aerobe; unlikely to be a gut coloniser. human faeces and air sample from Korea Yang2020 Proteobacteria Alphaproteobacteria Methylobacteriaceae neg SAER Sessile Rod No spore 62.2
Microvirga massiliensis Positive Rare Known Commensal Non/unknown Pathogen human faeces RajilicStojanovic2014, Lagier2016 Proteobacteria Alphaproteobacteria Methylobacteriaceae neg AER Sessile Rod No spore 63
Microvirgula aerodenitrificans 1 Unlikely Possible Commensal Non/unknown Pathogen human faeces (diarrhoea - CCUG), and activated sludge Forster2019, Byrd2020 Proteobacteria Betaproteobacteria Chromobacteriaceae neg AER Swimming Rod - curved No spore 65
Millionella massiliensis Rare Possible Commensal Non/unknown Pathogen human faeces Bacteroidetes Bacteroidia Rikenellaceae neg ANA Sessile Rod No spore
Miniphocaeibacter massiliensis Miniphocibacter massiliensis Rare Possible Commensal Non/unknown Pathogen human faeces (CCUG) Byrd2020 Firmicutes Tissierellia Peptoniphilaceae + ANA Coccus
Mitsuokella jalaludinii 1 Minor Possible Mutualist Non/unknown Pathogen In 16% of Europeans (unseenbio.com). Minor coloniser. human faeces, and bovine rumen RajilicStojanovic2014, Browne2016, Lagier2016, Forster2019, Byrd2020, Minerbi2019 Firmicutes Negativicutes Selenomonadaceae neg SANA Sessile Rod No spore 56.9
Mitsuokella multacida Bacteroides multiacidus 2 Moderate Known Commensal Opportunistic Pathogen Reported to ferment gluconate to acetate and lactate in pigs. human faeces and livestock animals Benno1986, Benno1989, Zupancic2012, Tyakht2013, Nielsen2014, RajilicStojanovic2014, Salonen2014, Lagier2016, Rothschild2018, Zou2019, Forster2019, Byrd2020, Dubinkina2017, Hu2019, Jie2017, Zeller2014, Vachida2019, Wang2020a Firmicutes Negativicutes Selenomonadaceae neg SANA Sessile Rod No spore 56-58 20(neg)
Mixta calida Rare Possible Commensal Possible Pathogen infant formula, clinical samples (wound, blood - CCUG) and human faeces (infant - CCUG) Lagier2016 Proteobacteria Gammaproteobacteria Erwiniaceae neg FANA Swimming Coccobacillus No spore 57.4
Mixta intestinalis Rare Possible Commensal Non/unknown Pathogen human faeces (Prakash2015) Proteobacteria Gammaproteobacteria Erwiniaceae neg FANA Swimming Rod No spore 59.1
Mobilibacterium massiliense Rare Possible Commensal Non/unknown Pathogen human faeces (Bilen2017d) Firmicutes Clostridia Eubacteriales Family XIII. Incertae Sedis neg ANA Rod
Mobilibacterium timonense Rare Possible Commensal Non/unknown Pathogen human faeces (CCUG) Firmicutes Clostridia Eubacteriales Family XIII. Incertae Sedis neg ANA Rod
Mobilicoccus massiliensis Rare Possible Commensal Non/unknown Pathogen the faeces of a child from Nigeria with kwashiorkor Lagier2016 Actinobacteria Actinomycetia Microbacteriaceae + FANA Swimming Coccus No spore 70.5
Mobiluncus curtisii 2 Rare Possible Commensal Non/unknown Pathogen human faeces, and vagina McLaughlin2010, RajilicStojanovic2014, Byrd2020, New2022, Zeller2014, Vachida2019 Actinobacteria Actinomycetia Actinomycetaceae vr ANA Swimming Rod - curved No spore 51-52
Moellerella wisconsensis 2 Rare Possible Commensal Opportunistic Pathogen human faeces and clinical sources (wound, sputum, peritoneum exsudate - CCUG) RajilicStojanovic2014, Lagier2016 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Sessile Rod No spore
Mogibacterium diversum 1 Opportunistic in immunocompromised patients Rare Transient Causes Illness dental disease and human faeces RajilicStojanovic2014, Byrd2020, New2022 Firmicutes Clostridia Mogibacteriaceae + SANA Sessile Rod No spore 42
Mogibacterium neglectum 2 Rare Possible Commensal Causes Illness dental disease and human faeces Wang2005, Bik2006, RajilicStojanovic2014 Firmicutes Clostridia Mogibacteriaceae + SANA Sessile Rod No spore 41-42
Mogibacterium pumilum 2 Rare Possible Commensal Opportunistic Pathogen Produces phenylacetate as the sole end product of PY or PYG broth; otherwise mostly inert to biochemical tests. periodontal pockets Byrd2020, Yang2020, New2022 Firmicutes Clostridia Mogibacteriaceae + SANA Sessile Rod No spore 45-46
Mogibacterium timidum Eubacterium timidum 2 Rare Transient Causes Illness dental disease and human faeces Woodmansey2004, RajilicStojanovic2014, Lagier2016, Byrd2020 Firmicutes Clostridia Mogibacteriaceae + SANA Sessile Rod No spore 45-46 20(neg)
Mogibacterium vescum 2 Unlikely Transient Causes Illness dental disease and human faeces RajilicStojanovic2014 Firmicutes Clostridia Mogibacteriaceae + SANA Sessile Rod No spore 46
Monoglobus pectinilyticus Minor Possible Commensal Non/unknown Pathogen In 34% of Europeans (unseenbio.com). Minor coloniser. human faeces (Kim2017) Byrd2020, New2022, Jeong2021, Wang2020a Firmicutes Clostridia Oscillospiraceae + ANA Sessile Coccus No spore 37.2
Moorella glycerini 1 Unlikely Transient Non/unknown Pathogen There is no growth at 42C or below, so unlikely to be a gut coloniser. Homoacetogen. Able to use the following electron donors: glycerol, sugars, pyruvate. hot springs, USA New2022 Firmicutes Clostridia Thermoanaerobacteraceae + ANA Swimming Rod Endospore 64.5
Moraxella catarrhalis Negative 2 Human and animal pathogen Unlikely Transient Opportunistic Pathogen Obligate aerobe; unlikely to be a gut coloniser. clinical sources (blood, sputum, wound - CCUG) and human faeces RajilicStojanovic2014, Vachida2019 Proteobacteria Gammaproteobacteria Moraxellaceae neg SAER Sessile Coccus No spore 40-43
Moraxella osloensis 2 Human and animal pathogen Unlikely Transient Opportunistic Pathogen Obligate aerobe; unlikely to be a gut coloniser. clinical sources (blood, sputum, cerebrospinal fluid - CCUG) and human faeces, and is parasitic Bik2006, McLaughlin2010, Dubourg2013, Pfleiderer2013, RajilicStojanovic2014, Lagier2016, De2020 Proteobacteria Gammaproteobacteria Moraxellaceae neg SAER Sessile Rod No spore 43-43.5
Mordavella massiliensis Rare Possible Commensal Non/unknown Pathogen human faeces (Bilen2018e) Firmicutes Clostridia Clostridiaceae neg SANA Swimming Rod No spore
Morganella morganii Proteus morganii Negative 2 Human and animal pathogen Minor Possible Commensal Opportunistic Pathogen human faeces, animals and clinical sources (trachea, blood, urine - CCUG) Finegold1974, Woodmansey2004, RajilicStojanovic2014, Lagier2016, Byrd2020, Yang2020, Vachida2019, Li2019b, PerezBrocal2015 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA vr Rod No spore 50
Moryella indoligenes 2 Rare Known Commensal Opportunistic Infection human faeces, human gut, and clinical sources (abscesses) RajilicStojanovic2014, Yang2020, PerezBrocal2015 Firmicutes Clostridia Lachnospiraceae + SANA Sessile Rod No spore 50.2
Mucispirillum schaedleri Rare Possible Commensal Non/unknown Pathogen the gastrointestinal mucus of rodents Deferribacteres Deferribacteres Mucispirillaceae neg SANA Swimming Vibrio No spore
Murdochiella asaccharolytica Rare Possible Commensal Opportunistic Pathogen wound specimens Lagier2016 Firmicutes Tissierellia Peptoniphilaceae + SANA Sessile Coccus
Murdochiella massiliensis Rare Possible Commensal Non/unknown Pathogen the faeces of a healthy child from Senegal Lagier2016, Byrd2020 Firmicutes Tissierellia Peptoniphilaceae + SANA Sessile Coccus No spore 48.9
Murdochiella vaginalis Rare Transient Opportunistic Pathogen In 4% of Europeans (unseenbio.com). Rare coloniser. a vaginal sample from an ill patient, France Byrd2020, New2022 Firmicutes Tissierellia Peptoniphilaceae + SANA Sessile Coccus No spore 49.5
Muribaculum gordoncarteri Unlikely Transient Non/unknown Pathogen mouse faeces New2022 Bacteroidetes Bacteroidia Muribaculaceae neg SANA Sessile Short Rod No spore 49.5
Muribaculum intestinale Minor Transient Non/unknown Pathogen In 31% of Europeans (unseenbio.com). Minor coloniser. the intestines of mice Byrd2020, New2022 Bacteroidetes Bacteroidia Muribaculaceae neg SANA Sessile Rod No spore 49.9
Murimonas intestini Rare Possible Commensal Non/unknown Pathogen human faeces and mouse gut Forster2019, Yang2020 Firmicutes Clostridia Lachnospiraceae + SANA Sessile Coccobacillus No spore 44.0
Mycobacterium abscessus Mycobacterium chelonae subsp. abscessus 2 Human and animal pathogen Unlikely Possible Commensal Opportunistic Pathogen clinical sources (sputum, respiratory tract, blood - CCUG) and human faeces RajilicStojanovic2014, Lagier2016 Actinobacteria Actinomycetia Mycobacteriaceae vr AER Sessile Rod No spore 64.1
Mycobacterium avium 2 Human and animal pathogen Unlikely Possible Commensal Opportunistic Pathogen human faeces, clinical sources (sputum), and bird TB RajilicStojanovic2014, Lagier2016, Zeller2014 Actinobacteria Actinomycetia Mycobacteriaceae vr AER Sessile Rod No spore 70
Mycobacterium avium subsp. paratuberculosis Mycobacterium paratuberculosis 2 Unlikely Possible Commensal Known Pathogen Difficult to cultivate. Pathogenic. Unlikely coloniser in healthy people. diseased cattle. Implicated as a contributing factor in Crohn's disease Lagier2016 Actinobacteria Actinomycetia Mycobacteriaceae vr AER Sessile Coccobacillus No spore 69.3
Mycobacterium colombiense 2 Rare Possible Commensal Opportunistic Pathogen the blood of an HIV patient Lagier2016, Zeller2014 Actinobacteria Actinomycetia Mycobacteriaceae vr AER Sessile Rod No spore
Mycobacterium florentinum 2 Rare Possible Commensal Opportunistic Pathogen human faeces, and clinical sources (sputum) RajilicStojanovic2014, Lagier2016 Actinobacteria Actinomycetia Mycobacteriaceae vr AER Sessile Rod No spore 66.4
Mycobacterium fortuitum 2 Rare Possible Commensal Opportunistic Pathogen human faeces and clinical sources (sputum, blood, abscess - CCUG) RajilicStojanovic2014, Lagier2016 Actinobacteria Actinomycetia Mycobacteriaceae vr AER Sessile Rod No spore 66.4
Mycobacterium gastri 2 Rare Possible Commensal Opportunistic Pathogen a gastric lavage (CCUG) Byrd2020 Actinobacteria Actinomycetia Mycobacteriaceae vr AER Sessile Rod No spore
Mycobacterium gordonae 1 Human and animal pathogen; opportunistic in immunocompromised patients Rare Possible Commensal Opportunistic Pathogen clinical sources (brochial lavage - CCUG) and gastric lavage (CCUG) Lagier2016 Actinobacteria Actinomycetia Mycobacteriaceae vr AER Sessile Rod No spore 66.6
Mycobacterium interjectum 2 Rare Possible Commensal Opportunistic Pathogen a child with cervical lymphadenitis Lagier2016 Actinobacteria Actinomycetia Mycobacteriaceae vr AER Sessile Rod No spore
Mycobacterium kansasii 2 Human and animal pathogen Unlikely Possible Commensal Known Pathogen Pathogenic; unlikely to be a coloniser in a healthy microbiome. pulmonary legions Lagier2016, Byrd2020, Zeller2014 Actinobacteria Actinomycetia Mycobacteriaceae vr AER Sessile Rod No spore
Mycobacterium lentiflavum 2 Rare Possible Commensal Opportunistic Pathogen a patient with spondylodiscitis Lagier2016 Actinobacteria Actinomycetia Mycobacteriaceae vr AER Sessile Rod No spore 66.8
Mycobacterium simiae 2 Human and animal pathogen Rare Possible Commensal Opportunistic Pathogen healthy monkeys and clinical sources (pulmonary disease) Lagier2016 Actinobacteria Actinomycetia Mycobacteriaceae vr AER Sessile Rod No spore
Mycobacterium terrae 1 Human and animal pathogen; opportunistic in immunocompromised patients Rare Possible Commensal Opportunistic Pathogen clinical sources (gastric lavage and sputum) and soil Lagier2016 Actinobacteria Actinomycetia Mycobacteriaceae vr AER Sessile Rod No spore
Mycobacterium tuberculosis 3 Vaccine available, zoonotic pathogen Non Transient Dangerous Pathogen cases of tuberculosis Lagier2016 Actinobacteria Actinomycetia Mycobacteriaceae vr AER Sessile Rod No spore 65.6
Mycobacterium tuberculosis variant africanum Mycobacterium africanum 3 Vaccine available, zoonotic pathogen Non Transient Dangerous Pathogen tuberculosis patients from Senegal Lagier2016 Actinobacteria Actinomycetia Mycobacteriaceae vr AER Sessile Rod No spore
Mycobacterium tuberculosis variant bovis Mycobacterium bovis 3 Vaccine available, zoonotic pathogen Unlikely Possible Commensal Dangerous Pathogen Pathogenic; unlikely to be a coloniser in a healthy microbiome. tuberculosis in cattle, man and other animals Lagier2016 Actinobacteria Actinomycetia Mycobacteriaceae + Micr Sessile Rod No spore 65.6
Mycobacteroides abscessus subsp. bolletii Mycobacterium bolletii 2 Unlikely Possible Commensal Known Pathogen Associated with chronic pneumonia. Multidrug-resistant species. Pathogenic; unlikely to be a coloniser in a healthy microbiome. sputum and stomach aspirate Lagier2016 Actinobacteria Actinomycetia Mycobacteriaceae + ANA Sessile Rod No spore
Mycolicibacterium aubagnense Mycobacterium aubagnense 2 Non Transient Rare Opportunist human faeces and bronchial aspirate Yang2020 Actinobacteria Actinomycetia Mycobacteriaceae + AER Sessile Rod No spore 65
Mycolicibacterium cosmeticum Mycobacterium cosmeticum 1 Opportunistic in immunocompromised patients Unlikely Possible Commensal Possible Pathogen human faeces (18-yr-old - CCUG) and clinical sources Actinobacteria Actinomycetia Mycobacteriaceae vr AER Sessile Rod No spore
Mycolicibacterium houstonense Mycobacterium houstonense 2 Rare Possible Commensal Opportunistic Pathogen face wound Byrd2020 Actinobacteria Actinobacteria Mycobacteriaceae + Micr Sessile Pleiomorph rod No spore 64
Mycolicibacterium mageritense Mycobacterium mageritense 2 Unlikely Possible Commensal Possible Pathogen sputum New2022 Actinobacteria Actinomycetia Mycobacteriaceae + AER Sessile Rod No spore 67
Mycolicibacterium neoaurum Mycobacterium neoaurum 1 Opportunistic in immunocompromised patients Rare Possible Commensal Known Pathogen clinical isolates and soil Byrd2020 Actinobacteria Actinobacteria Mycobacteriaceae + Micr Sessile Rod No spore
Mycoplasma hominis 2 Human and animal pathogen Rare Transient Opportunistic Pathogen human faeces and clinical sources (sinus, amniotic membrane - CCUG) Tyakht2013, RajilicStojanovic2014, Lagier2016, Yang2020, Hu2019, Zeller2014 Tenericutes Mollicutes Mycoplasmataceae neg FANA Coccobacillus No spore 33.7
Mycoplasma muris Malacoplasma muris 1 Rare Possible Commensal Non/unknown Pathogen mice De2020 Tenericutes Mycoplasmoidales Malacoplasma neg ANA Sessile Coccus No spore 24.9
Mycoplasma pneumoniae Negative 2 Rare Possible Commensal Known Pathogen human faeces and clinical sources RajilicStojanovic2014 Tenericutes Mollicutes Mycoplasmataceae neg FANA Gliding Filamentous No spore 38.6
Mycoplasmopsis arginini Mycoplasma arginini 2 Opportunistic in immunocompromised patients Unlikely Transient Known Pathogen Energy sources is arginine and not urea or glucose. Requires cholesterol. mammals, including septicaemia in immunocompromised patients New2022 Tenericutes Mollicutes Mycoplasmataceae neg FANA Coccus No spore 27.6
Mycoplasmopsis californica Mycoplasma californicum 2 Opportunistic in immunocompromised patients Unlikely Transient Possible Pathogen Causes bovine mastitis. Requires cholesterol. udders and milk of cows and ewes New2022 Tenericutes Mollicutes Mycoplasmataceae neg FANA Coccus No spore 31.9
Myroides odoratimimus Flavobacterium odoratum 2 Unlikely Transient Opportunistic Pathogen Obligate aerobe; unlikely to be a gut coloniser. clinical sources (wound, urine, pus) and water Lagier2016, Byrd2020 Bacteroidetes Flavobacteriia Flavobacteriaceae neg SAER Sessile Rod No spore 30-35
Myroides odoratus Flavobacterium odoratum 2 Unlikely Transient Opportunistic Pathogen Obligate aerobe; unlikely to be a gut coloniser. clinical sources (serum, urine) Lagier2016 Bacteroidetes Flavobacteriia Flavobacteriaceae neg SAER Sessile Rod No spore 35-38
Nakamurella multipartita Microsphaera multipartita 1 Unlikely Transient Non/unknown Pathogen Aerobic and low optimum growth temperature (25C) suggests this is an unlikely gut coloniser. an activated sludge reactor Zeller2014 Actinobacteria Actinomycetia Nakamurellaceae + AER Sessile Coccus No spore 67.5
Nanosynbacter lyticus Unlikely Transient Non/unknown Pathogen Obligate epibiotic parasite. the surface of other oral cavity-residing Actinomyces odontolyticus New2022 Candidatus Saccharibacteria Candidatus Saccharimonia Candidatus Nanosynbacteraceae + ANA Sessile Coccus
Natronorubrum bangense 1 Non Transient Non/unknown Pathogen Requires minimum 12% salt concentration and high pH to grow. Therefore likely to be a gut non-coloniser. a soda lake, Tibet New2022 Euryarchaeota Halobacteria Natrialbaceae neg SAER Sessile Pleiomorph rod No spore 59.9
Nautilia nitratireducens Unlikely Possible Commensal Non/unknown Pathogen Optimum growth temperature is 55C so unlikely to be a gut coloniser. Can use thiosulfate, sulfur and nitrate as terminal electron acceptors. a deep-sea hydrothermal vent Diamanti2020 Proteobacteria Epsilonproteobacteria Nautiliaceae neg SANA Swimming Rod No spore 36.0
Ndongobacter massiliensis Unlikely Transient Rare Opportunist a urine sample after a kidney transplant Byrd2020, New2022 Firmicutes Firmicutes sensu stricto incertae sedis neg ANA Sessile Coccus
Necropsobacter rosorum Rare Possible Commensal Possible Pathogen human faeces (CCUG) and clinical sources (blood, abscess - CCUG) Proteobacteria Gammaproteobacteria Pasteurellaceae neg Sessile Coccus No spore 52.5
Negativibacillus massiliensis Minor Possible Commensal Non/unknown Pathogen In 53% of Europeans (unseenbio.com). Minor coloniser. human left colon and human faeces (Bilen2018e) Byrd2020, Minerbi2019 Firmicutes Negativicutes Firmicutes sensu stricto incertae sedis neg SANA Sessile Rod Endospore 45.4
Negativicoccus massiliensis Rare Possible Commensal Non/unknown Pathogen human faeces (CCUG) Lagier2016, Byrd2020 Firmicutes Negativicutes Veillonellaceae neg Micr Sessile Coccus No spore
Negativicoccus succinicivorans Rare Possible Commensal Possible Pathogen clinical sources (wound, blood - CCUG) and human faeces Pfleiderer2013, RajilicStojanovic2014, Lagier2016 Firmicutes Negativicutes Veillonellaceae neg SANA Sessile Coccus No spore
Neglecta timonensis Rare Possible Commensal Non/unknown Pathogen human faeces (Bessis2016b) Lagier2016, Minerbi2019 Firmicutes Clostridia Eubacteriales incertae sedis + SANA Rod
Neisseria bacilliformis 2 Rare Possible Commensal Opportunistic Infection clinical specimens (sputa, lung abscess, oral infections, blood) Zeller2014 Proteobacteria Betaproteobacteria Neisseriaceae neg AER Sessile Rod No spore
Neisseria canis 1 Opportunistic in immunocompromised patients Rare Possible Commensal Opportunistic Infection throats of cats and clinical sources (cat bite) Lagier2016 Proteobacteria Betaproteobacteria Neisseriaceae neg AER Sessile Diplococci No spore 50
Neisseria cinerea 1 Opportunistic in immunocompromised patients Minor Possible Commensal Opportunistic Pathogen clinical sources (nasopharynx, eye, proctitis - CCUG) and human faeces. McLaughlin2010, Walker2011, RajilicStojanovic2014, Lagier2016, Byrd2020, Zeller2014, PerezBrocal2015 Proteobacteria Betaproteobacteria Neisseriaceae neg AER Sessile Diplococci No spore 49–51
Neisseria elongata 1 Minor Possible Commensal Opportunistic Pathogen human faeces, and clinical sources (appendix, nasopharynx, blood - CCUG) Bik2006, RajilicStojanovic2014, Lagier2016, De2020, Yang2020, New2022, Zeller2014, Vachida2019 Proteobacteria Betaproteobacteria Neisseriaceae neg AER Sessile Diplobacilli No spore 53
Neisseria flava 1 Opportunistic in immunocompromised patients Rare Possible Commensal Opportunistic Infection human faeces, oropharynx and nasopharynx Bik2006, RajilicStojanovic2014 Proteobacteria Betaproteobacteria Neisseriaceae neg AER Sessile Diplococci No spore 49
Neisseria flavescens 2 Minor Possible Commensal Opportunistic Pathogen clinical sources (nasopharynx, cerebrospinal fluid - CCUG) and human faeces Pfleiderer2013, RajilicStojanovic2014, Lagier2016, Byrd2020, De2020, New2022, Zeller2014, Vachida2019 Proteobacteria Betaproteobacteria Neisseriaceae neg AER Sessile Diplococci No spore 46–50
Neisseria gonorrhoeae 2 Non Transient Known Pathogen Found only in humans. patients with gonorrhoea (purulent venereal discharges), anorectal infections and other clinical sources Lagier2016, Zeller2014 Proteobacteria Betaproteobacteria Neisseriaceae neg AER Sessile Diplococci No spore 50-53
Neisseria lactamica Neisseria lactamicus 1 Opportunistic in immunocompromised patients Rare Possible Commensal Rare Opportunist Rarely pathogenic. The only Neisseria sp. to produce acid from lactose. the nasopharynx of younger people De2020, Zeller2014 Proteobacteria Betaproteobacteria Neisseriaceae neg AER Sessile Diplococci No spore 52
Neisseria macacae 1 Rare Possible Commensal Non/unknown Pathogen monkey isolates and human faeces Tyakht2013, RajilicStojanovic2014, Lagier2016, Forster2019, Zeller2014 Proteobacteria Betaproteobacteria Neisseriaceae neg AER Sessile Diplococci No spore 50–51
Neisseria meningitidis 2 Vaccine available Unlikely Possible Commensal Known Pathogen Frequently found in a commensal (asymptomatic) state in the nasopharynx. Pathogenic. Unlikely to be a gut coloniser in healthy people. causative agent of cerebrospinal meningitis, and other clinical sources (blood) Lagier2016, De2020, Zeller2014, Vachida2019 Proteobacteria Betaproteobacteria Neisseriaceae neg AER Sessile Diplococci No spore 50-52
Neisseria mucosa 2 Rare Possible Commensal Opportunistic Pathogen human faeces and clinical sources (blood, wound, cerebrospinal fluid - CCUG) RajilicStojanovic2014, Lagier2016, Byrd2020, New2022, Zeller2014 Proteobacteria Betaproteobacteria Neisseriaceae neg AER Sessile Diplococci No spore 50–52
Neisseria oralis Neisseria mucosa subsp. heidelbergensis Negative Rare Possible Commensal Rare Opportunist human faeces, clinical sources (blood - CCUG) and healthy gingiva Yang2020, PerezBrocal2015 Proteobacteria Betaproteobacteria Neisseriaceae neg FANA Sessile Coccus No spore 52.6
Neisseria perflava 1 Opportunistic in immunocompromised patients Rare Possible Commensal Opportunistic Pathogen human faeces and clinical sources (blood, wound, sputum - CCUG) Pfleiderer2013, RajilicStojanovic2014, Lagier2016, Byrd2020 Proteobacteria Betaproteobacteria Neisseriaceae neg AER Sessile Diplococci No spore
Neisseria polysaccharea 1 Rare Possible Commensal Non/unknown Pathogen Not known to cause human disease. the pharynx of a healthy person Zeller2014 Proteobacteria Betaproteobacteria Neisseriaceae neg AER Sessile Coccus No spore 53
Neisseria shayeganii Rare Possible Commensal Opportunistic Infection clinical sources (sputum, wound) De2020 Proteobacteria Betaproteobacteria Neisseriaceae neg FANA Sessile Diplococci No spore
Neisseria sicca 2 Rare Possible Commensal Opportunistic Pathogen human faeces and clinical sources (blood, nasopharynx, sputum - CCUG). Yang2020, Vachida2019 Proteobacteria Betaproteobacteria Neisseriaceae neg Micr Sessile Diplococci No spore 49-51.5
Neisseria subflava 2 Rare Transient Opportunistic Pathogen In 6% of Europeans (unseenbio.com). Rare coloniser. human faeces and clinical sources (urine, wound, sputum - CCUG) Wang2005, Bik2006, Walker2011, RajilicStojanovic2014, Lagier2016, Byrd2020, Yang2020, New2022, Zeller2014, Vachida2019, Li2019b, PerezBrocal2015 Proteobacteria Betaproteobacteria Neisseriaceae neg AER Sessile Diplococci No spore 48–51
Neoactinobaculum massilliense Rare Possible Commensal Non/unknown Pathogen the human oral cavity Actinobacteria Actinomycetia Actinomycetaceae + ANA Sessile Rod No spore 62.9
Neobacillus bataviensis Bacillus bataviensis 1 Rare Possible Commensal Non/unknown Pathogen soil, The Netherlands Lagier2016, Byrd2020 Firmicutes Bacilli Bacillaceae + FANA Swimming Rod Endospore 39.6-40.1
Neobacillus fumarioli Bacillus fumarioli 1 Unlikely Transient Non/unknown Pathogen Obligate aerobe and high optimum temperature suggest it is not a gut coloniser. Also requires low pH to grow. geothermal soils and active and inactive fumaroles, Antarctica Firmicutes Bacilli Bacillaceae + SAER Swimming Rod Endospore 40.7
Neobacillus jeddahensis Bacillus jeddahensis Rare Possible Commensal Non/unknown Pathogen human faeces (Bittar2015) Lagier2016 Firmicutes Bacilli Bacillaceae + FANA Sessile Rod Endospore 39.4
Neobacillus massiliamazoniensis Rare Possible Commensal Non/unknown Pathogen human faeces Firmicutes Bacilli Bacillaceae + FANA Sessile Rod No spore 34.1
Neobacillus niacini Bacillus niacini Positive 1 Rare Known Commensal Non/unknown Pathogen human faeces, and soil RajilicStojanovic2014, Lagier2016 Firmicutes Bacilli Bacillaceae + AER vr Rod Endospore 37-39
Neobacillus pocheonensis Bacillus pocheonensis 1 Unlikely Transient Non/unknown Pathogen Borderline cold mesophile, so unlikely to be a gut coloniser. a ginseng field, Korea Lagier2016 Firmicutes Bacilli Bacillaceae + SAER Sessile Rod Endospore 44.9
Neobacillus soli Bacillus soli 1 Rare Possible Commensal Non/unknown Pathogen soil, The Netherlands Lagier2016 Firmicutes Bacilli Bacillaceae + FANA Swimming Rod Endospore 40.1
Neobittarella massiliensis Moderate Possible Commensal Non/unknown Pathogen In 97% of Europeans (unseenbio.com). human faeces (Bilen2018) Firmicutes Clostridia Oscillospiraceae + SANA Coccobacillus
Neofamilia massiliensis Rare Possible Commensal Non/unknown Pathogen human faeces (Lagier2016, De2020) Lagier2016, De2020 Firmicutes Clostridia Eubacteriales incertae sedis
Nesterenkonia massiliensis Rare Possible Commensal Non/unknown Pathogen human faeces (Edouard2014a) Lagier2016 Actinobacteria Actinomycetia Micrococcaceae + AER Swimming Coccus No spore 62.5
Nevskia ramosa 1 Unlikely Transient Non/unknown Pathogen Optimum growth temp is low (20-25C), so unlikely to be a gut coloniser. human faeces, and aquatic sources RajilicStojanovic2014 Proteobacteria Gammaproteobacteria Nevskiaceae neg SAER Gliding No spore 67.8
Niallia nealsonii Bacillus nealsonii Positive 1 Rare Known Commensal Non/unknown Pathogen human faeces, and dust from clean area RajilicStojanovic2014, Lagier2016 Firmicutes Bacilli Bacillaceae + FANA Swimming Rod Endospore
Niameybacter massiliensis Rare Known Commensal Non/unknown Pathogen human faeces (Alou2017) Lagier2016, Byrd2020 Firmicutes Clostridia Lachnospiraceae + SANA Rod
Nigerium massiliense Rare Possible Commensal Non/unknown Pathogen the faeces of a Nigerian child with kwashiorkor Lagier2016 Actinobacteria Actinomycetia Propionibacteriaceae + FANA Coccus No spore
Nitriliruptor alkaliphilus Unlikely Transient Non/unknown Pathogen Obligate alkaliphilic, requiring at least pH 8 to grow; unlikely gut commensal. Utilises nitriles and amides for energy, C and N sources. soda lakes, Russia Forster2019 Actinobacteria Nitriliruptoria Nitriliruptoraceae + SAER Sessile Rod No spore 70.8
Nitrosomonas eutropha 1 Rare Possible Commensal Non/unknown Pathogen Can tolerate 0.6M ammonia concentrations. Contains carboxysomes. municipal and industrial sewage, eutrophic systems Proteobacteria Betaproteobacteria Nitrosomonadaceae neg AER Swimming Pleiomorph rod No spore 47.9-48.5
Nocardia asteroides 2 Human and animal pathogen Rare Possible Commensal Known Pathogen Contains aerial hyphae. soil, water sources, sewage sludge and clinical sources (mycetoma infections) Lagier2016 Actinobacteria Actinomycetia Nocardiaceae + AER Sessile Exospore 63-69
Nocardia brevicatena 1 Opportunistic in immunocompromised patients Rare Possible Commensal Non/unknown Pathogen Byrd2020 Actinobacteria Actinobacteria Nocardiaceae + AER Sessile Pleiomorph rod Exospore
Nocardia cyriacigeorgica Nocardia cyriacigeorgici 2 Rare Possible Commensal Non/unknown Pathogen a patient suffering chronic bronchitis Zeller2014 Actinobacteria Actinobacteria Nocardiaceae + AER Sessile Filamentous No spore 68.1
Nocardia mangyaensis Unlikely Transient Non/unknown Pathogen Borderline cold mesophile, with optimum growth temp of 28C. Unlikely gut coloniser. oil-contaminated soil, China New2022 Actinobacteria Actinomycetia Nocardiaceae + AER Sessile Pleiomorph rod No spore 68.1
Nocardia otitidiscaviarum 2 Human and animal pathogen Rare Possible Commensal Non/unknown Pathogen guinea pig ear infection, soil and clinical sources Byrd2020 Actinobacteria Actinobacteria Nocardiaceae + AER Sessile Filamentous 66-67
Nocardioides jensenii Pimelobacter jensenii 1 Unlikely Transient Non/unknown Pathogen Borderline cold mesophile, with optimum growth temp of 28C. Unlikely gut coloniser. soil Lagier2016 Actinobacteria Actinomycetia Nocardioidaceae + AER Sessile Rod-coccus cycle No spore 68.8
Nocardioides kribbensis 1 Unlikely Transient Non/unknown Pathogen Doesn't grow at 37C, has high optimum pH and is aerobic, so an unlikely gut coloniser. alkaline soil Frank2007 Actinobacteria Actinomycetia Nocardioidaceae + AER Sessile Rod-coccus cycle No spore 73-74
Nocardioides massiliensis Unlikely Transient Non/unknown Pathogen Obligate aerobe; unlikely to be a gut coloniser. human faeces (Dubourg2016) Lagier2016 Actinobacteria Actinomycetia Nocardioidaceae + SAER Sessile Rod No spore 71.0
Nosocomiicoccus massiliensis Rare Possible Commensal Rare Opportunist human faeces (Mishra2013c) and clinical sources (synovial fluid - CCUG) Lagier2016 Firmicutes Bacilli Staphylococcaceae + AER Swimming Coccus No spore 36.4
Noviherbaspirillum massiliense Herbaspirillum massiliense Positive Rare Known Commensal Non/unknown Pathogen human faeces RajilicStojanovic2014, Lagier2016, Forster2019 Proteobacteria Betaproteobacteria Oxalobacteraceae neg AER Swimming Rod - curved No spore 59.7
Novosphingobium capsulatum Flavobacterium capsulatum Unlikely Transient Non/unknown Pathogen Obligate aerobe; unlikely to be a gut coloniser. human faeces and distilled water Yang2020 Proteobacteria Alphaproteobacteria Sphingomonadaceae neg SAER Sessile Rod No spore 63.1
Numidum massiliense Rare Possible Commensal Non/unknown Pathogen human faeces (Alou2016d) Lagier2016 Firmicutes Bacilli Bacillaceae + FANA Sessile Rod Endospore 52.1
Obesumbacterium proteus Flavobacterium proteus 1 Rare Possible Commensal Non/unknown Pathogen human faeces Byrd2020, Yang2020 Proteobacteria Gammaproteobacteria Hafniaceae neg FANA Sessile Rod No spore
Oceanidesulfovibrio marinus Desulfovibrio marinus 1 Unlikely Transient Non/unknown Pathogen High salt required for optimum growth, so unlikely gut coloniser. phosphogypsum-contaminated marine sediment, Tunesia New2022 Proteobacteria Deltaproteobacteria Desulfovibrionaceae neg SANA Swimming Vibrio No spore 60.4
Oceanithermus profundus 1 Unlikely Transient Non/unknown Pathogen Doesn't grow below 40C, so unlikely to be a gut coloniser. a deep-sea hydrothermal vent New2022, Zeller2014 Deinococcus-Thermus Deinococci Thermaceae neg Micr Sessile Rod No spore 62.9
Oceanobacillus caeni 1 Rare Possible Commensal Non/unknown Pathogen human faeces (Hoyles2012), and activated sludge Hoyles2012, RajilicStojanovic2014, Lagier2016 Firmicutes Bacilli Bacillaceae + AER Swimming Rod Endospore 33.6
Oceanobacillus iheyensis 1 Unlikely Transient Non/unknown Pathogen Obligate aerobe; unlikely to be a gut coloniser. deep sea sediment Lagier2016 Firmicutes Bacilli Bacillaceae + SAER Swimming Rod Endospore 35.8
Oceanobacillus jeddahense Rare Possible Commensal Non/unknown Pathogen the faeces of an obese person from Saudi Arabia Lagier2016 Firmicutes Bacilli Bacillaceae + AER Swimming Rod Endospore 37.1
Oceanobacillus manasiensis Rare Possible Commensal Non/unknown Pathogen Apparently aerobic but lacks catalase and oxidase activities. salt lakes, China Lagier2016 Firmicutes Bacilli Bacillaceae + AER Swimming Rod Endospore 39.7
Oceanobacillus massiliensis Positive Rare Known Commensal Non/unknown Pathogen human faeces RajilicStojanovic2014, Lagier2016, Forster2019 Firmicutes Bacilli Bacillaceae + SAER Swimming Rod No spore 40.4
Oceanobacillus oncorhynchi 1 Non Transient Non/unknown Pathogen Likely gut non-coloniser because this organism doesn't grow below pH 9. the skin of a fish Lagier2016 Firmicutes Bacilli Bacillaceae + FANA Swimming Rod Endospore 38.5
Oceanobacillus picturae Virgibacillus picturae 1 Unlikely Transient Non/unknown Pathogen Obligate aerobe; unlikely to be a gut coloniser. old mural paintings Lagier2016 Firmicutes Bacilli Bacillaceae + SAER Swimming Rod Endospore 39.5
Oceanobacillus senegalensis Positive Unlikely Transient Non/unknown Pathogen High salt required for optimum growth, so unlikely gut coloniser. human faeces that are salty Firmicutes Bacilli Bacillaceae + Swimming Rod Endospore
Oceanobacillus sojae Rare Possible Commensal Non/unknown Pathogen soy sauce production equipment, Japan Lagier2016 Firmicutes Bacilli Bacillaceae + AER Swimming Rod Endospore 38.0
Oceanobacillus timonensis Positive Unlikely Transient Non/unknown Pathogen High salt required for optimum growth, so unlikely gut coloniser. human faeces that are salty Firmicutes Bacilli Bacillaceae + Swimming Rod Endospore
Ochrobactrum anthropi 2 Human and animal pathogen Unlikely Transient Opportunistic Pathogen Obligate aerobe; unlikely to be a gut coloniser. human faeces and clinical sources (sputum, blood, infection - CCUG) RajilicStojanovic2014, Lagier2016 Proteobacteria Alphaproteobacteria Brucellaceae neg SAER Swimming Rod No spore 56-59
Ochrobactrum intermedium 2 Unlikely Transient Opportunistic Pathogen Obligate aerobe; unlikely to be a gut coloniser. human faeces and clinical sources (blood, sputum, urine - CCUG) Pandey2012, RajilicStojanovic2014, Lagier2016, Zeller2014 Proteobacteria Alphaproteobacteria Brucellaceae neg SAER Swimming Rod No spore 58
Odoribacter laneus Minor Possible Commensal Non/unknown Pathogen human faeces Nielsen2014, RajilicStojanovic2014, Lagier2016, Rothschild2018, Forster2019, Byrd2020, Dubinkina2017, Jie2017, Vachida2019, Qin2012, Minerbi2019, Karlsson2013 Bacteroidetes Bacteroidia Odoribacteraceae neg SANA Sessile No spore 42.4 20(neg)
Odoribacter massiliensis Minor Isolation and characterisation not yet published. In 66% of Europeans (unseenbio.com). A minor coloniser. Byrd2020 Bacteroidetes Bacteroidia Odoribacteraceae
Odoribacter splanchnicus Bacteroides splanchnicus Positive 2 Widespread Known Commensal Opportunistic Pathogen human faeces and clinical samples (blood, wound, abscess - CCUG) Holdeman1976, Finegold1977, Benno1986, Benno1989, Mangin2004, MacFarlane2004, McLaughlin2010, Walker2011, Nielsen2014, RajilicStojanovic2014, Salonen2014, Lagier2016, Rothschild2018, Zou2019, Chung2019, Forster2019, King2019, Byrd2020, New2022, Chen2020, Dubinkina2017, Hu2019, Jeong2021, Jie2017, Zeller2014, Wang2018, Vachida2019, Wang2020a, Minerbi2019 Bacteroidetes Bacteroidia Odoribacteraceae neg SANA Sessile Rod No spore 43.3 20(+)
Oenococcus oeni Leuconostoc oenos 1 Unlikely Transient Non/unknown Pathogen Growth is not inhibited in the presence of 10% ethanol. Low optimum growth temperature and pH suggests this is an unlikely gut coloniser. wine fermentation Byrd2020, Zeller2014 Firmicutes Bacilli Leuconostocaceae + FANA Sessile Coccus No spore 38-42
Oerskovia turbata Cellulomonas turbata 1 Opportunistic in immunocompromised patients Rare Possible Commensal Opportunistic Infection Shows extensive branching, but lacks aerial hyphae. soil Lagier2016 Actinobacteria Actinomycetia Cellulomonadaceae + FANA Swimming Filamentous No spore 70.5-75
Okadaella gastrococcus Rare Possible Commensal Known Pathogen Intracellular parasite. Firmicutes Bacilli Streptococcaceae neg Swimming Coccus No spore
Olegusella massiliensis Rare Possible Commensal Non/unknown Pathogen the vaginal flora of a patient with bacterial vaginosis Byrd2020 Actinobacteria Coriobacteriia Coriobacteriaceae + SANA Sessile Coccobacillus No spore 49.2
Oleidesulfovibrio alaskensis Desulfovibrio alaskensis 1 Rare Possible Commensal Non/unknown Pathogen Can use sulfate, thiosulfate and sulfite to oxidise organic acids and alcohols. oilfields, Alaska, United States Tyakht2013, New2022, Zeller2014 Proteobacteria Deltaproteobacteria Desulfovibrionaceae neg SANA Swimming Vibrio No spore 64.1
Oleidesulfovibrio vietnamensis Desulfovibrio vietnamensis 1 Rare Possible Commensal Non/unknown Pathogen production fluids from offshore oil fields, Vietnam Proteobacteria Deltaproteobacteria Desulfovibrionaceae neg SANA Swimming Vibrio No spore 60.6
Oligella urethralis Moraxella urethralis 1 Human and animal pathogen; opportunistic in immunocompromised patients Rare Possible Commensal Opportunistic Pathogen the urinary tract and ear Lagier2016, Byrd2020 Proteobacteria Betaproteobacteria Alcaligenaceae neg AER vr Short Rod No spore 47
Olsenella congonensis Rare Possible Commensal Non/unknown Pathogen human faeces (Bilen2018e) Actinobacteria Coriobacteriia Atopobiaceae + SANA Rod
Olsenella massiliensis Rare Possible Commensal Non/unknown Pathogen human faeces (Lagier2016) Lagier2016 Actinobacteria Coriobacteriia Atopobiaceae + SANA Sessile Coccus No spore 63-64
Olsenella phocaeensis Olsenella phoceensis Rare Possible Commensal Non/unknown Pathogen the right colon of a 60 yo patient Lagier2016, Byrd2020 Actinobacteria Coriobacteriia Atopobiaceae + SANA Coccus Endospore
Olsenella profusa 2 Rare Possible Commensal Opportunistic Pathogen Differences in enzyme activities between published reports are labelled 'vr' and might represent strain variability. human faeces, and oral cavity RajilicStojanovic2014, Byrd2020, Vachida2019 Actinobacteria Coriobacteriia Atopobiaceae + Micr Sessile Rod No spore 64
Olsenella timonensis Rare Possible Commensal Non/unknown Pathogen human faeces (Bilen2018e) Lagier2016, New2022 Actinobacteria Coriobacteriia Atopobiaceae + SANA Sessile Rod No spore
Olsenella uli Lactobacillus uli 2 Rare Possible Commensal Opportunistic Pathogen human faeces RajilicStojanovic2014, Lagier2016, Byrd2020, New2022, Zeller2014, Vachida2019 Actinobacteria Coriobacteriia Atopobiaceae + Micr Sessile Rod No spore 64
Olsenella urininfantis Rare Possible Commensal Non/unknown Pathogen urine of a baby, France Byrd2020 Actinobacteria Coriobacteriia Atopobiaceae + SANA Rod No spore
Oribacterium asaccharolyticum Rare Possible Commensal Non/unknown Pathogen Requires yeast extract for growth. subgingival dental plaque Byrd2020 Firmicutes Clostridia Lachnospiraceae vr SANA Swimming Rod No spore 43.3 S
Oribacterium parvum Rare Possible Commensal Opportunistic Pathogen subgingival plaque Firmicutes Clostridia Lachnospiraceae vr SANA Swimming Oval-shaped No spore 42.0-42.1
Oribacterium sinus 1 Opportunistic in immunocompromised patients Minor Transient Opportunistic Infection human faeces, and oral cavity (sinus) Walker2011, RajilicStojanovic2014, Byrd2020, Yang2020, Hu2019, Jie2017, Zeller2014, Vachida2019 Firmicutes Clostridia Lachnospiraceae vr SANA Swimming Oval-shaped No spore 42.4
Ornithinibacillus contaminans Unlikely Transient Opportunistic Infection Obligate aerobe; unlikely to be a gut coloniser. a blood sample Lagier2016 Firmicutes Bacilli Bacillaceae + SAER Sessile Rod Endospore
Ornithinibacillus massiliensis Rare Possible Commensal Non/unknown Pathogen human faeces (Pham2017) Firmicutes Bacilli Bacillaceae + AER Rod
Ornithobacterium rhinotracheale 2 Animal pathogen Rare Unknown Opportunistic Pathogen human faeces and avian respiratory system Forster2019, King2019, New2022 Bacteroidetes Flavobacteriia Weeksellaceae neg Micr Sessile Rod No spore 37-39
Oscillibacter massiliensis Oscilibacter massiliensis Rare Possible Commensal Non/unknown Pathogen human faeces (Bilen2018e) Lagier2016, Minerbi2019 Firmicutes Clostridia Oscillospiraceae neg SANA Sessile Rod No spore
Oscillibacter ruminantium Rare Possible Commensal Non/unknown Pathogen rumen of cattle, Korea Byrd2020 Firmicutes Clostridia Oscillospiraceae neg SANA Swimming Rod No spore 54.6
Oscillibacter valericigenes 1 Minor Known Commensal Non/unknown Pathogen Homoacetogen. human faeces, and clam gut RajilicStojanovic2014, Chung2019, King2019, Byrd2020, New2022, Zeller2014, Qin2012, Karlsson2013 Firmicutes Clostridia Oscillospiraceae neg SANA Swimming Rod No spore 52.9
Oscillospira guillermondii 1 Rare Possible Commensal Non/unknown Pathogen caecal contents of guinea pigs and rumen. It has also been detected in human faeces Zupancic2012, Salonen2014 Firmicutes Clostridia Oscillospiraceae + ANA Swimming Rod Endospore
Ottowia massiliensis Rare Possible Commensal Non/unknown Pathogen human faeces (healthy) Pseudomonadota Betaproteobacteria Comamonadaceae neg AER Sessile Short Rod No spore 63.5
Oxalobacter formigenes 1 Moderate Possible Commensal Non/unknown Pathogen human faeces, animal faeces, lakes and marine sediments Tyakht2013, RajilicStojanovic2014, Salonen2014, Lagier2016, Rothschild2018, Almeida2019, Forster2019, Byrd2020, De2020, Yang2020, New2022, Chen2020, Dubinkina2017, Hu2019, Jie2017, Zeller2014, Wang2018, Vachida2019, Wang2020a, Minerbi2019, Li2019b, PerezBrocal2015 Proteobacteria Betaproteobacteria Oxalobacteraceae neg SANA Sessile Rod No spore 48-51
Pacaella massiliensis Rare Possible Commensal Non/unknown Pathogen the faeces of an adult patient, France Lagier2016 Synergistetes Synergistia Synergistaceae neg SANA Sessile Rod No spore
Paenarthrobacter aurescens Arthrobacter aurescens 1 Rare Possible Commensal Non/unknown Pathogen soil Lagier2016 Actinobacteria Actinomycetia Micrococcaceae + AER Sessile Rod-coccus cycle No spore 61.5
Paenarthrobacter ilicis Arthrobacter ilicis 1 Non Transient Non/unknown Pathogen Unlikely gut coloniser because this organism doesn't grow at 37C. blighted foliage of some trees Lagier2016 Actinobacteria Actinomycetia Micrococcaceae + AER Swimming Rod-coccus cycle No spore 61.5
Paenibacillus alvei Bacillus alvei 1 Opportunistic in immunocompromised patients, invertebrate pathogen Unlikely Transient Opportunistic Infection Borderline cold mesophile, with optimum growth temp of 28C. Unlikely gut coloniser. a beehive and human faeces RajilicStojanovic2014, Lagier2016 Firmicutes Bacilli Paenibacillaceae + FANA Swimming Rod Endospore 45–47
Paenibacillus amylolyticus Bacillus amylolyticus 1 Rare Possible Commensal Non/unknown Pathogen soil Lagier2016, Byrd2020, PerezBrocal2015 Firmicutes Bacilli Paenibacillaceae + FANA Swimming Rod Endospore 46.3-46.6
Paenibacillus anaericanus Paenibacillus ginsengisoli 1 Rare Possible Commensal Non/unknown Pathogen the gut of an earthworm, Germany Lagier2016 Firmicutes Bacilli Paenibacillaceae neg FANA Swimming Rod Endospore 42.6
Paenibacillus antibioticophila Rare Possible Commensal Non/unknown Pathogen human faeces (woman with multiresistant TB) Dubourg2013, RajilicStojanovic2014, Lagier2016 Firmicutes Bacilli Paenibacillaceae + FANA Swimming Rod Endospore 49.1
Paenibacillus azoreducens 1 Rare Possible Commensal Non/unknown Pathogen Can reduce the azo dye remazol and decolourise it. azo dye waste water Lagier2016 Firmicutes Bacilli Paenibacillaceae vr FANA Swimming Rod Endospore 47
Paenibacillus barcinonensis 1 Unlikely Transient Non/unknown Pathogen Obligate aerobe; unlikely to be a gut coloniser. rice field and human faeces Pfleiderer2013, RajilicStojanovic2014, Lagier2016 Firmicutes Bacilli Paenibacillaceae + SAER Swimming Rod Endospore 45
Paenibacillus barengoltzii 1 Unlikely Transient Opportunistic Pathogen Obligate aerobe; unlikely to be a gut coloniser. spacecraft facility, clinical sources (cerebrospinal fluid, blood - CCUG) and human faeces Pfleiderer2013, RajilicStojanovic2014, Lagier2016, Forster2019 Firmicutes Bacilli Paenibacillaceae + SAER Swimming Rod Endospore
Paenibacillus borealis 1 Unlikely Transient Non/unknown Pathogen Fixes N2. Borderline cold mesophile, with optimum growth temp of 28C. Unlikely gut coloniser. acid humus, Finland Lagier2016 Firmicutes Bacilli Paenibacillaceae neg FANA Swimming Rod Endospore 54
Paenibacillus bouchesdurhonensis Rare Possible Commensal Non/unknown Pathogen human faeces (severe acute marasmus - Pham2017b) Lagier2016 Firmicutes Bacilli Paenibacillaceae neg FANA Swimming Rod Endospore 47.4
Paenibacillus chibensis 1 Unlikely Transient Non/unknown Pathogen Obligate aerobe; unlikely to be a gut coloniser. Hoyles2012 Firmicutes Bacilli Paenibacillaceae + SAER Swimming Rod Endospore 52.5-53.2
Paenibacillus chitinolyticus Bacillus chitinolyticus 1 Rare Possible Commensal Rare Opportunist human faeces, clinical samples (pleural fluid - CCUG) and forest soil from Japan Forster2019 Firmicutes Bacilli Paenibacillaceae vr AER Swimming Rod Endospore 51-53
Paenibacillus cineris 1 Rare Possible Commensal Non/unknown Pathogen soil near a volcano in Antarctica Lagier2016 Firmicutes Bacilli Paenibacillaceae vr FANA Swimming Rod Endospore 51.5
Paenibacillus cookii 1 Unlikely Transient Non/unknown Pathogen Antarctic volcanic soils Hoyles2012 Firmicutes Bacilli Paenibacillaceae vr FANA Swimming Rod Endospore 51.6
Paenibacillus daejeonensis Positive 1 Rare Known Commensal Non/unknown Pathogen alkaline soil and human faeces RajilicStojanovic2014, Lagier2016 Firmicutes Bacilli Paenibacillaceae vr FANA Swimming Rod Endospore 53
Paenibacillus dendritiformis 1 Rare Possible Commensal Non/unknown Pathogen soil Lagier2016 Firmicutes Bacilli Paenibacillaceae neg FANA Swimming Rod Endospore 55
Paenibacillus donghaensis Unlikely Transient Non/unknown Pathogen Can't grow at 35C or above, so unlikely to be a gut coloniser. sea sediment, Korea New2022 Firmicutes Bacilli Paenibacillaceae + FANA Swimming Rod Endospore 53.1
Paenibacillus durus Clostridium durum 1 Rare Possible Commensal Non/unknown Pathogen human faeces, and deep sea sediment Benno1986, RajilicStojanovic2014 Firmicutes Bacilli Paenibacillaceae + FANA Swimming Rod Endospore 50
Paenibacillus faecis Positive Rare Known Commensal Non/unknown Pathogen human faeces (Clermont2015a) Firmicutes Bacilli Paenibacillaceae + FANA Swimming Rod Endospore 52.9
Paenibacillus favisporus 1 Rare Possible Commensal Non/unknown Pathogen Xylanolytic. old cow manure, Spain Lagier2016 Firmicutes Bacilli Paenibacillaceae vr FANA Swimming Rod Endospore 53
Paenibacillus glucanolyticus Bacillus glucanolyticus 1 Rare Possible Commensal Non/unknown Pathogen human faeces, and soil RajilicStojanovic2014, Lagier2016 Firmicutes Bacilli Paenibacillaceae neg FANA Swimming Rod Endospore 48.3-48.6
Paenibacillus graminis 1 Unlikely Transient Non/unknown Pathogen Borderline cold mesophile, with optimum growth temp of 28C. Unlikely gut coloniser. human faeces, rhizosphere, and soil RajilicStojanovic2014 Firmicutes Bacilli Paenibacillaceae + FANA Swimming Rod Endospore 52.1
Paenibacillus ihuae Rare Possible Commensal Non/unknown Pathogen the faeces of an ill patient, France Lagier2016 Firmicutes Bacilli Paenibacillaceae + FANA Swimming Rod Endospore 49.6
Paenibacillus ihumii Rare Possible Commensal Non/unknown Pathogen human faeces (obese patient - Togo2016c) Lagier2016 Firmicutes Bacilli Paenibacillaceae neg FANA Swimming Rod Endospore 50.2
Paenibacillus illinoisensis Positive 1 Rare Known Commensal Non/unknown Pathogen human faeces, and soil RajilicStojanovic2014, Lagier2016 Firmicutes Bacilli Paenibacillaceae + FANA Swimming Rod Endospore 47.6–48.3
Paenibacillus jamilae 1 Rare Possible Commensal Non/unknown Pathogen corn compost, olive-mill waste Lagier2016 Firmicutes Bacilli Paenibacillaceae vr FANA Swimming Rod Endospore 40.6-40.8
Paenibacillus kribbensis 1 Rare Possible Commensal Non/unknown Pathogen soil, Korea Zou2019, Byrd2020 Firmicutes Bacilli Paenibacillaceae vr FANA Swimming Rod Endospore 48
Paenibacillus lactis Positive 1 Rare Known Commensal Non/unknown Pathogen raw and heat-treated milk and human faeces RajilicStojanovic2014, Lagier2016, Qin2012 Firmicutes Bacilli Paenibacillaceae neg FANA Swimming Rod Endospore 51.7
Paenibacillus larvae Bacillus larvae 1 Rare Possible Commensal Non/unknown Pathogen honeybee larva, and causes American foulbrood disease Lagier2016 Firmicutes Bacilli Paenibacillaceae + FANA Swimming Rod Endospore 42-43
Paenibacillus lautus Bacillus lautus Positive 1 Rare Known Commensal Rare Opportunist human faeces, clinical sources (cornea, blood - CCUG), soil and rat ticks RajilicStojanovic2014, Lagier2016, Forster2019 Firmicutes Bacilli Paenibacillaceae vr FANA Swimming Rod Endospore 50–52
Paenibacillus macerans Bacillus macerans 1 Opportunistic in immunocompromised patients Rare Possible Commensal Opportunistic Infection Can fix N2 under anaerobic conditions. composting plant material Lagier2016 Firmicutes Bacilli Paenibacillaceae + FANA Swimming Rod Endospore 52-53
Paenibacillus motobuensis 1 Rare Possible Commensal Possible Pathogen human faeces, clinical sources (blood, tissue - CCUG) and soil from Japan Lagier2016, Forster2019 Firmicutes Bacilli Paenibacillaceae neg FANA Swimming Rod Endospore 47.0
Paenibacillus mucilaginosus Unlikely Transient Non/unknown Pathogen Obligate aerobe; unlikely to be a gut coloniser. soil New2022, Zeller2014 Firmicutes Bacilli Paenibacillaceae neg SAER Sessile Rod Endospore 55.1-56.8
Paenibacillus naphthalenovorans 1 Unlikely Transient Non/unknown Pathogen Can utilise naphthalene as a sole carbon source. Obligate aerobe; unlikely to be a gut coloniser. estuarine sediments and salt marsh rhizosphere Lagier2016 Firmicutes Bacilli Paenibacillaceae + SAER Swimming Rod Endospore 49
Paenibacillus odorifer 1 Unlikely Transient Non/unknown Pathogen Can fix N2 under anaerobic conditions. Colonies produce a fruity odour. Borderline cold mesophile, with optimum growth temp of 28C. Unlikely gut coloniser. wheat roots and vegetable purees Lagier2016, Byrd2020 Firmicutes Bacilli Paenibacillaceae + FANA Swimming Rod Endospore 44
Paenibacillus pabuli Bacillus pabuli 1 Rare Possible Commensal Non/unknown Pathogen soil and fodder Lagier2016 Firmicutes Bacilli Paenibacillaceae + FANA Swimming Rod Endospore 48-50
Paenibacillus pasadenensis 1 Rare Possible Commensal Non/unknown Pathogen an entrance floor Lagier2016 Firmicutes Bacilli Paenibacillaceae + Swimming Rod Endospore
Paenibacillus phocaensis Paenibacillus phoceensis Rare Possible Commensal Non/unknown Pathogen the faeces of a healthy infant, Niger Lagier2016 Firmicutes Bacilli Paenibacillaceae neg FANA Swimming Rod Endospore
Paenibacillus polymyxa Clostridium polymyxa 1 Rare Possible Commensal Rare Opportunist rhizosphere, clinical sources (blood - CCUG) and human faeces Lagier2016 Firmicutes Bacilli Paenibacillaceae neg FANA Swimming Rod Endospore 43-46
Paenibacillus provencensis 1 Opportunistic in immunocompromised patients Rare Possible Commensal Opportunistic Infection human faeces and clinical samples (cerebrospinal fluid) RajilicStojanovic2014, Lagier2016 Firmicutes Bacilli Paenibacillaceae neg AER Swimming Rod Endospore
Paenibacillus pueri Positive Rare Known Commensal Non/unknown Pathogen pu'er tea and human faeces RajilicStojanovic2014, Lagier2016 Firmicutes Bacilli Paenibacillaceae + AER Swimming Rod Endospore 56.6-58.4
Paenibacillus rhizosphaerae Positive 1 Unlikely Transient Non/unknown Pathogen Borderline cold mesophile, with optimum growth temp of 28C. Unlikely gut coloniser. rhizosphere, soil and human faeces RajilicStojanovic2014, Lagier2016 Firmicutes Bacilli Paenibacillaceae + SAER Swimming Rod Endospore 50.9-51.3
Paenibacillus riograndensis Unlikely Transient Non/unknown Pathogen Borderline cold mesophile, with optimum growth temp of 28C. Unlikely gut coloniser. a plant rhizosphere, Brazil New2022 Firmicutes Bacilli Paenibacillaceae vr FANA Swimming Rod Endospore 55.1
Paenibacillus rubinfantis Positive Rare Known Commensal Non/unknown Pathogen human faeces (Pham2017b) that are salty Lagier2016 Firmicutes Bacilli Paenibacillaceae neg FANA Swimming Rod Endospore 53.0
Paenibacillus sabinae 1 Rare Transient Non/unknown Pathogen human faeces, rhizosphere, and soil King2019 Firmicutes Bacilli Paenibacillaceae + FANA Swimming Rod Endospore 51.9-52.9
Paenibacillus senegalensis Bacillus senegalensis Positive Rare Known Commensal Non/unknown Pathogen human faeces Pfleiderer2013, RajilicStojanovic2014, Lagier2016, Forster2019 Firmicutes Bacilli Paenibacillaceae neg FANA Swimming Rod Endospore 48.2
Paenibacillus senegalimassiliensis Positive Rare Known Commensal Non/unknown Pathogen human faeces (Pham2017b) Lagier2016 Firmicutes Bacilli Paenibacillaceae vr FANA Swimming Rod Endospore 49.2
Paenibacillus stellifer 1 Unlikely Transient Non/unknown Pathogen Borderline cold mesophile, with optimum growth temp of 28C. Unlikely gut coloniser. food packaging Lagier2016 Firmicutes Bacilli Paenibacillaceae + FANA Swimming Rod Endospore 55.6
Paenibacillus thiaminolyticus Bacillus thiaminolyticus Positive 1 Opportunistic in immunocompromised patients Unlikely Transient Opportunistic Infection Borderline cold mesophile, with optimum growth temp of 28C. Unlikely gut coloniser. human faeces, honey bee, and clinical sources RajilicStojanovic2014, Lagier2016 Firmicutes Bacilli Paenibacillaceae + FANA Swimming Rod Endospore 52–54
Paenibacillus timonensis 1 Opportunistic in immunocompromised patients Rare Possible Commensal Rare Opportunist clinical sources (blood - CCUG) and human faeces RajilicStojanovic2014, Lagier2016 Firmicutes Bacilli Paenibacillaceae + FANA Swimming Rod Endospore
Paenibacillus tuaregi Positive Rare Known Commensal Non/unknown Pathogen human faeces (Pham2017b) Firmicutes Bacilli Paenibacillaceae vr FANA Swimming Rod Endospore 49.1
Paenibacillus typhae Rare Possible Commensal Non/unknown Pathogen an artificial wetland, China Lagier2016 Firmicutes Bacilli Paenibacillaceae + FANA Swimming Rod Endospore 47.9
Paenibacillus urinalis 1 Opportunistic in immunocompromised patients Rare Possible Commensal Opportunistic Infection urine Lagier2016 Firmicutes Bacilli Paenibacillaceae neg FANA Swimming Rod Endospore
Paenibacillus xylanilyticus 1 Rare Possible Commensal Non/unknown Pathogen Xylanolytic. air samples, Spain Lagier2016 Firmicutes Bacilli Paenibacillaceae + FANA Swimming Rod Endospore 50.5
Paeniclostridium ghonii Clostridium ghonii Rare Possible Commensal Opportunistic Pathogen human faeces, clinical sources, and soil Finegold1974, RajilicStojanovic2014, Lagier2016 Firmicutes Clostridia Clostridiaceae + SANA Swimming Rod Endospore 30.2 20(neg)
Paeniclostridium sordellii Clostridium sordellii 2 Human and animal pathogen Minor Known Commensal Opportunistic Pathogen human faeces, clinical sources (wounds, abscesses), and animal sources Finegold1974, Benno1989, Woodmansey2004, McLaughlin2010, Zupancic2012, Pfleiderer2013, RajilicStojanovic2014, Lagier2016, Zou2019, King2019, Byrd2020, New2022, Hu2019, Vachida2019 Firmicutes Clostridia Peptostreptococcaceae + SANA vr Rod Endospore 26 20(neg)
Paenisporosarcina quisquiliarum Unlikely Transient Non/unknown Pathogen Obligate aerobe; unlikely to be a gut coloniser. human faeces and landfill sites in India Forster2019 Firmicutes Bacilli Planococcaceae + SAER Sessile Rod Endospore 46.0
Paludibacter jiangxiensis Rare Possible Commensal Non/unknown Pathogen a rice paddy field, China De2020 Bacteroidetes Bacteroidia Paludibacteraceae neg SANA Sessile Short Rod No spore 42.8
Paludibacter propionicigenes 1 Unlikely Transient Non/unknown Pathogen Growth is poor at 33C or above, so unlikely to be a gut coloniser. plant residue, Japan New2022 Bacteroidetes Bacteroidia Paludibacteraceae neg SANA Sessile Short Rod No spore 39.3 neg
Paludibaculum fermentans Unlikely Transient Non/unknown Pathogen Optimum growth temp is low (20-28C), so unlikely to be a gut coloniser. littoral wetland, Russia New2022 Acidobacteria Acidobacteriia Bryobacteraceae neg FANA Sessile Rod No spore 60.5
Paludicola psychrotolerans Rare Possible Commensal Non/unknown Pathogen Chitinolytic, growing on chitin as the only carbon source wetland soil, Tibet Firmicutes Clostridia Oscillospiraceae + ANA Rod Endospore 35.4
Pannonibacter phragmitetus 2 Unlikely Transient Rare Opportunist soda lake and clinical sources (blood - CCUG) Yang2020 Proteobacteria Alphaproteobacteria Stappiaceae neg FANA Swimming Rod No spore 64.6
Pantoea agglomerans Enterobacter agglomerans 2 Minor Known Commensal Possible Pathogen aka Erwinia herbicola. Can reduce Fe(III) with acetate as an electron donor. clinical sources (blood, sputum - CCUG) and human faeces (including ulcerative colitis patients) Taylor1985, Dubourg2013, Pfleiderer2013, RajilicStojanovic2014, Lagier2016, Byrd2020, De2020, Vachida2019 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Swimming Rod No spore 49.7-60.6
Pantoea conspicua Rare Possible Commensal Opportunistic Infection blood, France De2020 Proteobacteria Gammaproteobacteria Erwiniaceae neg FANA Swimming Rod No spore 55.7
Pantoea eucalypti Rare Possible Commensal Possible Pathogen eucalyptus dieback. Has also been detected in human faeces (Alkhalil2017) Proteobacteria Gammaproteobacteria Erwiniaceae neg FANA Swimming Rod No spore 54.5
Pantoea rodasii Unlikely Transient Non/unknown Pathogen human faeces and as Eucalypt leaf blight Yang2020 Proteobacteria Betaproteobacteria Erwiniaceae neg FANA Swimming Rod No spore 53.2
Pantoea septica Rare Possible Commensal Known Pathogen human faeces (CCUG), and clinical sources (blood, urine - CCUG) Lagier2016 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Swimming Rod No spore 59.3
Pantoea vagans Rare Possible Commensal Non/unknown Pathogen eucalyptus showing blight, Uganda Zeller2014 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Swimming Short Rod No spore 55.4
Papillibacter cinnamivorans 1 Rare Possible Commensal Non/unknown Pathogen human faeces and an anaerobic digester RajilicStojanovic2014, Salonen2014, Byrd2020 Firmicutes Clostridia Oscillospiraceae + SANA Sessile Rod No spore 56
Parabacteroides bouchesdurhonensis Minor Possible Commensal Non/unknown Pathogen In 15% of Europeans (unseenbio.com). Minor coloniser. human faeces (CCUG, Yimagou2020) Byrd2020 Bacteroidetes Bacteroidia Tannerellaceae neg ANA Sessile Rod No spore 40.8
Parabacteroides chinchillae Minor Possible Commensal Non/unknown Pathogen In 48% of Europeans (unseenbio.com). Minor coloniser. chinchilla (Chincilla lanigera) faeces Byrd2020 Bacteroidetes Bacteroidia Tannerellaceae neg ANA Sessile Rod No spore 42.8 R
Parabacteroides distasonis Bacteroides distasonis 2 Widespread Known Commensal Rare Opportunist human faeces and clinical sources (blood - CCUG) Finegold1974, Holdeman1976, Finegold1977, Benno1984, Benno1986, Benno1989, Mangin2004, MacFarlane2004, Woodmansey2004, Wang2005, McLaughlin2010, Walker2011, Zupancic2012, Pfleiderer2013, Tyakht2013, Nielsen2014, RajilicStojanovic2014, Salonen2014, Browne2016, Lagier2016, Rothschild2018, Zou2019, Chung2019, Forster2019, King2019, Byrd2020, Yang2020, New2022, Chen2020, Dubinkina2017, Hu2019, Jeong2021, Jie2017, Zeller2014, Wang2018, Vachida2019, Wang2020a, Urban2020, Qin2012, Minerbi2019, Moore1995, Li2019b, PerezBrocal2015 Bacteroidetes Bacteroidia Tannerellaceae neg SANA Sessile Rod No spore 44 20(+)
Parabacteroides faecis Rare Possible Commensal Non/unknown Pathogen human faeces (CCUG) Lagier2016, Yang2020 Bacteroidetes Bacteroidia Tannerellaceae neg SANA Sessile Rod No spore 48.1 20(+)
Parabacteroides goldsteinii Bacteroides goldsteinii 2 Moderate Known Commensal Opportunistic Pathogen In 69% of Europeans (unseenbio.com). human faeces and clinical sources (wound, abdominal fluid - CCUG) Pfleiderer2013, RajilicStojanovic2014, Lagier2016, Rothschild2018, Zou2019, Forster2019, Byrd2020, Yang2020, Chen2020, Hu2019, Jeong2021, Vachida2019, Urban2020, Minerbi2019 Bacteroidetes Bacteroidia Tannerellaceae neg SANA Sessile Rod No spore 43 +
Parabacteroides gordonii Minor Possible Commensal Possible Pathogen human faeces, and clinical sources (wound, blood - CCUG) RajilicStojanovic2014, Lagier2016, Zou2019, Forster2019, Byrd2020, Yang2020, Minerbi2019, Li2019b, PerezBrocal2015 Bacteroidetes Bacteroidia Tannerellaceae neg SANA Sessile Rod No spore 44.6 20(+)
Parabacteroides johnsonii Moderate Known Commensal Non/unknown Pathogen human faeces Walker2011, Zupancic2012, Tyakht2013, Nielsen2014, RajilicStojanovic2014, Lagier2016, Rothschild2018, Forster2019, Byrd2020, Yang2020, Chen2020, Dubinkina2017, Hu2019, Jie2017, Vachida2019, Qin2012, Minerbi2019, Karlsson2013 Bacteroidetes Bacteroidia Tannerellaceae neg SANA Sessile Rod No spore 45.2 20(+)
Parabacteroides massiliensis Rare Possible Commensal Non/unknown Pathogen human faeces (Bilen2018e) Lagier2016, Chen2020 Bacteroidetes Bacteroidia Tannerellaceae neg SANA Sessile Rod No spore 42.7
Parabacteroides merdae Bacteroides merdae 1 Opportunistic in immunocompromised patients Widespread Known Commensal Rare Opportunist human faeces (Alkhalil2017) and clinical sources (infection - CCUG) Benno1989, McLaughlin2010, Walker2011, Pfleiderer2013, Tyakht2013, Nielsen2014, RajilicStojanovic2014, Browne2016, Lagier2016, Rothschild2018, Zou2019, Almeida2019, Forster2019, Byrd2020, Yang2020, Chen2020, Dubinkina2017, Hu2019, Jeong2021, Jie2017, Zeller2014, Wang2018, Vachida2019, Wang2020a, Urban2020, Minerbi2019, Karlsson2013 Bacteroidetes Bacteroidia Tannerellaceae neg ANA Sessile Rod No spore 43-46 20(+)
Parabacteroides pacaensis Rare Possible Commensal Non/unknown Pathogen human faeces (healthy) Bacteroidetes Bacteroidia Tannerellaceae neg SANA Sessile Rod No spore 39.2
Parabacteroides pekinense Rare Possible Commensal Non/unknown Pathogen human faeces (healthy) Bacteroidetes Bacteroidia Tannerellaceae neg SANA Swimming Rod No spore 46.5
Parabacteroides provencensis Rare Possible Commensal Non/unknown Pathogen human faeces (healthy) Bacteroidetes Bacteroidia Tannerellaceae neg SANA Sessile Rod No spore 40.8
Parabacteroides timonensis Minor Possible Commensal Non/unknown Pathogen In 12% of Europeans (unseenbio.com). Minor coloniser. human faeces (Bilen2016a) Byrd2020 Bacteroidetes Bacteroidia Tannerellaceae neg SANA Sessile Rod No spore
Paraburkholderia fungorum Burkholderia fungorum 1 Opportunistic in immunocompromised patients Rare Possible Commensal Opportunistic Pathogen human faeces, clinical samples (lung, cerebrospinal fluid - CCUG) and fungi Yang2020 Proteobacteria Betaproteobacteria Burkholderiaceae neg Swimming Rod No spore 62
Paraburkholderia phytofirmans Burkholderia phytofirmans 1 Unlikely Transient Non/unknown Pathogen Inability to grow at 37C suggests this is unlikely to be a gut coloniser. onion roots, Canada Proteobacteria Betaproteobacteria Burkholderiaceae neg FANA Swimming Rod No spore 61.0-62.1
Paracholeplasma brassicae Acholeplasma brassicae 1 Unlikely Transient Non/unknown Pathogen Cholesterol is not required. broccoli New2022 Tenericutes Mollicutes Acholeplasmataceae neg Sessile Coccus No spore 35.5
Paraclostridium benzoelyticum Rare Possible Commensal Non/unknown Pathogen Produces antimicrobials. marine sediment samples, India Firmicutes Clostridia Clostridiaceae + SANA Swimming Rod Endospore 28.3
Paraclostridium bifermentans Clostridium bifermentans 2 Human and animal pathogen Moderate Known Commensal Opportunistic Pathogen human faeces, clinical specimens including wounds, abscesses, and blood, and animal sources Finegold1974, Finegold1977, Taylor1985, Benno1986, Benno1989, MacFarlane2004, Woodmansey2004, Pfleiderer2013, RajilicStojanovic2014, Cassir2015, Lagier2016, Zou2019, Yang2020, New2022, Vachida2019 Firmicutes Clostridia Clostridiaceae + SANA Swimming Rod Endospore 27 20(neg)
Paracoccus aminovorans 1 Rare Possible Commensal Non/unknown Pathogen soil, Japan PerezBrocal2015 Proteobacteria Alphaproteobacteria Rhodobacteraceae neg AER Sessile Coccus No spore 67-68
Paracoccus carotinifaciens 1 Unlikely Transient Non/unknown Pathogen human faeces, and soil McLaughlin2010, RajilicStojanovic2014 Proteobacteria Alphaproteobacteria Rhodobacteraceae neg AER Swimming Coccobacillus No spore 67
Paracoccus denitrificans 1 Rare Possible Commensal Non/unknown Pathogen sewage, soil, manure and mud Hu2019 Proteobacteria Alphaproteobacteria Rhodobacteraceae neg AER Sessile Coccobacillus No spore 65-67
Paracoccus haeundaensis 1 Unlikely Transient Non/unknown Pathogen Borderline cold mesophile, so unlikely to be a gut coloniser. human faeces and a Korean beach Yang2020 Proteobacteria Alphaproteobacteria Rhodobacteraceae neg AER Sessile Rod No spore 66.9
Paracoccus marcusii 1 Non Transient Non/unknown Pathogen Aerobic and poor growth at 35C suggests this not a gut coloniser. an agar plate (contamination) PerezBrocal2015 Proteobacteria Alphaproteobacteria Rhodobacteraceae neg AER Sessile Coccus No spore 66
Paracoccus marinus 1 Unlikely Possible Commensal Non/unknown Pathogen human faeces, and seawater McLaughlin2010, Pandey2012, RajilicStojanovic2014 Proteobacteria Alphaproteobacteria Rhodobacteraceae neg AER Sessile Rod No spore 69
Paracoccus sphaerophysae Unlikely Transient Non/unknown Pathogen Borderline cold mesophile, with optimum growth temp of 28C. Unlikely gut coloniser. root nodules and human faeces Yang2020 Proteobacteria Alphaproteobacteria Rhodobacteraceae neg AER Sessile Rod No spore 67.1
Paracoccus yeei 2 Rare Possible Commensal Opportunistic Pathogen human faeces, bile, and clinical sources (blood, eye, peritonitis - CCUG) McLaughlin2010, RajilicStojanovic2014, Lagier2016 Proteobacteria Alphaproteobacteria Rhodobacteraceae neg AER Sessile Coccus No spore 62
Paraeggerthella hongkongensis Eggerthella hongkongensis 2 Rare Possible Commensal Possible Pathogen human faeces (Alkhalil2017), and clinical sources (blood - CCUG) RajilicStojanovic2014 Actinobacteria Coriobacteriia Eggerthellaceae + SANA Sessile Coccobacillus No spore 61.1-61.8
Parafannyhessea umbonata Olsenella umbonata Unlikely Transient Non/unknown Pathogen Byrd2020, New2022 Actinobacteria Coriobacteriia Atopobiaceae + Micr Sessile No spore 20(+)
Paraliobacillus quinghaiensis Non Transient Non/unknown Pathogen Obligate aerobe and high salt required for optimum growth, so likely a gut non-coloniser. a salt lake, China Lagier2016 Firmicutes Bacilli Bacillaceae + SAER Swimming Rod Endospore 39.5
Paramuribaculum intestinale Rare Possible Commensal Non/unknown Pathogen mouse gastrointestinal tract Byrd2020 Bacteroidetes Bacteroidia Muribaculaceae neg SANA Sessile Rod No spore 53.1
Paraprevotella clara Moderate Possible Commensal Non/unknown Pathogen In 91% of Europeans (unseenbio.com). human faeces Nielsen2014, RajilicStojanovic2014, Lagier2016, Rothschild2018, Zou2019, Byrd2020, Chen2020, Hu2019, Jie2017, Vachida2019, Minerbi2019 Bacteroidetes Bacteroidia Prevotellaceae neg SANA Sessile No spore 48.1
Paraprevotella xylaniphila Moderate Possible Commensal Non/unknown Pathogen human faeces Tyakht2013, RajilicStojanovic2014, Lagier2016, Rothschild2018, Forster2019, Byrd2020, New2022, Chen2020, Dubinkina2017, Hu2019, Jie2017, Zeller2014, Vachida2019, Wang2020a, Minerbi2019 Bacteroidetes Bacteroidia Prevotellaceae neg SANA Sessile Rod No spore 49.0
Pararheinheimera texasensis Rheinheimera texasensis 1 Rare Possible Commensal Non/unknown Pathogen a freshwater lake, United States Forster2019 Proteobacteria Gammaproteobacteria Chromatiaceae neg AER Swimming Rod No spore 48.2
Parascardovia denticolens Bifidobacterium denticolens 1 Opportunistic in immunocompromised patients Rare Possible Commensal Rare Opportunist In 6% of Europeans (unseenbio.com). Rare coloniser. Found in human breast milk (Jeurink2013). dental caries Byrd2020, New2022, Hu2019, Zeller2014, Vachida2019 Actinobacteria Actinomycetia Bifidobacteriaceae + ANA Sessile Rod No spore 55
Parasphingorhabdus flavimaris Sphingopyxis flavimaris 1 Unlikely Transient Non/unknown Pathogen Strictly aerobic and inability to grow at 37C suggests this not a gut coloniser. sea water, Korea Proteobacteria Alphaproteobacteria Sphingomonadaceae neg SAER Swimming Rod No spore 58
Parasporobacterium paucivorans 1 Rare Transient Non/unknown Pathogen human faeces and eutrophic lake sediment Nam2008a, RajilicStojanovic2014, Byrd2020, De2020 Firmicutes Clostridia Lachnospiraceae neg SANA Diplobacilli No spore
Parasutterella excrementihominis Moderate Known Commensal Non/unknown Pathogen human faeces (CCUG) Tyakht2013, Nielsen2014, RajilicStojanovic2014, Lagier2016, Rothschild2018, Zou2019, Forster2019, Byrd2020, De2020, Yang2020, Chen2020, Dubinkina2017, Hu2019, Jie2017, Zeller2014, Wang2018, Vachida2019, Wang2020a, Urban2020, Minerbi2019 Proteobacteria Betaproteobacteria Sutterellaceae neg SANA Sessile Coccobacillus No spore 49.8 +
Parasutterella secunda Rare Possible Commensal Non/unknown Pathogen human faeces RajilicStojanovic2014, Lagier2016, Yang2020, Jeong2021 Proteobacteria Betaproteobacteria Sutterellaceae neg SANA Sessile Coccobacillus No spore 48.2
Paratractidigestivibacter faecalis Olsenella faecalis Rare Possible Commensal Non/unknown Pathogen human faeces (CCUG) Actinobacteria Coriobacteriia Atopobiaceae + SANA Sessile Rod No spore 65.5
Paremcibacter congregatus Emcibacter congregatus Unlikely Transient Non/unknown Pathogen Low maximum growth temperature (30C) and aerobic requirements makes this a very unlikely gut coloniser. coastal sediment, China New2022 Proteobacteria Alphaproteobacteria Emcibacteraceae neg AER Swimming Rod No spore 51.5
Parolsenella catena Rare Possible Commensal Non/unknown Pathogen human faeces (Sakamoto2018c) New2022 Actinobacteria Coriobacteriia Atopobiaceae + SANA Sessile Coccobacillus No spore 68.4 20(+)
Parolsenella massiliensis Libanicoccus massiliensis Rare Possible Commensal Non/unknown Pathogen human faeces (Bilen2017e) Byrd2020, De2020, New2022 Actinobacteria Coriobacteriia Atopobiaceae + ANA Sessile Coccobacillus No spore 65.5 20(+)
Parvibacter caecicola Rare Possible Commensal Non/unknown Pathogen mouse caecum. Has been detected in human faeces (Alkhalil2017) Actinobacteria Coriobacteriia Coriobacteriaceae + SANA Sessile Rod No spore 62.5
Parvimonas micra Peptostreptococcus micros 2 Human and animal pathogen Moderate Known Commensal Opportunistic Pathogen marine sediment, human faeces and clinical sources (abscesses, blood, vagina - CCUG) Finegold1974, Benno1986, Benno1989, Walker2011, Zupancic2012, Tyakht2013, Nielsen2014, RajilicStojanovic2014, Salonen2014, Lagier2016, Zou2019, Forster2019, King2019, Byrd2020, Yang2020, New2022, Dubinkina2017, Jie2017, Zeller2014, Vachida2019 Firmicutes Clostridia Peptoniphilaceae + SANA Coccus No spore 27–28
Pasteurella aerogenes 2 Zoonotic pathogen Rare Possible Commensal Non/unknown Pathogen pigs, including intestines Proteobacteria Gammaproteobacteria Pasteurellaceae neg FANA Sessile Filamentous No spore 41.8
Pasteurella dagmatis 2 Zoonotic pathogen Rare Possible Commensal Opportunistic Pathogen animal bites causing local and systemic infections Lagier2016 Proteobacteria Gammaproteobacteria Pasteurellaceae neg ANA Sessile Coccus No spore 38.9-41.5
Pasteurella multocida Pasteurella canis 2 Zoonotic pathogen Rare Possible Commensal Known Pathogen many animal and human infections Lagier2016, De2020, New2022, Zeller2014 Proteobacteria Gammaproteobacteria Pasteurellaceae neg AER Sessile Coccobacillus No spore 40.8-43.9
Paucilactobacillus oligofermentans Lactobacillus oligofermentans 1 Non Transient Non/unknown Pathogen Unlikely gut coloniser because this organism doesn't grow at 37C. expired food, food packaging Lagier2016 Firmicutes Bacilli Lactobacillaceae + FANA Sessile Pleiomorph rod No spore 35.3-39.9
Paucilactobacillus suebicus Lactobacillus suebicus 1 Unlikely Transient Non/unknown Pathogen fruit mashes, Germany Firmicutes Bacilli Lactobacillaceae + Micr Sessile Rod No spore 40.4
Paucilactobacillus vaccinostercus Lactobacillus vaccinostercus 1 Unlikely Transient Non/unknown Pathogen fermentation products Lagier2016 Firmicutes Bacilli Lactobacillaceae + FANA Sessile Rod No spore 41-44
Paucisalibacillus globulus 1 Unlikely Transient Non/unknown Pathogen Obligate aerobe; unlikely to be a gut coloniser. potting soil Lagier2016 Firmicutes Bacilli Bacillaceae + SAER Swimming Rod Endospore 37.9
Pauljensenia bouchesdurhonensis Minor Isolation and characterisation not yet published. In 22% of Europeans (unseenbio.com). A minor coloniser. Byrd2020 Actinobacteria Actinobacteria Actinomycetaceae + AER Rod
Pauljensenia cellulosilytica Rare Isolation and characterisation not yet published. Byrd2020 Actinobacteria Actinobacteria Actinomycetaceae + AER Rod
Pauljensenia hongkongensis Actinomyces hongkongensis 2 Rare Possible Commensal Opportunistic Pathogen the pus of a patient with pelvic actinomycosis Byrd2020, New2022 Actinobacteria Actinomycetia Actinomycetaceae + SANA Sessile Rod No spore
Pauljensenia keddieii Minor Isolation and characterisation not yet published. In 22% of Europeans (unseenbio.com). A minor coloniser. Byrd2020 Actinobacteria Actinobacteria Sanguibacteraceae + AER Rod
Pauljensenia odontolyticus Rare Isolation and characterisation not yet published. Byrd2020, Chen2020 Actinobacteria Actinobacteria Actinomycetaceae + AER Rod
Pauljensenia turicensis Rare Isolation and characterisation not yet published. Byrd2020 Actinobacteria Actinobacteria Actinomycetaceae + Rod
Pectobacterium wasabiae Pectobacterium carotovorum subsp. wasabiae 1 Plant pathogen Unlikely Transient Non/unknown Pathogen Low optimum temperatures (27-30C) and inability to grow at 37C makes this an unlikely gut coloniser. rotting horseradish, Japan Byrd2020, Zeller2014 Proteobacteria Gammaproteobacteria Pectobacteriaceae neg FANA Swimming Rod No spore 51.4-51.7
Pediococcus acidilactici Positive 1 Opportunistic in immunocompromised patients Rare Transient Opportunistic Pathogen In 1% of Europeans (unseenbio.com). Rare coloniser. A probiotic. food fermentation, human faeces and clinical sources (abscess, fistula, blood) Dubourg2013, Tyakht2013, RajilicStojanovic2014, Lagier2016, Almeida2019, Forster2019, Byrd2020, Dubinkina2017, Zeller2014, Vachida2019 Firmicutes Bacilli Lactobacillaceae + FANA Sessile Diplococci No spore 41-43.5
Pediococcus claussenii 1 Rare Possible Commensal Non/unknown Pathogen Firmicutes Bacilli Lactobacillaceae
Pediococcus damnosus 1 Unlikely Transient Non/unknown Pathogen Can't grow at 31C or above, so unlikely to be a gut coloniser. human faeces, and beer, wine fermentation RajilicStojanovic2014 Firmicutes Bacilli Lactobacillaceae + FANA Sessile Diplococci No spore 37-42
Pediococcus pentosaceus 1 Opportunistic in immunocompromised patients Minor Known Commensal Rare Opportunist Found in human breast milk (Jeurink2013). food fermentation, human faeces and clinical sources (blood, wound) Mangin2004, DalBello2006, RajilicStojanovic2014, Lagier2016, Zou2019, Byrd2020, Zeller2014 Firmicutes Bacilli Lactobacillaceae + FANA Sessile Diplococci No spore 38
Pedobacter cryoconitis 1 Non Transient Non/unknown Pathogen Low optimum temperatures (25C) makes this likely not a gut coloniser. alpine glacier cryoconite, Austria New2022 Proteobacteria Alphaproteobacteria Sphingobacteriaceae neg AER Gliding Rod No spore 43.4
Pedobacter daejeonensis Unlikely Transient Non/unknown Pathogen Borderline cold mesophile, so unlikely to be a gut coloniser. human faeces, and tree trunks McLaughlin2010, RajilicStojanovic2014 Proteobacteria Alphaproteobacteria Sphingobacteriaceae neg AER Sessile Rod No spore 35.5
Pedobacter panaciterrae 1 Unlikely Transient Non/unknown Pathogen Low temperature range (4-30C) for growth makes this an unlikely gut coloniser. soil of a ginseng field, Korea Byrd2020 Bacteroidetes Sphingobacteriia Sphingobacteriaceae neg FANA Sessile Rod No spore 44.2
Pedobacter terricola 1 Non Transient Non/unknown Pathogen Not likely to be a gut coloniser because this organism doesn't grow at 37C. island soil, Korea De2020 Bacteroidetes Sphingobacteriia Sphingobacteriaceae neg AER Sessile Pleiomorph rod No spore 36.8
Pedomicrobium ferrugineum 1 Rare Possible Commensal Non/unknown Pathogen human faeces, soils, and aquatic sources Bik2006, RajilicStojanovic2014 Proteobacteria Alphaproteobacteria Hyphomicrobiaceae neg AER Swimming Filamentous No spore 63-66.8
Pelistega indica Rare Possible Commensal Non/unknown Pathogen human faeces (Prakash2014) Lagier2016 Proteobacteria Betaproteobacteria Alcaligenaceae neg AER Swimming Coccus No spore 42
Pelobacter propionicus 1 Rare Possible Commensal Non/unknown Pathogen Produces butyrate, but only from butanol. anoxic muds of freshwater origin; sewage sludge digesters, Germany Zeller2014 Proteobacteria Deltaproteobacteria Desulfuromonadaceae neg SANA Sessile Rod No spore 57.4
Pelomonas aquatica 1 Rare Possible Commensal Non/unknown Pathogen human faeces Yang2020 Proteobacteria Betaproteobacteria Comamonadaceae neg No spore
Pelomonas puraquae 1 Rare Possible Commensal Non/unknown Pathogen human faeces Yang2020 Proteobacteria Betaproteobacteria Comamonadaceae neg No spore
Pelomonas saccharophila Pseudomonas saccharophila 1 Rare Possible Commensal Non/unknown Pathogen human faeces, and mud RajilicStojanovic2014 Proteobacteria Betaproteobacteria Comamonadaceae neg AER Swimming Rod No spore 69.1
Peptacetobacter hiranonis Clostridium hiranonis Positive 1 Minor Known Commensal Non/unknown Pathogen human faeces Tyakht2013, RajilicStojanovic2014, Lagier2016, Zou2019, Yang2020, New2022, Hu2019, Zeller2014, Vachida2019 Firmicutes Clostridia Clostridiaceae + SANA Sessile Rod - curved Endospore 31.1
Peptoclostridium acidaminophilum Eubacterium acidaminophilum 1 Unlikely Transient Non/unknown Pathogen Co-culture with Desulfovibrio vulgaris allows for fermentation of alanine, L-malate, valine and aspartate/H2. black, anaerobic mud, Germany New2022 Firmicutes Clostridia Peptostreptococcaceae + SANA Swimming Rod No spore 44
Peptococcus niger 2 Human and animal pathogen Rare Known Commensal Opportunistic Pathogen human faeces, and vagina Woodmansey2004, Walker2011, RajilicStojanovic2014, Salonen2014, Lagier2016, Byrd2020 Firmicutes Clostridia Peptococcaceae + SANA Sessile Coccus No spore 50-51
Peptoniphilus asaccharolyticus Peptostreptococcus asaccharolyticus 2 Minor Known Commensal Opportunistic Pathogen human faeces, and clinical sources (vaginal discharge and various abscesses) Moore1974, Finegold1974, Finegold1977, Benno1986, Benno1989, RajilicStojanovic2014, Lagier2016, Byrd2020 Firmicutes Tissierellia Peptoniphilaceae + SANA Sessile Coccus No spore 31-32
Peptoniphilus catoniae Positive Rare Known Commensal Non/unknown Pathogen human faeces (CCUG, Patel2016) Firmicutes Tissierellia Peptoniphilaceae + SANA Sessile Coccus No spore 34.4
Peptoniphilus colimassiliensis Unknown Rare Possible Commensal Non/unknown Pathogen human faeces (healthy) Firmicutes Tissierellia Peptoniphilaceae + SANA Sessile Oval-shaped No spore 48.6
Peptoniphilus duerdenii Rare Transient Rare Opportunist human faeces and clinical sources (vaginal abscess) Byrd2020, Yang2020, Zeller2014, Vachida2019 Firmicutes Tissierellia Peptoniphilaceae + SANA Coccus 33.4
Peptoniphilus gorbachii Rare Possible Commensal Opportunistic Infection clinical sources deGoffau2013, Lagier2016 Firmicutes Tissierellia Peptoniphilaceae + SANA Sessile Coccus No spore
Peptoniphilus grossensis Rare Known Commensal Non/unknown Pathogen human faeces Pfleiderer2013, RajilicStojanovic2014, Lagier2016, Byrd2020 Firmicutes Tissierellia Peptoniphilaceae + SANA Sessile Coccus Endospore 33.9
Peptoniphilus harei Peptostreptococcus harei 2 Minor Known Commensal Opportunistic Pathogen clinical sources (sacral ulcer) and human faeces RajilicStojanovic2014, Lagier2016, Forster2019, Byrd2020, Yang2020, New2022, Jie2017, Zeller2014, Vachida2019 Firmicutes Tissierellia Peptoniphilaceae + SANA Sessile Coccus No spore 25
Peptoniphilus indolicus 2 Opportunistic in immunocompromised patients Rare Known Commensal Opportunistic Pathogen human faeces, animal sources and clinical specimens Benno1984, RajilicStojanovic2014, Byrd2020 Firmicutes Tissierellia Peptoniphilaceae + SANA Sessile Coccus No spore 32-34
Peptoniphilus ivorii 2 Rare Possible Commensal Opportunistic Pathogen Carbohydrates are not fermented. a leg ulcer New2022 Firmicutes Tissierellia Peptoniphilaceae + SANA Sessile Coccus No spore 29
Peptoniphilus koenoeneniae Rare Possible Commensal Rare Opportunist human faeces (Bilen2018e) and clinical sources (vaginal abscess, buttock abscess - CCUG) Lagier2016 Firmicutes Tissierellia Peptoniphilaceae + SANA Sessile Coccus No spore 32.4
Peptoniphilus lacrimalis Peptostreptococcus lacrimalis 2 Minor Known Commensal Opportunistic Pathogen clinical sources (abscess, blood, vagina, eye - CCUG) and human faeces Walker2011, RajilicStojanovic2014, Lagier2016, Byrd2020, Dubinkina2017, Hu2019, Zeller2014, Vachida2019 Firmicutes Tissierellia Peptoniphilaceae + SANA Sessile Coccus No spore 30-31
Peptoniphilus obesi Rare Known Commensal Non/unknown Pathogen human faeces (obese patient) Lagier2016, Forster2019 Firmicutes Tissierellia Peptoniphilaceae + SANA Sessile Coccus No spore 30.1
Peptoniphilus pacaensis Rare Possible Commensal Non/unknown Pathogen the vagina Lagier2016 Firmicutes Tissierellia Peptoniphilaceae + SANA Sessile Coccus No spore 49.4
Peptoniphilus phoceensis Unknown Rare Possible Commensal Non/unknown Pathogen human faeces (healthy, Bilen2018e) Lagier2016, Byrd2020 Firmicutes Tissierellia Peptoniphilaceae + ANA Swimming Coccus No spore 31.2
Peptoniphilus senegalensis Positive Rare Known Commensal Non/unknown Pathogen human faeces RajilicStojanovic2014, Lagier2016, Forster2019, Byrd2020 Firmicutes Tissierellia Peptoniphilaceae + SANA Sessile Coccus No spore 32.2
Peptoniphilus timonensis Positive Rare Known Commensal Non/unknown Pathogen human faeces Pfleiderer2013, RajilicStojanovic2014, Lagier2016, Forster2019 Firmicutes Tissierellia Peptoniphilaceae + SANA Sessile Coccus Endospore 30.7
Peptostreptococcus anaerobius 2 Human and animal pathogen Moderate Known Commensal Opportunistic Pathogen human faeces, vagina and clinical sources (various abscesses) Benno1984, Benno1986, Benno1989, Mangin2004, MacFarlane2004, Wang2005, Nielsen2014, RajilicStojanovic2014, Salonen2014, Lagier2016, Almeida2019, Byrd2020, Yang2020, Dubinkina2017, Hu2019, Jie2017, Zeller2014, Vachida2019 Firmicutes Clostridia Peptostreptococcaceae + SANA Coccus No spore 34-36
Peptostreptococcus russellii Rare Possible Commensal Non/unknown Pathogen pig manure and has been detected in human faeces (Bilen2018e) Lagier2016, Byrd2020 Firmicutes Clostridia Peptostreptococcaceae + SANA Sessile Coccus No spore 35.6
Peptostreptococcus stomatis Negative 2 Minor Transient Opportunistic Pathogen dental disease (oral infections), clinical sources (abscess, blood, tissue - CCUG) and human faeces McLaughlin2010, Walker2011, RajilicStojanovic2014, Byrd2020, Yang2020, Dubinkina2017, Hu2019, Jie2017, Zeller2014, Vachida2019 Firmicutes Clostridia Peptostreptococcaceae + SANA Coccus No spore 36
Peribacillus psychrosaccharolyticus Bacillus psychrosaccharolyticus 1 Unlikely Possible Commensal Non/unknown Pathogen Unlikely gut coloniser because this organism doesn't grow at 37C. soil and lowland marshes Lagier2016 Firmicutes Bacilli Bacillaceae vr FANA Sessile Pleiomorph rod Endospore 43-44
Peribacillus simplex Bacillus simplex Positive 1 Rare Known Commensal Rare Opportunist human faeces, various clinical specimens and soil Hoyles2012, Pfleiderer2013, RajilicStojanovic2014, Lagier2016, Forster2019, Yang2020 Firmicutes Bacilli Bacillaceae vr AER Swimming Rod Endospore 39.5-41.6
Petrimonas mucosa Unlikely Transient Non/unknown Pathogen a reactor fed with pig and cattle faeces Byrd2020, New2022 Bacteroidetes Bacteroidia Dysgonomonadaceae neg FANA Sessile Rod No spore 48.2
Petrimonas sulfuriphila 1 Rare Possible Commensal Non/unknown Pathogen Reduces elemental sulfur. a biodegraded oil reservoir, Canada Lagier2016 Bacteroidetes Bacteroidia Dysgonomonadaceae neg SANA Sessile Rod No spore 40.8
Petrobacter succinatimandens 1 Rare Possible Commensal Non/unknown Pathogen an oil well, Australia PerezBrocal2015 Proteobacteria Hydrogenophilalia Hydrogenophilaceae neg SAER Swimming Rod No spore 58.6
Petrocella atlantisensis Unlikely Transient Non/unknown Pathogen Borderline cold mesophile, so unlikely to be a gut coloniser. rock drills, Mid-Atlantic Ridge New2022 Firmicutes Clostridia Vallitaleaceae + SANA Swimming Rod No spore 37.7
Phascolarctobacterium faecium 1 Minor Known Commensal Non/unknown Pathogen human faeces, and Koala faeces Mangin2004, McLaughlin2010, Walker2011, RajilicStojanovic2014, Salonen2014, Lagier2016, Zou2019, Yang2020, New2022, Jeong2021, Wang2020a, Minerbi2019 Firmicutes Negativicutes Acidaminococcaceae neg SANA Sessile Pleiomorph rod No spore 41-42
Phascolarctobacterium succinatutens Positive Moderate Known Commensal Non/unknown Pathogen human faeces Nielsen2014, RajilicStojanovic2014, Lagier2016, Rothschild2018, Forster2019, Byrd2020, Yang2020, Chen2020, Hu2019, Jie2017, Zeller2014, Wang2018, Vachida2019, Wang2020a, Minerbi2019, LeChatelier2013, Karlsson2013 Firmicutes Negativicutes Acidaminococcaceae neg SANA Sessile Rod No spore 46.5-47.3 neg
Phenylobacterium falsum 1 Unlikely Transient Non/unknown Pathogen Obligate aerobe; unlikely to be a gut coloniser. human faeces and groundwater from Portugal Yang2020 Proteobacteria Alphaproteobacteria Caulobacteraceae neg SAER Sessile Rod No spore 66.9
Phenylobacterium haematophilum Rare Possible Commensal Rare Opportunist human faeces, freshwater, and clinical sources (blood - CCUG) RajilicStojanovic2014 Proteobacteria Alphaproteobacteria Caulobacteraceae neg Filamentous No spore 67.8
Phenylobacterium lituiforme 1 Unlikely Transient Non/unknown Pathogen Grows best with yeast extract as sole source of energy and carbon. a free-flowing bore well, Australia Frank2007 Proteobacteria Alphaproteobacteria Caulobacteraceae neg FANA Swimming Rod No spore 66.5
Phocaeicola barnesiae Bacteroides barnesiae Moderate Possible Commensal Non/unknown Pathogen In 79% of Europeans (unseenbio.com). human faeces Walker2011, Byrd2020, Yang2020, Vachida2019, Urban2020, Li2019b, PerezBrocal2015 Bacteroidetes Bacteroidia bacteroidaceae neg SANA Sessile Rod No spore 46.8
Phocaeicola coprocola Bacteroides coprocola 1 Widespread Known Commensal Non/unknown Pathogen In 95% of Europeans (unseenbio.com). human faeces McLaughlin2010, Walker2011, Zupancic2012, Tyakht2013, Nielsen2014, RajilicStojanovic2014, Lagier2016, Rothschild2018, Zou2019, Byrd2020, Chen2020, Dubinkina2017, Hu2019, Jeong2021, Jie2017, Zeller2014, Vachida2019, Wang2020a, Urban2020, Qin2012, Minerbi2019, Karlsson2013 Bacteroidetes Bacteroidia Bacteroidaceae neg SANA Sessile Rod No spore 42.4 +
Phocaeicola coprophilus Bacteroides coprophilus 1 Widespread Known Commensal Non/unknown Pathogen In 87% of Europeans (unseenbio.com). human faeces (CCUG) Zupancic2012, Tyakht2013, Nielsen2014, RajilicStojanovic2014, Lagier2016, Rothschild2018, Zou2019, Forster2019, Byrd2020, Yang2020, New2022, Dubinkina2017, Hu2019, Jie2017, Zeller2014, Vachida2019, Wang2020a, Urban2020, Minerbi2019, Li2019b, PerezBrocal2015 Bacteroidetes Bacteroidia Bacteroidaceae neg ANA Sessile Rod No spore 44.2-45.2 +
Phocaeicola dorei Bacteroides dorei Mixed 1 Widespread Known Commensal Rare Opportunist human faeces (Alkhalil2017) and clinical sources (blood - CCUG) McLaughlin2010, PerisBondia2011, Walker2011, Zupancic2012, Tyakht2013, Nielsen2014, RajilicStojanovic2014, Lagier2016, Rothschild2018, Zou2019, Almeida2019, Forster2019, King2019, Byrd2020, Yang2020, New2022, Chen2020, Dubinkina2017, Hu2019, Jeong2021, Jie2017, Wang2018, Vachida2019, Wang2020a, Urban2020, Minerbi2019, LeChatelier2013, Karlsson2013 Bacteroidetes Bacteroidia Bacteroidaceae neg ANA Sessile Rod No spore 43 +
Phocaeicola massiliensis Bacteroides massiliensis 1 Opportunistic in immunocompromised patients Minor Possible Commensal Opportunistic Pathogen clinical sources (blood, brain abscess - CCUG) and human faeces Walker2011, Zupancic2012, RajilicStojanovic2014, Lagier2016, Rothschild2018, Zou2019, Byrd2020, Hu2019, Jie2017, Vachida2019, Urban2020, Minerbi2019 Bacteroidetes Bacteroidia Bacteroidaceae neg SANA Sessile Rod No spore 49 +
Phocaeicola paurosaccharolyticus Bacteroides paurosaccharolyticus Rare Possible Commensal Non/unknown Pathogen a cow waste methane generator, Japan Byrd2020, De2020, Urban2020 Bacteroidetes Bacteroidia Bacteroidaceae neg SANA Sessile Rod No spore 41.0 neg
Phocaeicola plebeius Bacteroides plebeius 1 Widespread Known Commensal Non/unknown Pathogen human faeces Walker2011, Tyakht2013, Nielsen2014, RajilicStojanovic2014, Salonen2014, Lagier2016, Rothschild2018, Zou2019, Forster2019, Byrd2020, De2020, Yang2020, Chen2020, Dubinkina2017, Hu2019, Jeong2021, Jie2017, Zeller2014, Wang2018, Vachida2019, Wang2020a, Urban2020, Minerbi2019, Li2019b, Karlsson2013, PerezBrocal2015 Bacteroidetes Bacteroidia Bacteroidaceae neg SANA Sessile Rod No spore 43.9 +
Phocaeicola salanitronis Bacteroides salanitronis Minor Known Commensal Non/unknown Pathogen In 34% of Europeans (unseenbio.com). Minor coloniser. caeca of chickens and human faeces Byrd2020, New2022, Jie2017, Zeller2014, Vachida2019, Urban2020 Bacteroidetes Bacteroidia Bacteroidaceae neg SANA Sessile Rod No spore 46.9 +
Phocaeicola sartorii Bacteroides sartorii Moderate Possible Commensal Non/unknown Pathogen In 99% of Europeans (unseenbio.com). human faeces and mice caeca Byrd2020, Yang2020, Urban2020, Minerbi2019 Bacteroidetes Bacteroidia Bacteroidaceae neg SANA Sessile Rod No spore 41.5 0.5(+)
Phocaeicola vulgatus Bacteroides vulgatus 1 Opportunistic in immunocompromised patients Widespread Known Commensal Opportunistic Infection human faeces (CCUG) and clinical sources (blood, lymph node, abscess - CCUG) Finegold1974, Holdeman1976, Finegold1977, Benno1984, Benno1986, Benno1989, Mangin2004, MacFarlane2004, Woodmansey2004, McLaughlin2010, Walker2011, Zupancic2012, deGoffau2013, Pfleiderer2013, Tyakht2013, Nielsen2014, RajilicStojanovic2014, Salonen2014, Browne2016, Lagier2016, Rothschild2018, Zou2019, Almeida2019, Forster2019, King2019, Byrd2020, De2020, Yang2020, New2022, Chen2020, Dubinkina2017, Hu2019, Jeong2021, Jie2017, Zeller2014, Wang2018, Vachida2019, Wang2020a, Urban2020, Minerbi2019, Moore1995, LeChatelier2013, Karlsson2013 Bacteroidetes Bacteroidia Bacteroidaceae neg SANA Sessile Rod No spore 40-42 20(+)
Phocea massiliensis Minor Possible Commensal Non/unknown Pathogen In 61% of Europeans (unseenbio.com). Minor coloniser. human faeces (Bilen2018e) and brain abscess Lagier2016, Byrd2020, Minerbi2019 Firmicutes Clostridia Oscillospiraceae neg SANA Swimming Rod No spore
Phoenicibacter congonensis Phoenicibacter massiliensis Rare Possible Commensal Non/unknown Pathogen human faeces (Bilen2018d) New2022 Actinobacteria Coriobacteriia Eggerthellaceae + SANA Sessile Coccobacillus No spore 43.4
Phyllobacterium myrsinacearum 1 Rare Possible Commensal Non/unknown Pathogen human faeces RajilicStojanovic2014, Yang2020 Proteobacteria Alphaproteobacteria Phyllobacteriaceae neg AER Swimming Rod No spore 60.3-61.3
Pigmentiphaga kullae 1 Rare Possible Commensal Non/unknown Pathogen human faeces (CCUG) and soil Proteobacteria Betaproteobacteria Alcaligenaceae neg AER Swimming Rod No spore 68.5
Planococcus massiliensis Unlikely Transient Non/unknown Pathogen Obligate aerobe; unlikely to be a gut coloniser. human faeces Lagier2016 Firmicutes Bacilli Caryophanaceae + SAER Swimming Rod No spore 46.0
Planococcus rifietoensis 1 Unlikely Transient Non/unknown Pathogen Unlikely gut coloniser because its optimum growth is with high salt. an algal mat and human faeces RajilicStojanovic2014, Lagier2016, Yang2020 Firmicutes Bacilli Caryophanaceae + AER Swimming Diplococci No spore 47.9
Planomicrobium chinense 1 Unlikely Transient Non/unknown Pathogen Obligate aerobe; unlikely to be a gut coloniser. marine sediment and human faeces RajilicStojanovic2014, Lagier2016, Yang2020 Firmicutes Bacilli Caryophanaceae + SAER Swimming Coccus No spore 34.8
Planomicrobium koreense Planococcus koreense 1 Unlikely Transient Non/unknown Pathogen Obligate aerobe; unlikely to be a gut coloniser. human faeces and Korean fermented food Yang2020 Firmicutes Bacilli Planococcaceae + SAER Swimming Rod No spore 47
Planomicrobium okeanokoites Planococcus okeanokoites 1 Unlikely Transient Non/unknown Pathogen Obligate aerobe; unlikely to be a gut coloniser. human faeces, blood and marine mud Lagier2016, Yang2020 Firmicutes Bacilli Planococcaceae + SAER Swimming Rod No spore 46
Plesiomonas shigelloides 2 Human and animal pathogen Rare Possible Commensal Opportunistic Pathogen human faeces, and aquatic sources RajilicStojanovic2014, Lagier2016, Byrd2020, Yang2020, Hu2019, PerezBrocal2015 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Swimming Rod No spore 51
Pluralibacter gergoviae Enterobacter gergoviae 2 Rare Transient Opportunistic Pathogen In 6% of Europeans (unseenbio.com). Rare coloniser. clinical sources (sputum, urine, blood - CCUG) and human faeces (CCUG) Byrd2020 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Swimming Rod No spore 60
Pontibacillus litoralis Rare Possible Commensal Non/unknown Pathogen a sea anemone, China Byrd2020 Firmicutes Bacilli Bacillaceae + FANA Swimming Rod Endospore 41.3
Porphyromonas asaccharolytica Bacteroides asaccharolyticus 2 Human and animal pathogen Minor Known Commensal Known Pathogen human faeces and pelvic abscess RajilicStojanovic2014, Lagier2016, Almeida2019, Forster2019, King2019, Byrd2020, New2022, Chen2020, Hu2019, Jie2017, Zeller2014, Vachida2019 Bacteroidetes Bacteroidia Porphyromonadaceae neg SANA Sessile Coccobacillus No spore 52-54
Porphyromonas bennonis Rare Possible Commensal Opportunistic Pathogen human faeces (Bilen2018e) and clinical sources (shoulder abscess - CCUG) Lagier2016, Byrd2020, Yang2020, Chen2020, Hu2019, Vachida2019 Bacteroidetes Bacteroidia Porphyromonadaceae neg SANA Rod No spore 58 neg
Porphyromonas cangingivalis 2 Animal pathogen Unlikely Transient Non/unknown Pathogen periodontal pockets of dogs Byrd2020, New2022 Bacteroidetes Bacteroidia Porphyromonadaceae neg ANA Sessile Rod No spore 55
Porphyromonas canoris 2 Human and animal pathogen Rare Possible Commensal Non/unknown Pathogen subgingival pockets of dogs Byrd2020 Bacteroidetes Bacteroidia Porphyromonadaceae neg SANA Sessile Short Rod No spore 49-51
Porphyromonas crevioricanis Porphyromonas cansulci 2 Animal pathogen Unlikely Transient Non/unknown Pathogen Asaccharolytic. Byrd2020, New2022 Bacteroidetes Bacteroidia Porphyromonadaceae neg SANA Sessile Short Rod No spore 44-45.9
Porphyromonas endodontalis Bacteroides endodontalis 2 Minor Possible Commensal Opportunistic Pathogen dental disease and human faeces Walker2011, RajilicStojanovic2014, Byrd2020, Yang2020, Zeller2014, Vachida2019, PerezBrocal2015 Bacteroidetes Bacteroidia Porphyromonadaceae neg SANA Sessile Coccobacillus No spore 49-51
Porphyromonas gingivalis Bacteroides gingivalis 2 Human and animal pathogen Unlikely Possible Commensal Known Pathogen Pathogenic; unlikely to be a coloniser in a healthy microbiome. dental disease and human faeces Bik2006, Tyakht2013, RajilicStojanovic2014, King2019, Byrd2020, New2022, Dubinkina2017, Zeller2014, Vachida2019 Bacteroidetes Bacteroidia Porphyromonadaceae neg SANA Sessile Coccobacillus No spore 46-48
Porphyromonas levii Bacteroides levii 2 Human and animal pathogen Rare Possible Commensal Non/unknown Pathogen cattle Byrd2020 Bacteroidetes Bacteroidia Porphyromonadaceae neg SANA Sessile Coccobacillus No spore 46-48 S(20)
Porphyromonas macacae Bacteroides macacae 2 Human and animal pathogen Rare Possible Commensal Opportunistic Pathogen oral cavities, subcutaneous abscesses, and pyothoraxes of animals, including cats and monkeys Byrd2020 Bacteroidetes Bacteroidia Porphyromonadaceae neg ANA Sessile Coccobacillus No spore 43-44
Porphyromonas somerae 2 Minor Possible Commensal Rare Opportunist human faeces and leg ulcer Walker2011, Pfleiderer2013, RajilicStojanovic2014, Lagier2016, Byrd2020, Hu2019, Jie2017, Vachida2019 Bacteroidetes Bacteroidia Porphyromonadaceae neg SANA Sessile Rod No spore 47.8
Porphyromonas uenonis 2 Minor Possible Commensal Opportunistic Pathogen clinical sources (infection, ulcer, abscess - CCUG) and human faeces RajilicStojanovic2014, Lagier2016, Forster2019, Byrd2020, Dubinkina2017, Zeller2014, Vachida2019 Bacteroidetes Bacteroidia Porphyromonadaceae neg SANA Sessile Rod No spore 52.5 neg
Pragia fontium 1 Rare Possible Commensal Non/unknown Pathogen human faeces (CCUG), and aquatic sources Proteobacteria Gammaproteobacteria Budviciaceae neg FANA Swimming Rod No spore 46-47
Prevotella albensis 2 Rare Possible Commensal Opportunistic Pathogen human faeces, and Sheep rumen RajilicStojanovic2014, Lagier2016, Byrd2020 Bacteroidetes Bacteroidia Prevotellaceae neg ANA Sessile Rod No spore 39-43 20(neg)
Prevotella amnii 1 Opportunistic in immunocompromised patients Rare Possible Commensal Opportunistic Infection human faeces, and human amniotic fluid RajilicStojanovic2014, Byrd2020, Jeong2021, Zeller2014, Vachida2019 Bacteroidetes Bacteroidia Prevotellaceae neg ANA Sessile Rod No spore 36.6 20(neg)
Prevotella aurantiaca Rare Possible Commensal Opportunistic Infection periodontal pockets of a patient with periodontitis Urban2020 Bacteroidetes Bacteroidia Prevotellaceae neg SANA Sessile Rod No spore 39.7 S(20)
Prevotella baroniae 2 Rare Possible Commensal Opportunistic Pathogen human oral cavity, blood and human faeces Forster2019, Byrd2020, Yang2020, Vachida2019 Bacteroidetes Bacteroidia Prevotellaceae neg SANA Sessile Coccus No spore 52 20(neg)
Prevotella bergensis 2 Moderate Possible Commensal Opportunistic Pathogen In 86% of Europeans (unseenbio.com). human faeces and clinical sources (soft tissue abscess - CCUG) Lagier2016, Byrd2020, Yang2020, Zeller2014, Urban2020 Bacteroidetes Bacteroidia Prevotellaceae neg SANA Sessile Rod No spore 48 20(neg)
Prevotella bivia Bacteroides bivius 2 Human and animal pathogen Moderate Known Commensal Opportunistic Pathogen the vagina microbiome, clinical sources (abscess, urine - CCUG) and human faeces Benno1984, Benno1989, MacFarlane2004, McLaughlin2010, Walker2011, RajilicStojanovic2014, Lagier2016, Rothschild2018, Forster2019, Byrd2020, Yang2020, Chen2020, Hu2019, Zeller2014, Vachida2019 Bacteroidetes Bacteroidia Prevotellaceae neg SANA Sessile Rod No spore 40 20(neg)
Prevotella brevis Bacteroides ruminicola subsp. brevis 2 Human and animal pathogen Minor Possible Commensal Opportunistic Pathogen human faeces, and bovine rumen Finegold1974, Holdeman1976, Finegold1977, RajilicStojanovic2014, Lagier2016, Byrd2020, Urban2020 Bacteroidetes Bacteroidia Prevotellaceae neg ANA Sessile Oval-shaped No spore 45-52 20(neg)
Prevotella bryantii 2 Rare Possible Commensal Opportunistic Pathogen human faeces, and rumen RajilicStojanovic2014, Byrd2020, Dubinkina2017, Zeller2014, Urban2020 Bacteroidetes Bacteroidia Prevotellaceae neg ANA Sessile Oval-shaped No spore 40-43 20(neg)
Prevotella buccae Bacteroides buccae 2 Human and animal pathogen Minor Known Commensal Opportunistic Pathogen human faeces, dental disease, and oral flora Benno1986, Benno1989, McLaughlin2010, Walker2011, RajilicStojanovic2014, Lagier2016, Almeida2019, Chung2019, Byrd2020, Dubinkina2017, Zeller2014, Vachida2019, Wang2020a, Minerbi2019 Bacteroidetes Bacteroidia Prevotellaceae neg ANA Sessile Rod No spore 52 20(neg)
Prevotella buccalis Bacteroides buccalis 2 Minor Possible Commensal Rare Opportunist human faeces (Bilen2018e), dental plaque and umbilical drainage Lagier2016, Byrd2020, Yang2020, Hu2019, Zeller2014, Vachida2019, Urban2020 Bacteroidetes Bacteroidia Prevotellaceae neg SANA Sessile Rod No spore 45-46
Prevotella conceptionensis Rare Possible Commensal Rare Opportunist human faeces RajilicStojanovic2014, Lagier2016, Byrd2020, Urban2020 Bacteroidetes Bacteroidia Prevotellaceae neg ANA Sessile Pleiomorphic No spore 20(neg)
Prevotella copri 1 Widespread Known Commensal Non/unknown Pathogen human faeces (CCUG) McLaughlin2010, Walker2011, Zupancic2012, Tyakht2013, Nielsen2014, RajilicStojanovic2014, Browne2016, Lagier2016, Rothschild2018, Zou2019, Forster2019, Byrd2020, De2020, Yang2020, New2022, Chen2020, Dubinkina2017, Hu2019, Jie2017, Zeller2014, Wang2018, Vachida2019, Wang2020a, Urban2020, Minerbi2019, Li2019b, Karlsson2013, PerezBrocal2015 Bacteroidetes Bacteroidia Prevotellaceae neg SANA Sessile Rod No spore 44-45 20(neg)
Prevotella corporis Bacteroides corporis 2 Moderate Possible Commensal Opportunistic Pathogen In 99% of Europeans (unseenbio.com). clinical sources (cervical swab - CCUG) and human faeces Walker2011, RajilicStojanovic2014, Lagier2016, Byrd2020, Yang2020, Urban2020 Bacteroidetes Bacteroidia Prevotellaceae neg SANA Sessile Coccus No spore 43-46 20(neg)
Prevotella dentalis Mitsuokella dentalis 1 Opportunistic in immunocompromised patients Minor Possible Commensal Opportunistic Pathogen human faeces and dental disease Forster2019, King2019, Yang2020, New2022, Zeller2014, Vachida2019, Urban2020 Bacteroidetes Bacteroidia Prevotellaceae neg SANA Sessile Oval-shaped No spore 56-60 20(neg)
Prevotella dentasini Rare Possible Commensal Non/unknown Pathogen oral cavity of donkeys Byrd2020 Bacteroidetes Bacteroidia Prevotellaceae neg SANA Sessile Rod No spore 50.2 S(20)
Prevotella denticola Bacteroides denticola 2 Human and animal pathogen Minor Possible Commensal Opportunistic Pathogen oral cavity and human faeces Bik2006, Walker2011, RajilicStojanovic2014, Chung2016, Lagier2016, Almeida2019, King2019, Byrd2020, New2022, Zeller2014, Vachida2019 Bacteroidetes Bacteroidia Prevotellaceae neg ANA Sessile Rod No spore 49-51 20(neg)
Prevotella disiens Bacteroides disiens 2 Minor Possible Commensal Opportunistic Pathogen clinical sources (abscess, vagina, wound - CCUG) and human faeces McLaughlin2010, RajilicStojanovic2014, Lagier2016, Zou2019, Byrd2020, Yang2020, Dubinkina2017, Hu2019, Jeong2021, Jie2017, Zeller2014, Vachida2019, Urban2020 Bacteroidetes Bacteroidia Prevotellaceae neg ANA Sessile Rod No spore 40-42 20(neg)
Prevotella enoeca 1 Opportunistic in immunocompromised patients Rare Possible Commensal Opportunistic Infection oral cavity and human faeces Woodmansey2004, RajilicStojanovic2014, Lagier2016, Byrd2020, De2020, New2022 Bacteroidetes Bacteroidia Prevotellaceae neg ANA Sessile Filamentous No spore 47 20(neg)
Prevotella falsenii Rare Isolation and characterisation not yet published. Byrd2020 Bacteroidetes Bacteroidia Prevotellaceae
Prevotella fusca Unlikely Transient Non/unknown Pathogen the oral cavity Byrd2020, New2022 Bacteroidetes Bacteroidia Prevotellaceae neg SANA Sessile Rod No spore 43 20(neg)
Prevotella herbatica Unlikely Transient Non/unknown Pathogen a methanogenic reactor plant residue New2022 Bacteroidetes Bacteroidia Prevotellaceae neg SANA Sessile Rod No spore 37.5
Prevotella histicola Rare Possible Commensal Non/unknown Pathogen the oral cavity Byrd2020, Vachida2019 Bacteroidetes Bacteroidia Prevotellaceae neg SANA Sessile Rod No spore 43 S(20)
Prevotella ihumii Rare Possible Mutualist Non/unknown Pathogen a stool specimen of a healthy adult Byrd2020, Urban2020 Bacteroidetes Bacteroidia Prevotellaceae neg SANA Sessile Rod No spore 42.1
Prevotella intermedia Bacteroides intermedius 2 Human and animal pathogen Minor Possible Commensal Opportunistic Pathogen human faeces, clinical sources (blood, abscess - CCUG), and dental disease Benno1984, Benno1989, Bik2006, Walker2011, RajilicStojanovic2014, Lagier2016, King2019, Byrd2020, De2020, New2022, Vachida2019, Urban2020 Bacteroidetes Bacteroidia Prevotellaceae neg ANA Sessile Rod No spore 41-44 20(neg)
Prevotella jejuni Rare Possible Commensal Non/unknown Pathogen the jejunum of a child with coeliac disease Lagier2016, Byrd2020, New2022, Urban2020 Bacteroidetes Bacteroidia Prevotellaceae neg SANA Sessile Rod No spore 41.7
Prevotella lascolaii Minor Possible Commensal Possible Pathogen In 70% of Europeans (unseenbio.com). Minor coloniser. a patient suffering from BV Byrd2020 Bacteroidetes Bacteroidia Prevotellaceae neg SANA Sessile Coccobacillus No spore 48.7
Prevotella loescheii Bacteroides loescheii 2 Rare Possible Commensal Opportunistic Pathogen human faeces Woodmansey2004, RajilicStojanovic2014, Lagier2016, Byrd2020 Bacteroidetes Bacteroidia Prevotellaceae neg SANA Sessile Rod No spore 46.6 20(neg)
Prevotella maculosa 1 Opportunistic in immunocompromised patients Rare Possible Commensal Possible Pathogen the oral cavity Byrd2020, Urban2020 Bacteroidetes Bacteroidia Prevotellaceae neg SANA Sessile Rod No spore 48
Prevotella marseillensis Rare Possible Commensal Non/unknown Pathogen human faeces (Clostridioides difficile infection) Bacteroidetes Bacteroidia Prevotellaceae neg ANA Sessile Coccobacillus No spore 45.8
Prevotella marshii 2 Rare Possible Commensal Opportunistic Pathogen an oral cavity Byrd2020, De2020, Zeller2014 Bacteroidetes Bacteroidia Prevotellaceae neg SANA Sessile Rod No spore 47.5 20(neg)
Prevotella melaninogenica Bacteroides melaninogenicus 2 Human and animal pathogen Moderate Known Commensal Opportunistic Pathogen In 86% of Europeans (unseenbio.com). dental, clinical sources (wound - CCUG) and human faeces Wang2005, Bik2006, Zupancic2012, RajilicStojanovic2014, Salonen2014, Lagier2016, King2019, Byrd2020, New2022, Dubinkina2017, Zeller2014, Vachida2019, PerezBrocal2015 Bacteroidetes Bacteroidia Prevotellaceae neg ANA Sessile Rod No spore 36-40 20(neg)
Prevotella merdae Rare Possible Commensal Non/unknown Pathogen human faeces (healthy) Bacteroidetes Bacteroidia Prevotellaceae neg ANA Sessile Rod No spore 44.4
Prevotella micans Rare Possible Commensal Opportunistic Infection an oral cavity Forster2019, De2020 Bacteroidetes Bacteroidia Prevotellaceae neg SANA Sessile Rod No spore 46 20(neg)
Prevotella multiformis 2 Rare Possible Commensal Non/unknown Pathogen subgingival plaque Byrd2020, Zeller2014, Vachida2019 Bacteroidetes Bacteroidia Prevotellaceae neg SANA Sessile Rod No spore 51.1 S(20)
Prevotella multisaccharivorax 2 Minor Possible Commensal Opportunistic Pathogen In 14% of Europeans (unseenbio.com). Minor coloniser. subgingival dental plaque from patients with periodontitis Forster2019, Byrd2020, Zeller2014, Vachida2019, Urban2020 Bacteroidetes Bacteroidia Prevotellaceae neg SANA Sessile Rod No spore 48.5-49.9
Prevotella nanceiensis 2 Rare Possible Commensal Possible Pathogen clinical sources (blood, bacteremia - CCUG) and human faeces RajilicStojanovic2014, Lagier2016, Byrd2020, Vachida2019 Bacteroidetes Bacteroidia Prevotellaceae neg SANA Sessile Coccobacillus No spore 42.6 20(neg)
Prevotella nigrescens 2 Minor Possible Commensal Opportunistic Pathogen clinical sources (dental disease, wound - CCUG) and human faeces MacFarlane2004, Bik2006, RajilicStojanovic2014, Lagier2016, Byrd2020, De2020, Zeller2014, Vachida2019, Urban2020 Bacteroidetes Bacteroidia Prevotellaceae neg SANA Sessile Rod No spore 40-44 20(neg)
Prevotella oralis Bacteroides oralis 2 Human and animal pathogen Minor Known Commensal Known Pathogen human faeces, clinical sources (blood, drainage fluid - CCUG), oral flora, and chicken gut Finegold1974, Benno1984, Benno1986, Benno1989, Walker2011, Bik2006, RajilicStojanovic2014, Salonen2014, Lagier2016, Forster2019, Byrd2020, Zeller2014, Vachida2019, Urban2020 Bacteroidetes Bacteroidia Prevotellaceae neg ANA Sessile Rod No spore 42-46 20(neg)
Prevotella oris Bacteroides oris 2 Moderate Possible Commensal Opportunistic Pathogen In 94% of Europeans (unseenbio.com). the gingival sulcus of a patient with periodontitis. Also, from clinical sources (systemic infections) and chicken intestines MacFarlane2004, Bik2006, Lagier2016, Byrd2020, New2022, Zeller2014, Vachida2019, Urban2020 Bacteroidetes Bacteroidia Prevotellaceae neg SANA Sessile Rod No spore 42-46 10(d(neg))
Prevotella oryzae Xylanibacter oryzae 1 Unlikely Transient Non/unknown Pathogen Growth at 37C is significantly delayed. This is an unlikely gut coloniser rice-plant residue in flooded rice-field soil in Japan Byrd2020 Bacteroidetes Bacteroidia Prevotellaceae neg SANA Sessile Filamentous No spore 43.6 S
Prevotella oulorum Bacteroides oulorum 1 Rare Possible Commensal Non/unknown Pathogen human faeces, dental disease, and oral flora Bik2006, Zupancic2012, RajilicStojanovic2014, Byrd2020, Vachida2019 Bacteroidetes Bacteroidia Prevotellaceae neg SANA Sessile Rod No spore 45-46 20(neg)
Prevotella pallens 2 Rare Possible Commensal Opportunistic Pathogen oral flora and human faeces Bik2006, RajilicStojanovic2014, Lagier2016, Byrd2020, Zeller2014, Vachida2019 Bacteroidetes Bacteroidia Prevotellaceae neg SANA Sessile Rod No spore 37.4 20(neg)
Prevotella paludivivens 1 Rare Possible Commensal Non/unknown Pathogen Haemin significantly stimulates growth. Growth at 37C is delayed compared with that at 30C. irrigated rice-field soil in Japan Byrd2020 Bacteroidetes Bacteroidia Prevotellaceae neg SANA Sessile Short Rod No spore 39.2 S
Prevotella phocaeensis Rare Possible Commensal Non/unknown Pathogen human faeces (Afouda2017a) Urban2020 Bacteroidetes Bacteroidia Prevotellaceae neg SANA Sessile Rod No spore 44.6 20(neg)
Prevotella pleuritidis 1 Opportunistic in immunocompromised patients Rare Possible Commensal Opportunistic Infection pleural fluid from a patient with suppurative pleuritis Vachida2019 Bacteroidetes Bacteroidia Prevotellaceae neg SANA Sessile Rod No spore 45.4 S(20)
Prevotella rara Rare Possible Commensal Non/unknown Pathogen human faeces (Efimov2018) Bacteroidetes Bacteroidia Prevotellaceae neg SANA Sessile Rod No spore 45.7 20(neg)
Prevotella rectalis Rare Possible Commensal Non/unknown Pathogen the rectum Bacteroidetes Bacteroidia Prevotellaceae neg SANA Sessile Rod No spore 43.3
Prevotella ruminicola Bacteroides ruminicola 2 Minor Known Commensal Opportunistic Pathogen human faeces, rumen, and chicken gut Finegold1974, Holdeman1976, Finegold1977, Woodmansey2004, Walker2011, RajilicStojanovic2014, Salonen2014, Lagier2016, King2019, Byrd2020, New2022, Zeller2014, Urban2020 Bacteroidetes Bacteroidia Prevotellaceae neg SANA Sessile Rod No spore 45-52 20(neg)
Prevotella saccharolytica Rare Possible Commensal Non/unknown Pathogen the oral cavity Byrd2020, Urban2020 Bacteroidetes Bacteroidia Prevotellaceae neg SANA Sessile Rod No spore 44 S(20)
Prevotella salivae 1 Opportunistic in immunocompromised patients Rare Possible Commensal Opportunistic Infection Homoacetogen. human faeces and saliva of patient with chronic periodontitis Tyakht2013, Lagier2016, Forster2019, Byrd2020, Zeller2014, Vachida2019 Bacteroidetes Bacteroidia Prevotellaceae neg SANA Sessile Rod No spore 41.3 20(neg)
Prevotella scopos Unlikely Transient Non/unknown Pathogen the oral cavity Byrd2020, New2022 Bacteroidetes Bacteroidia Prevotellaceae neg SANA Sessile Rod No spore 41
Prevotella seregens Rare Is 'Prevotella seregens' actually Hallella seregens (Moore and Moore)? No record of Prevotella seregens published. Byrd2020 Bacteroidetes Bacteroidia Prevotellaceae
Prevotella shahii 1 Rare Possible Commensal Non/unknown Pathogen oral cavity and human faeces RajilicStojanovic2014, Byrd2020 Bacteroidetes Bacteroidia Prevotellaceae neg ANA Sessile Rod No spore 44-45 20(neg)
Prevotella stercorea 1 Moderate Possible Commensal Non/unknown Pathogen human faeces Walker2011, Nielsen2014, RajilicStojanovic2014, Lagier2016, Rothschild2018, Zou2019, Forster2019, Byrd2020, De2020, Dubinkina2017, Hu2019, Jeong2021, Jie2017, Vachida2019, Urban2020, Minerbi2019, Li2019b, PerezBrocal2015 Bacteroidetes Bacteroidia Prevotellaceae neg ANA Sessile Rod No spore 48.2 20(neg)
Prevotella timonensis 1 Opportunistic in immunocompromised patients Minor Possible Commensal Opportunistic Pathogen clinical sources (abscess, urine, ulcer - CCUG) and human faeces RajilicStojanovic2014, Byrd2020, Yang2020, Chen2020, Hu2019, Zeller2014, Vachida2019 Bacteroidetes Bacteroidia Prevotellaceae neg ANA Sessile Rod No spore 42.4 20(neg)
Prevotella veroralis Bacteroides veroralis 1 Minor Possible Commensal Non/unknown Pathogen dental disease and human faeces Benno1986, Wang2005, RajilicStojanovic2014, Lagier2016, Forster2019, Byrd2020, Vachida2019 Bacteroidetes Bacteroidia Prevotellaceae neg ANA Sessile Rod No spore 42 20(neg)
Prevotellamassilia timonensis Minor Possible Commensal Non/unknown Pathogen In 50% of Europeans (unseenbio.com). Minor coloniser. human faeces (Bilen2018e) Lagier2016, Byrd2020, De2020, Minerbi2019 Bacteroidetes Bacteroidia Prevotellaceae neg SANA Swimming Coccus No spore
Priestia flexa Bacillus flexus Positive 1 Rare Known Commensal Non/unknown Pathogen human faeces, and soil Pfleiderer2013, RajilicStojanovic2014, Lagier2016, Yang2020 Firmicutes Bacilli Bacillaceae vr SAER Rod Endospore 37-39
Priestia koreensis Bacillus koreensis 1 Unlikely Transient Non/unknown Pathogen Obligate aerobe; unlikely to be a gut coloniser. the rhizosphere of a willow, Korea Lagier2016 Firmicutes Bacilli Bacillaceae + SAER Swimming Rod Endospore 36
Priestia megaterium Bacillus megaterium 1 Opportunistic in immunocompromised patients Rare Possible Commensal Opportunistic Pathogen May be able to persist in the gut, albeit in low numbers, by residing in niches close to epithelial cells (Ilinskaya2017). human faeces, cow faeces, food and clinical specimens Taylor1985, Pfleiderer2013, RajilicStojanovic2014, Lagier2016, New2022 Firmicutes Bacilli Bacillaceae + FANA Swimming Rod Endospore 37.0-38.1
Prochlorococcus marinus Rare Possible Commensal Non/unknown Pathogen human faeces and is oxygenic marine organism Yang2020 Cyanobacteria Cyanobacteria Prochlorococcaceae neg AER Rod No spore
Prolixibacter bellariivorans 1 Unlikely Transient Non/unknown Pathogen Optimum growth temp is low (22C), so unlikely to be a gut coloniser. Tested neg for glucose fermentation and utilisation, yet fermentation from glucose was reported. human faeces Walker2011 Bacteroidetes Bacteroidia Prolixibacteraceae neg FANA Sessile Filamentous No spore 44.9
Propionibacterium acidifaciens Rare Possible Commensal Opportunistic Infection oral carious lesions Lagier2016, Byrd2020, New2022 Actinobacteria Actinomycetia Propionibacteriaceae + ANA Sessile Pleiomorph rod No spore 70
Propionibacterium freudenreichii 1 Rare Possible Commensal Non/unknown Pathogen human faeces RajilicStojanovic2014, Lagier2016, Forster2019, Byrd2020, Zeller2014 Actinobacteria Actinomycetia Propionibacteriaceae + ANA Rod No spore
Propionimicrobium lymphophilum Propionibacterium lymphophilum 2 Rare Possible Commensal Known Pathogen lymph nodes and is associated with Hodgkin's disease Lagier2016, Forster2019 Actinobacteria Actinomycetia Propionibacteriaceae neg ANA Sessile Pleiomorph rod No spore 53-54
Prosthecobacter fluviatilis 1 Rare Possible Commensal Non/unknown Pathogen human faeces, and oligotrophic aquatic environments McLaughlin2010, RajilicStojanovic2014 Verrucomicrobia Verrucomicrobiae Verrucomicrobiaceae neg AER Fusobacterium No spore 62.9
Proteiniphilum saccharofermentans Unlikely Transient Non/unknown Pathogen a wheat and maize-fed biogas reactor Byrd2020, New2022 Bacteroidetes Bacteroidia Dysgonomonadaceae neg FANA Rod No spore 45.1
Proteus mirabilis Negative 2 Human and animal pathogen Moderate Possible Commensal Opportunistic Pathogen clinical sources (urine, vagina - CCUG) and human faeces (including ulcerative colitis patients) Finegold1977, Benno1984, MacFarlane2004, Woodmansey2004, McLaughlin2010, Walker2011, Pfleiderer2013, RajilicStojanovic2014, Cassir2015, Lagier2016, Almeida2019, Forster2019, Byrd2020, De2020, Yang2020, Jie2017, Zeller2014, Vachida2019 Proteobacteria Gammaproteobacteria Morganellaceae neg FANA Swimming Rod No spore 39.3
Proteus penneri Proteus vulgaris Indole Negative 2 Rare Possible Commensal Known Pathogen human faeces, and clinical sources (urine, blood, atherosclerotic plaques) Tyakht2013, RajilicStojanovic2014, Lagier2016, Vachida2019 Proteobacteria Gammaproteobacteria Morganellaceae neg FANA Swimming Rod No spore 38
Proteus vulgaris 2 Rare Possible Commensal Opportunistic Pathogen human faeces and clinical sources (urine, sputum, wound - CCUG). Implicated in accelerating CVD progression Woodmansey2004, RajilicStojanovic2014, Lagier2016, Byrd2020 Proteobacteria Gammaproteobacteria Morganellaceae neg FANA vr Rod No spore 39.3
Provencibacterium massiliense Moderate Possible Commensal Non/unknown Pathogen In 75% of Europeans (unseenbio.com). human faeces (Traore2017b) Byrd2020 Firmicutes Clostridia Oscillospiraceae neg SANA Sessile Rod - curved
Providencia alcalifaciens Proteus inconstans 2 Minor Known Commensal Opportunistic Pathogen human faeces, including diarrhoea, and clinical sources (blood, abscess - CCUG) Finegold1974, Tyakht2013, RajilicStojanovic2014, Lagier2016, Forster2019, Zeller2014, Vachida2019 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Swimming Rod No spore 43
Providencia heimbachae 1 Opportunistic in immunocompromised patients Rare Possible Commensal Possible Pathogen from animals and has been detected in human faeces (Bilen2018e) Lagier2016 Proteobacteria Gammaproteobacteria Morganellaceae neg FANA vr Rod No spore 39.6
Providencia rettgeri Proteus rettgeri Negative 2 Minor Possible Commensal Opportunistic Pathogen human faeces and clinical sources (blood, urine, sputum, wound, atherosclerotic plaques) Finegold1974, Tyakht2013, RajilicStojanovic2014, Lagier2016, Forster2019, Byrd2020, Vachida2019 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Swimming Rod No spore 40.5
Providencia rustigianii Providencia alcalifaciens Biogroup 3 2 Rare Possible Commensal Rare Opportunist human faeces, and clinical sources (urine - CCUG) Tyakht2013, RajilicStojanovic2014, Lagier2016, Forster2019 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA vr Rod No spore 41.8
Providencia stuartii Proteus stuartii 1 Rare Possible Commensal Opportunistic Pathogen human faeces, and clinical sources (urine, abdominal fluid, wound - CCUG) Woodmansey2004, Tyakht2013, RajilicStojanovic2014, Lagier2016 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Swimming Rod No spore 40.7
Pseudarthrobacter oxydans Arthrobacter oxydans 1 Rare Possible Commensal Possible Pathogen clinical sources and human faeces RajilicStojanovic2014, Lagier2016 Actinobacteria Actinomycetia Micrococcaceae + AER Sessile No spore 63.1
Pseudarthrobacter polychromogenes Arthrobacter polychromogenes 1 Unlikely Transient Non/unknown Pathogen Borderline cold mesophile, so unlikely to be a gut coloniser. human faeces RajilicStojanovic2014, Lagier2016, Yang2020 Actinobacteria Actinomycetia Micrococcaceae vr AER Sessile No spore
Pseudescherichia vulneris Escherichia vulneris 2 Rare Possible Commensal Opportunistic Pathogen clinical sources (wound, blood, urine - CCUG) and human faeces (CCUG; including ulcerative colitis patients - Alkhalil2017) Byrd2020 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Swimming Rod No spore 58.5-58.7
Pseudobutyrivibrio ruminis 1 Rare Possible Commensal Non/unknown Pathogen bovine rumen Firmicutes Clostridia Lachnospiraceae neg SANA Swimming Rod - curved No spore 40.5
Pseudobutyrivibrio xylanivorans 1 Unlikely Transient Non/unknown Pathogen rumen Byrd2020, New2022 Firmicutes Clostridia Lachnospiraceae neg ANA Swimming Rod - curved No spore 42.7
Pseudochrobactrum asaccharolyticum Rare Possible Commensal Opportunistic Infection a knee aspirate Lagier2016 Proteobacteria Alphaproteobacteria Brucellaceae neg FANA Sessile Rod No spore 50.9
Pseudochrobactrum saccharolyticum 1 Rare Possible Commensal Non/unknown Pathogen industrial glue Yang2020 Proteobacteria Brucellaceae neg AER Sessile Rod No spore
Pseudocitrobacter anthropi Rare Possible Commensal Non/unknown Pathogen human faeces (Kaempfer2014) Lagier2016, Yang2020 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Swimming Rod No spore 57.1
Pseudocitrobacter faecalis Rare Possible Commensal Non/unknown Pathogen human faeces (Kaempfer2014) Lagier2016 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Swimming Rod No spore 54.2
Pseudoclavibacter alba Zimmermannella alba Rare Possible Commensal Opportunistic Pathogen urine Lagier2016 Actinobacteria Actinomycetia Microbacteriaceae + AER Sessile Pleiomorph rod No spore 68
Pseudoclavibacter helvolus Zimmermannella helvola 1 Unlikely Transient Non/unknown Pathogen Obligate aerobe; unlikely to be a gut coloniser. butter Yang2020 Actinobacteria Actinomycetia Microbacteriaceae + SAER Sessile Rod No spore 67
Pseudoclavibacter sp. Timone Pseudoclavibacter massiliense Rare Possible Commensal Possible Pathogen human faeces and clinical sources RajilicStojanovic2014, Lagier2016 Actinobacteria Actinomycetia Microbacteriaceae + AER Rod No spore 67
Pseudoclostridium thermosuccinogenes Clostridium thermosuccinogenes 1 Unlikely Transient Non/unknown Pathogen High optimum growth temperature so unlikely to be a gut coloniser. human faeces, cow manure and food sources Walker2011, New2022 Firmicutes Clostridia Oscillospiraceae neg ANA Swimming Rod Endospore 35.9
Pseudodesulfovibrio aespoeensis Desulfovibrio aespoeensis 1 Unlikely Transient Non/unknown Pathogen subterranean groundwater, Sweden New2022, Zeller2014 Proteobacteria Deltaproteobacteria Desulfovibrionaceae neg SANA Swimming Vibrio No spore 61
Pseudodesulfovibrio indicus Unlikely Transient Non/unknown Pathogen a hydrothermal vent New2022 Proteobacteria Deltaproteobacteria Desulfovibrionaceae neg SANA Swimming Vibrio No spore 63.5
Pseudoflavonifractor capillosus Bacteroides capillosus 2 Moderate Known Commensal Opportunistic Pathogen human faeces Moore1974, Finegold1974, Holdeman1976, Finegold1977, Benno1986, Benno1989, Walker2011, Zupancic2012, Tyakht2013, RajilicStojanovic2014, Lagier2016, Rothschild2018, Forster2019, Byrd2020, Chen2020, Dubinkina2017, Hu2019, Zeller2014, Vachida2019, Urban2020, Qin2012, LeChatelier2013 Firmicutes Clostridia Oscillospiraceae neg SANA Sessile Rod No spore 60 20(neg)
Pseudoglutamicibacter albus Arthrobacter albus 2 Rare Possible Commensal Rare Opportunist clinical sources (blood - CCUG) and human faeces RajilicStojanovic2014, Lagier2016 Actinobacteria Actinomycetia Micrococcaceae + AER Swimming Rod No spore
Pseudoglutamicibacter cumminsii Arthrobacter cumminsii 2 Unlikely Transient Opportunistic Pathogen Strict aerobe, so unlikely to be a gut coloniser. clinical specimens (wounds, UTI, amniotic fluid, blood, infections) Lagier2016 Actinobacteria Actinomycetia Micrococcaceae + SAER Sessile Coryneform No spore 60-62
Pseudomonas aeruginosa Negative 2 Human and animal pathogen Rare Possible Commensal Opportunistic Pathogen In 7% of Europeans (unseenbio.com). Rare coloniser. clinical sources (abscess, respiratory tract, wound, blood, others - CCUG) and human faeces (CCUG) Finegold1977, Benno1984, Taylor1985, Benno1986, Benno1989, MacFarlane2004, Woodmansey2004, RajilicStojanovic2014, Lagier2016, Almeida2019, Forster2019, Byrd2020, New2022, Zeller2014, Vachida2019 Proteobacteria Gammaproteobacteria Pseudomonadaceae neg AER Swimming Rod No spore 67.2
Pseudomonas alcaligenes 2 Non Transient Opportunistic Pathogen swimming pool water Lagier2016 Proteobacteria Gammaproteobacteria Pseudomonadaceae neg AER Swimming Rod No spore 64-68
Pseudomonas alcaliphila 1 Rare Possible Commensal Non/unknown Pathogen human faeces, and seawater RajilicStojanovic2014 Proteobacteria Gammaproteobacteria Pseudomonadaceae neg AER Swimming Rod No spore 62.3-63.2
Pseudomonas asiatica Rare Possible Commensal Non/unknown Pathogen human faeces (Tohya2019) Proteobacteria Gammaproteobacteria Pseudomonadaceae neg AER Swimming Rod No spore 62.3
Pseudomonas asplenii 1 Plant pathogen Unlikely Transient Non/unknown Pathogen Unlikely gut coloniser. bird's nest fern (pathogen) Byrd2020 Proteobacteria Gammaproteobacteria Pseudomonadaceae neg AER Swimming Rod No spore
Pseudomonas boreopolis 1 Non Transient Non/unknown Pathogen soil Lagier2016 Proteobacteria Gammaproteobacteria Xanthomonadaceae incertae sedis neg AER Swimming Rod No spore 67.8
Pseudomonas caricapapayae 1 Plant pathogen Non Transient Non/unknown Pathogen clay and dead beetle larvae Lagier2016 Proteobacteria Gammaproteobacteria Pseudomonadaceae neg AER Swimming Rod No spore 63.5-63.6
Pseudomonas chlororaphis 1 Non Transient Non/unknown Pathogen clay and dead beetle larvae Lagier2016 Proteobacteria Gammaproteobacteria Pseudomonadaceae neg AER Swimming Rod No spore 63
Pseudomonas citronellolis 1 Rare Possible Commensal Possible Pathogen In 1% of Europeans (unseenbio.com). Rare coloniser. human appendix (CCUG), human rectum, clinical sources (blood - CCUG) and soil Proteobacteria Gammaproteobacteria Pseudomonadaceae neg AER Swimming Rod No spore
Pseudomonas fluorescens 1 Opportunistic in immunocompromised patients, invertebrate pathogen Unlikely Transient Possible Pathogen human faeces, clinical sources (sputum, blood - CCUG), soil, water and spoilt food McLaughlin2010, RajilicStojanovic2014, Lagier2016, Zeller2014 Proteobacteria Gammaproteobacteria Pseudomonadaceae neg AER Swimming Rod No spore 59-61
Pseudomonas fragi 1 Rare Possible Commensal Non/unknown Pathogen In 9% of Europeans (unseenbio.com). Rare coloniser. human faeces (CCUG) Lagier2016, Byrd2020, Yang2020, Vachida2019 Proteobacteria Gammaproteobacteria Pseudomonadaceae neg AER Swimming Rod No spore 60.6
Pseudomonas fulva 1 Rare Transient Possible Pathogen paddy fields in Japan and has been detected in human faeces (Bilen2018e) Lagier2016, Zeller2014 Proteobacteria Gammaproteobacteria Pseudomonadaceae neg AER Swimming Rod No spore
Pseudomonas gessardii 1 Non Transient Non/unknown Pathogen natural mineral waters Lagier2016, Yang2020 Proteobacteria Gammaproteobacteria Pseudomonadaceae neg AER Swimming Rod No spore 58
Pseudomonas japonica Non Transient Non/unknown Pathogen activated sludge, Japan McLaughlin2010, Lagier2016 Proteobacteria Gammaproteobacteria Pseudomonadaceae neg AER Swimming Rod No spore 66
Pseudomonas libanensis 1 Non Transient Non/unknown Pathogen spring water, Lebanon Lagier2016 Proteobacteria Gammaproteobacteria Pseudomonadaceae neg AER Swimming Rod No spore 58
Pseudomonas lundensis 1 Non Transient Rare Opportunist Borderline cold mesophile, so likely not a gut coloniser. meat, clinical specimens (sputum, tonsil - CCUG) and has been detected in human faeces (Bilen2018e) Lagier2016, Byrd2020 Proteobacteria Gammaproteobacteria Pseudomonadaceae neg AER Swimming Rod No spore 59
Pseudomonas luteola Chryseomonas luteola 2 Unlikely Transient Possible Pathogen Obligate aerobe; unlikely to be a gut coloniser. human faeces and clinical sources (wound, cerebrospinal fluid - CCUG) Lagier2016, Forster2019 Proteobacteria Gammaproteobacteria Pseudomonadaceae neg SAER Swimming Rod No spore 54.6
Pseudomonas massiliensis Non Transient Non/unknown Pathogen faeces of a healthy volunteer, Brazil Lagier2016 Proteobacteria Gammaproteobacteria Pseudomonadaceae neg AER Swimming Short Rod No spore 62.3
Pseudomonas mendocina 2 Rare Possible Commensal Opportunistic Pathogen soil and water; clinical specimens McLaughlin2010, Zeller2014 Proteobacteria Gammaproteobacteria Pseudomonadaceae neg AER Swimming Rod No spore 62.8-64.3
Pseudomonas migulae 1 Non Transient Non/unknown Pathogen natural mineral waters Lagier2016 Proteobacteria Gammaproteobacteria Pseudomonadaceae neg AER Swimming Rod No spore 58
Pseudomonas monteilii 1 Opportunistic in immunocompromised patients Unlikely Transient Rare Opportunist clinical sources (bronchial aspirate - CCUG) and human faeces RajilicStojanovic2014, Lagier2016 Proteobacteria Gammaproteobacteria Pseudomonadaceae neg AER Swimming Rod No spore 60.5
Pseudomonas mosselii 1 Opportunistic in immunocompromised patients Non Transient Opportunistic Pathogen clinical sources Lagier2016 Proteobacteria Gammaproteobacteria Pseudomonadaceae neg AER Swimming Rod No spore 63
Pseudomonas nitroreducens 1 Unlikely Transient Non/unknown Pathogen human faeces, and oil brine McLaughlin2010, RajilicStojanovic2014, Byrd2020 Proteobacteria Gammaproteobacteria Pseudomonadaceae neg AER Swimming Rod No spore
Pseudomonas oleovorans 1 Unlikely Transient Rare Opportunist clinical sources (blood, sinus - CCUG) and human faeces RajilicStojanovic2014, Lagier2016 Proteobacteria Gammaproteobacteria Pseudomonadaceae neg AER Swimming Coccobacillus No spore 63.5
Pseudomonas oryzihabitans 2 Unlikely Transient Opportunistic Pathogen human faeces (18-yr-old - CCUG), clinical sources (blood, urine, wound - CCUG) and rice paddies Lagier2016 Proteobacteria Gammaproteobacteria Pseudomonadaceae neg AER Swimming Rod No spore 65.1
Pseudomonas parafulva 1 Unlikely Transient Non/unknown Pathogen human faeces and rice paddies Yang2020 Proteobacteria Gammaproteobacteria Pseudomonadaceae neg AER Swimming Rod No spore 60
Pseudomonas protegens Unlikely Transient Non/unknown Pathogen Strictly aerobic and reduced growth at 37C suggests this is unlikely to be a gut coloniser. soil and plant roots Zeller2014 Proteobacteria Gammaproteobacteria Pseudomonadaceae neg SAER Sessile Rod No spore 60.1-63.3
Pseudomonas putida Biovar A Pseudomonas putida 2 Rare Possible Commensal Opportunistic Pathogen In 4% of Europeans (unseenbio.com). Rare coloniser. human faeces, soil, and rhizosphere Wang2005, Frank2007, RajilicStojanovic2014, Lagier2016, Zeller2014 Proteobacteria Gammaproteobacteria Pseudomonadaceae neg AER Swimming Rod No spore 60.8
Pseudomonas putida Biovar B Pseudomonas putida 2 Rare Possible Commensal Opportunistic Pathogen In 4% of Europeans (unseenbio.com). Rare coloniser. soil, rhizosphere, human faeces Wang2005, Frank2007, RajilicStojanovic2014, Lagier2016 Proteobacteria Gammaproteobacteria Pseudomonadaceae neg AER Swimming Rod No spore 60.8
Pseudomonas rhodesiae 1 Non Transient Non/unknown Pathogen natural mineral waters Lagier2016, Byrd2020 Proteobacteria Gammaproteobacteria Pseudomonadaceae neg AER Swimming Rod No spore 61
Pseudomonas saudiphocaensis Rare Possible Commensal Non/unknown Pathogen paper money, Saudi Arabia Lagier2016 Proteobacteria Gammaproteobacteria Pseudomonadaceae neg AER Swimming Rod No spore
Pseudomonas straminea 1 Unlikely Transient Non/unknown Pathogen No growth at 37C, so not likely to be a gut coloniser. rice paddies, Japan Frank2007 Proteobacteria Gammaproteobacteria Pseudomonadaceae neg AER Swimming Rod No spore 62.5-63.7
Pseudomonas stutzeri 1 Opportunistic in immunocompromised patients Unlikely Transient Opportunistic Pathogen soil, clinical sources (sputum, infection, wound - CCUG) and human faeces McLaughlin2010, RajilicStojanovic2014, Cassir2015, Lagier2016, Zeller2014 Proteobacteria Gammaproteobacteria Pseudomonadaceae neg AER Swimming Rod No spore 60.6-66.3
Pseudomonas taetrolens 1 Non Transient Non/unknown Pathogen foods with musty odour Lagier2016 Proteobacteria Gammaproteobacteria Pseudomonadaceae neg AER Swimming Short Rod No spore 59.8
Pseudomonas tolaasii 1 Plant pathogen Unlikely Transient Non/unknown Pathogen Borderline cold mesophile, so unlikely to be a gut coloniser. mushroom disease and has been detected in human faeces Lagier2016, King2019, Byrd2020, Yang2020 Proteobacteria Gammaproteobacteria Pseudomonadaceae neg AER Swimming Rod No spore 61
Pseudomonas veronii 1 Rare Possible Commensal Non/unknown Pathogen natural mineral waters PerezBrocal2015 Proteobacteria Gammaproteobacteria Pseudomonadaceae neg AER Swimming Rod No spore 61-62
Pseudomonas weihenstephanensis Unlikely Transient Non/unknown Pathogen Maximum growth temperature of 33C suggests this is an unlikely gut coloniser. raw cow’s milk Byrd2020 Proteobacteria Gammaproteobacteria Pseudomonadaceae neg AER Swimming Rod No spore 57.3
Pseudomonas xanthomarina 1 Non Transient Non/unknown Pathogen coastal waters, Sea of Japan Cassir2015, Lagier2016 Proteobacteria Gammaproteobacteria Pseudomonadaceae neg AER Swimming Rod No spore 59.1-63.7
Pseudomonas yamanorum Unlikely Transient Non/unknown Pathogen Borderline cold mesophile, with optimum growth temp of 28C. Unlikely gut coloniser. soil, Argentina Yang2020 Proteobacteria Gammaproteobacteria Pseudomonadaceae neg AER Swimming Rod No spore 59.8
Pseudomonas zhaodongensis Unlikely Transient Non/unknown Pathogen Borderline cold mesophile, with optimum growth temp of 28C. Unlikely gut coloniser. saline and alkaline soils, China Yang2020 Proteobacteria Gammaproteobacteria Pseudomonadaceae neg AER Swimming Rod No spore 65
Pseudonocardia dioxanivorans 1 Unlikely Transient Non/unknown Pathogen Can degrade 1,4-dioxane, THF, tetrahydropyran, 1,3-dioxane, methyl t-butyl ether and diethyl ether. Strict aerobe so unlikely to be a gut coloniser. a 1,4-dioxane-contaminated site, USA Zeller2014 Actinobacteria Actinomycetia Pseudonocardiaceae + SAER Sessile Filamentous No spore 74
Pseudoprevotella muciniphila Rare Possible Commensal Non/unknown Pathogen Mucin-degrading bacterium the mucine of bovine rumen epithelium New2022 Bacteroidetes Bacteroidia Prevotellaceae neg SANA Sessile Coccus No spore 46.4
Pseudopropionibacterium massiliense Rare Possible Commensal Non/unknown Pathogen the human oral cavity Actinobacteria Actinomycetia Propionibacteriaceae + ANA Swimming Rod No spore 54.3
Pseudoramibacter alactolyticus Eubacterium alactolyticum 2 Rare Possible Commensal Opportunistic Pathogen dental disease and human faeces Benno1986, RajilicStojanovic2014, Lagier2016, Byrd2020, Zeller2014, Vachida2019 Firmicutes Clostridia Eubacteriaceae + SANA Sessile Rod No spore 61 20(neg)
Pseudoruegeria marinistellae Tropicimonas marinistellae Rare Possible Commensal Non/unknown Pathogen a starfish, China De2020 Proteobacteria Alphaproteobacteria Roseobacteraceae neg FANA Sessile Rod No spore 63
Pseudoruminococcus massiliensis Rare Possible Commensal Non/unknown Pathogen human faeces (Bilen2018e) Firmicutes Clostridia Oscillospiraceae neg SANA Sessile Coccus 37.6
Pseudoxanthomonas broegbernensis 1 Unlikely Transient Non/unknown Pathogen Can't grow at 37C, so unlikely to be a gut coloniser. human faeces and a biofilter from waste gas Yang2020 Proteobacteria Gammaproteobacteria Xanthomonadaceae neg AER Swimming Rod No spore 66.5
Pseudoxanthomonas japonensis 1 Unlikely Transient Non/unknown Pathogen Obligate aerobe; unlikely to be a gut coloniser. polluted urban soil, Japan Yang2020 Proteobacteria Gammaproteobacteria Xanthomonadaceae neg SAER Swimming Rod No spore 65.2
Pseudoxanthomonas mexicana 1 Rare Possible Commensal Non/unknown Pathogen human faeces, and urine McLaughlin2010, Walker2011, RajilicStojanovic2014 Proteobacteria Gammaproteobacteria Lysobacteraceae neg AER Swimming Rod No spore 67.8
Pseudoxanthomonas spadix 1 Rare Possible Commensal Non/unknown Pathogen an oil-contaminated site, Taiwan. Zeller2014 Proteobacteria Gammaproteobacteria Lysobacteraceae neg AER Sessile Rod - curved No spore 68.5
Pseudoxanthomonas suwonensis 1 Rare Possible Commensal Non/unknown Pathogen cotton waste composts, Korea Zeller2014 Proteobacteria Gammaproteobacteria Lysobacteraceae neg AER Swimming Rod No spore 66.6-68.4
Pseudoxanthomonas taiwanensis 1 Rare Possible Commensal Non/unknown Pathogen hot springs, Taiwan PerezBrocal2015 Proteobacteria Gammaproteobacteria Lysobacteraceae neg AER Sessile Rod No spore 69.9-70.1
Psychrobacter alimentarius 1 Unlikely Transient Non/unknown Pathogen human faeces and traditional Korean fermented seafood Yang2020 Proteobacteria Gammaproteobacteria Moraxellaceae + AER Sessile Coccus No spore 44
Psychrobacter arenosus 1 Unlikely Transient Non/unknown Pathogen Borderline cold mesophile, so unlikely to be a gut coloniser. marine sediment and human faeces RajilicStojanovic2014, Lagier2016 Proteobacteria Gammaproteobacteria Moraxellaceae neg AER Sessile Oval-shaped No spore 45.0
Psychrobacter cibarius 1 Unlikely Transient Non/unknown Pathogen human faeces and traditional Korean fermented seafood Byrd2020, Yang2020 Proteobacteria Gammaproteobacteria Moraxellaceae neg AER Sessile Coccobacillus No spore 43-43.5
Psychrobacter faecalis 1 Unlikely Transient Opportunistic Infection Low optimum growth temp, so unlikely gut coloniser. pigeon faeces, clinical sources (blood, wound, bone - CCUG) and has been detected in human faeces (Bilen2018e) Lagier2016 Proteobacteria Gammaproteobacteria Moraxellaceae neg AER Sessile Rod No spore 5(neg)
Psychrobacter fulvigenes Rare Possible Commensal Non/unknown Pathogen marine crustaceans, Sea of Japan Proteobacteria Gammaproteobacteria Moraxellaceae neg AER Sessile Oval-shaped No spore
Psychrobacter maritimus 1 Unlikely Transient Non/unknown Pathogen Borderline cold mesophile, so unlikely to be a gut coloniser. human faeces and coastal sediment from Japan Yang2020 Proteobacteria Gammaproteobacteria Moraxellaceae neg AER Sessile Oval-shaped No spore 44.6-44.9
Psychrobacter namhaensis 1 Unlikely Transient Non/unknown Pathogen sea water off South Korea and human faeces Yang2020 Proteobacteria Gammaproteobacteria Moraxellaceae neg AER Sessile No spore 45.3
Psychrobacter phenylpyruvicus Moraxella phenylpyruvica 2 Rare Possible Commensal Opportunistic Infection skin and mucous membranes. Also from clinical sources (blood, pus, cerebrospinal fluid, UTI) Lagier2016 Proteobacteria Gammaproteobacteria Moraxellaceae neg AER Sessile Pleiomorph rod No spore 43 5(+)
Psychrobacter pulmonis 2 Animal pathogen Unlikely Transient Possible Pathogen Obligate aerobe; unlikely to be a gut coloniser. lungs of lambs Lagier2016 Proteobacteria Gammaproteobacteria Moraxellaceae neg SAER Sessile Coccus No spore
Pusillimonas faecalis Rare Possible Commensal Non/unknown Pathogen human faeces Firmicutes Clostridia Oscillospiraceae neg SANA Sessile Rod No spore 55.2
Pygmaiobacter massiliensis Minor Possible Commensal Non/unknown Pathogen In 30% of Europeans (unseenbio.com). Minor coloniser. human faeces (Bilen2017g) Byrd2020 Firmicutes Clostridia Oscillospiraceae + Rod
Pyramidobacter piscolens Minor Possible Commensal Non/unknown Pathogen dental disease, abscesses and human faeces RajilicStojanovic2014, Lagier2016, Byrd2020, Yang2020, Hu2019, Jie2017, Zeller2014, Vachida2019, Wang2020a, Li2019b, PerezBrocal2015 Synergistetes Synergistia Synergistaceae neg SANA Sessile Rod No spore 59 20(neg)
Rahnella aquatilis 1 Opportunistic in immunocompromised patients Unlikely Transient Possible Pathogen human faeces (CCUG) and clinical sources (blood, urine - CCUG) Byrd2020, Yang2020, Zeller2014, Vachida2019 Proteobacteria Gammaproteobacteria Yersiniaceae neg FANA vr Rod No spore 51-56
Ralstonia mannitolilytica 2 Rare Possible Commensal Opportunistic Pathogen clinical sources (sputum, blood, nasopharynx - CCUG) and human faeces RajilicStojanovic2014 Proteobacteria Betaproteobacteria Burkholderiaceae neg AER Sessile Rod No spore 66.2
Ralstonia pickettii Biovar Va-1&2 Burkholderia pickettii 2 Rare Possible Commensal Opportunistic Pathogen Biovars Va-1 and Va-2 combined. the small intestine (28-yr-old female - CCUG) and clinical sources (trachea, crebrospinal fluid, blood - CCUG) McLaughlin2010, Forster2019, Yang2020, Zeller2014, Vachida2019 Proteobacteria Betaproteobacteria Burkholderiaceae neg AER Sessile Rod No spore 66.2
Raoultella ornithinolytica Klebsiella ornithinolytica 2 Minor Possible Commensal Possible Pathogen human faeces (Alkhalil2017 - can be high load in ulcerative colitis patients), clinical sources (throat, urine) and food Zupancic2012, Lagier2016, King2019, Byrd2020, Yang2020, New2022, Vachida2019 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Sessile Rod No spore 57
Raoultella planticola Klebsiella planticola 1 Human and animal pathogen; opportunistic in immunocompromised patients Rare Possible Commensal Opportunistic Pathogen human faeces (ulceritive colitis - Alkhalil2017), urine, and plants RajilicStojanovic2014, Lagier2016, Byrd2020, Wang2020a Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Sessile Rod No spore 53.9-55.4
Raoultella terrigena Klebsiella terrigena 1 Human and animal pathogen; opportunistic in immunocompromised patients Rare Possible Commensal Opportunistic Pathogen human faeces (Alkhalil2017 - ulceritive colitis), soils, and freshwater RajilicStojanovic2014, Lagier2016, Byrd2020 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Sessile Rod No spore 56.7
Raoultibacter massiliensis Rare Possible Commensal Non/unknown Pathogen human faeces (Traore2019) Lagier2016, Byrd2020 Actinobacteria Coriobacteriia Eggerthellaceae + Micr Swimming Rod No spore 59.0
Raoultibacter timonensis Rare Possible Commensal Non/unknown Pathogen human faeces (Traore2019) Byrd2020, De2020 Actinobacteria Coriobacteriia Eggerthellaceae + Micr Swimming Rod No spore 59.6
Rheinheimera perlucida 1 Unlikely Transient Non/unknown Pathogen Borderline cold mesophile, so unlikely to be a gut coloniser. surface water, Baltic Sea Forster2019 Proteobacteria Gammaproteobacteria Chromatiaceae neg AER Swimming Rod No spore 48.9
Rhizobium metallidurans Unlikely Transient Non/unknown Pathogen seedlings and human faeces Yang2020 Proteobacteria Alphaproteobacteria Rhizobiaceae neg AER Sessile Rod No spore 58.9
Rhizorhabdus wittichii Sphingomonas wittichii 1 Unlikely Transient Non/unknown Pathogen Aerobic and optimum growth temperature of 30C suggests this is an unlikely gut coloniser. water of the River Elbe, Europe Byrd2020, Zeller2014 Proteobacteria Alphaproteobacteria Sphingomonadaceae neg AER Swimming Rod No spore 67
Rhodanobacter ginsenosidimutans Unlikely Transient Non/unknown Pathogen human faeces, and soil RajilicStojanovic2014 Proteobacteria Gammaproteobacteria Rhodanobacteraceae neg AER Sessile Rod No spore 65.5
Rhodococcus erythropolis Mycobacterium erythropolis 1 Rare Possible Commensal Opportunistic Pathogen human faeces and clinical sources (wound, blood, tissue - CCUG) Walker2011, RajilicStojanovic2014, Lagier2016, Zeller2014 Actinobacteria Actinomycetia Nocardiaceae + AER Sessile No spore 65.2
Rhodococcus hoagii Rhodococcus equi 2 Human and animal pathogen Rare Possible Commensal Opportunistic Pathogen human faeces Taylor1985, RajilicStojanovic2014, Lagier2016, Zeller2014 Actinobacteria Actinomycetia Nocardiaceae + AER Sessile No spore
Rhodococcus jostii 1 Non Transient Non/unknown Pathogen Aerobic and no growth at 37C suggests this not a gut coloniser. the bones in an old grave, Czechia/Moravia Zeller2014 Actinobacteria Actinomycetia Nocardiaceae + AER Sessile Filamentous No spore 67.4
Rhodococcus opacus 1 Unlikely Transient Non/unknown Pathogen Strictly aerobic suggests this is unlikely to be a gut coloniser. a soil sample from a leaking gas pipe Zeller2014 Actinobacteria Actinomycetia Nocardiaceae + SAER Sessile Rod-coccus cycle No spore 67.6
Rhodococcus qingshengii 1 Unlikely Transient Non/unknown Pathogen carbendazim-contaminated soil, China Yang2020 Actinobacteria Actinomycetia Nocardiaceae + AER Sessile Rod-coccus cycle No spore 59.1
Rhodococcus rhodochrous 1 Opportunistic in immunocompromised patients Rare Possible Commensal Opportunistic Infection human faeces, and soil RajilicStojanovic2014, Lagier2016 Actinobacteria Actinomycetia Nocardiaceae + AER Sessile Coccus No spore 67-70
Rhodoplanes serenus Unlikely Transient Non/unknown Pathogen Phototrophic and prefers anaerobic photoorganotrophy, using nitrate as a terminal electron acceptor. Photolithic growth with thiosulfate. Can fix N2 and use sulfate as a S source. pond water Yang2020 Proteobacteria Alphaproteobacteria Hyphomicrobiaceae neg FANA Swimming Rod No spore 69.5
Rhodothermus marinus 1 Non Transient Non/unknown Pathogen High minimum growth temperature (55C) and strict aerobic nature suggests this organism is likely a gut non-coloniser. submarine hot springs, Iceland New2022, Zeller2014 Bacteroidetes Rhodothermaceae neg SAER Sessile Rod No spore 64
Riemerella columbina 2 Animal pathogen Rare Possible Commensal Possible Pathogen a pigeon palatine cleft, Germany Forster2019 Bacteroidetes Flavobacteriia Weeksellaceae neg AER Sessile Rod No spore 36
Rikenella microfusus Bacteroides microfusus 1 Rare Possible Mutualist Non/unknown Pathogen faecal or caecal specimens from calves, chickens, and Japanese quails Byrd2020, Minerbi2019 Bacteroidetes Bacteroidia Rikenellaceae neg SANA Sessile Short Rod No spore 57.0 20(R)
Risungbinella massiliensis Rare Possible Commensal Non/unknown Pathogen human faeces (Dubourg2016a) Lagier2016 Firmicutes Bacilli Thermoactinomycetaceae + AER Sessile Filamentous Endospore 40.1
Robertmurraya andreesenii Bacillus andreesenii Unlikely Transient Non/unknown Pathogen Obligate aerobe; unlikely to be a gut coloniser. a compost bioreactor Lagier2016 Firmicutes Bacilli Bacillaceae + SAER Swimming Rod Endospore 39
Robertmurraya kyonggiensis Bacillus kyonggiensis Rare Possible Commensal Non/unknown Pathogen soil from a lettuce field, Korea Lagier2016 Firmicutes Bacilli Bacillaceae + FANA Sessile Rod Endospore 36.3
Robertmurraya massiliosenegalensis Bacillus massiliosenegalensis Positive Rare Known Commensal Non/unknown Pathogen human faeces RajilicStojanovic2014, Lagier2016, Forster2019 Firmicutes Bacilli Bacillaceae + AER Swimming Rod Endospore 37.6
Robinsoniella peoriensis Rare Possible Commensal Opportunistic Pathogen human faeces, clinical sources (blood, deep wound - CCUG), and pig faeces RajilicStojanovic2014, Lagier2016, Byrd2020, PerezBrocal2015 Firmicutes Clostridia Lachnospiraceae + SANA Sessile Oval-shaped Endospore 49
Romboutsia hominis Rare Transient Non/unknown Pathogen ileostoma effluent, Germany New2022 Firmicutes Clostridia Peptostreptococcaceae + SANA Swimming Rod No spore 27.8
Romboutsia ilealis Rare Possible Commensal Non/unknown Pathogen rat gastrointestinal tract and human faeces Yang2020, New2022, Wang2020a Firmicutes Clostridia Peptostreptococcaceae vr SANA Sessile Rod Endospore 28.1 5(neg)
Romboutsia lituseburensis Clostridium lituseburense 1 Minor Possible Commensal Non/unknown Pathogen human faeces and soil McLaughlin2010, Walker2011, RajilicStojanovic2014, Lagier2016, Forster2019, Byrd2020, Yang2020 Firmicutes Clostridia Peptostreptococcaceae + ANA Swimming Rod Endospore 27 20(neg)
Romboutsia maritimum Rare Possible Commensal Non/unknown Pathogen Full characterisation of this organism hasn't been published. a coastal estuarine mud sample in New Zealand Byrd2020 Firmicutes Clostridia Peptostreptococcaceae + SANA Rod Endospore 27.1
Romboutsia timonensis Moderate Possible Commensal Non/unknown Pathogen In 78% of Europeans (unseenbio.com). human faeces (Ricaboni2016) Lagier2016, Byrd2020 Firmicutes Clostridia Peptostreptococcaceae + SANA Rod Endospore
Romboutsia weinsteinii Rare Possible Commensal Non/unknown Pathogen Characterisation not yet published. a water sample harvested in Québec City, Canada Byrd2020 Firmicutes Clostridia Peptostreptococcaceae + SANA Rod Endospore 29.3
Roseburia faecis Agathobacter faecis Positive 1 Widespread Known Commensal Non/unknown Pathogen In 99% of Europeans (unseenbio.com). human faeces McLaughlin2010, PerisBondia2011, Walker2011, Zupancic2012, deGoffau2013, RajilicStojanovic2014, Browne2016, Lagier2016, Zou2019, Forster2019, Byrd2020, Yang2020, Jeong2021, Minerbi2019, Li2019b, PerezBrocal2015 Firmicutes Clostridia Lachnospiraceae vr SANA Swimming Rod - curved 42.0
Roseburia hominis Positive 1 Widespread Known Commensal Non/unknown Pathogen human faeces PerisBondia2011, Walker2011, Tyakht2013, Nielsen2014, RajilicStojanovic2014, Browne2016, Lagier2016, Rothschild2018, Zou2019, King2019, Byrd2020, De2020, Yang2020, New2022, Chen2020, Dubinkina2017, Hu2019, Jeong2021, Jie2017, Zeller2014, Wang2018, Vachida2019, Wang2020a, Qin2012, Minerbi2019 Firmicutes Clostridia Lachnospiraceae vr SANA Swimming Rod - curved 47.4
Roseburia intestinalis Positive 1 Widespread Known Commensal Non/unknown Pathogen human faeces McLaughlin2010, PerisBondia2011, Walker2011, Tyakht2013, Nielsen2014, RajilicStojanovic2014, Salonen2014, Browne2016, Lagier2016, Rothschild2018, Zou2019, Forster2019, King2019, Byrd2020, Yang2020, New2022, Chen2020, Dubinkina2017, Hu2019, Jeong2021, Jie2017, Zeller2014, Wang2018, Vachida2019, Wang2020a, Qin2012, Minerbi2019, LeChatelier2013, Karlsson2013 Firmicutes Clostridia Lachnospiraceae vr SANA Swimming Rod - curved 42.6
Roseburia inulinivorans Positive 1 Widespread Known Commensal Non/unknown Pathogen human faeces McLaughlin2010, PerisBondia2011, Walker2011, Tyakht2013, Nielsen2014, RajilicStojanovic2014, Browne2016, Lagier2016, Rothschild2018, Zou2019, Forster2019, Byrd2020, Yang2020, Chen2020, Dubinkina2017, Hu2019, Jeong2021, Jie2017, Zeller2014, Wang2018, Vachida2019, Wang2020a, Qin2012, Minerbi2019, LeChatelier2013, Karlsson2013 Firmicutes Clostridia Lachnospiraceae vr SANA Swimming Rod - curved 41.4
Roseobacter denitrificans 1 Non Transient Non/unknown Pathogen Aerobic and low growth temperatures of 20-30C suggests this is not a gut coloniser. high-tide seaweed Zeller2014 Proteobacteria Alphaproteobacteria Roseobacteraceae neg AER Swimming Coccobacillus No spore 59.6
Roseomonas gilardii 2 Rare Possible Commensal Known Pathogen potable water and clinical sources Lagier2016 Proteobacteria Alphaproteobacteria Acetobacteraceae neg FANA vr Coccobacillus No spore 67.6-71.2
Roseomonas mucosa 2 Rare Possible Commensal Possible Pathogen human faeces, clinical sources (blood, eye - CCUG), and aquatic origins RajilicStojanovic2014, Lagier2016, PerezBrocal2015 Proteobacteria Alphaproteobacteria Acetobacteraceae neg AER Coccus No spore
Rossellomorea aquimaris Bacillus aquimaris 1 Unlikely Transient Non/unknown Pathogen Obligate aerobe; unlikely to be a gut coloniser. tidal flats from Korea and has been detected in human faeces (Bilen2018e) Lagier2016 Firmicutes Bacilli Bacillaceae vr SAER Swimming Rod Endospore 38
Rossellomorea marisflavi Bacillus marisflavi 1 Rare Possible Commensal Non/unknown Pathogen human faeces (Pfleiderer2013) and tidal flats from Korea Pfleiderer2013, RajilicStojanovic2014, Lagier2016 Firmicutes Bacilli Bacillaceae vr AER Swimming Rod Endospore 49
Rossellomorea vietnamensis Bacillus vietnamensis 1 Rare Possible Commensal Non/unknown Pathogen fish sauce, Vietnam Lagier2016 Firmicutes Bacilli Bacillaceae + AER Swimming Rod Endospore 43-44
Rothia aeria 1 Opportunistic in immunocompromised patients Minor Possible Commensal Opportunistic Pathogen air samples, clinical sources (sputum, blood, peritonean fluid - CCUG) and human faeces Pfleiderer2013, RajilicStojanovic2014, Lagier2016, Byrd2020, De2020, New2022, Hu2019, Vachida2019, Li2019b, PerezBrocal2015 Actinobacteria Actinomycetia Micrococcaceae + AER Coccus No spore 57.8
Rothia dentocariosa 2 Minor Possible Commensal Opportunistic Pathogen clinical sources (pleural fluid, infection, blood, sputum, bucca - CCUG) and human faeces Taylor1985, Bik2006, Dubourg2013, Pfleiderer2013, RajilicStojanovic2014, Lagier2016, Byrd2020, De2020, New2022, Zeller2014, Vachida2019, Li2019b, PerezBrocal2015 Actinobacteria Actinomycetia Micrococcaceae + AER Sessile Filamentous No spore
Rothia halotolerans Kocuria halotolerans Unlikely Transient Non/unknown Pathogen High salt required for optimum growth, so unlikely gut coloniser. saline soil and human faeces RajilicStojanovic2014, Lagier2016 Actinobacteria Actinomycetia Micrococcaceae + AER Sessile Coccus No spore 68.0
Rothia koreensis Kocuria koreensis Rare Possible Commensal Non/unknown Pathogen traditional fermented seafood, Korea Lagier2016 Actinobacteria Actinomycetia Micrococcaceae + AER Sessile Coccus No spore 65.2
Rothia kristinae Kocuria kristinae 1 Opportunistic in immunocompromised patients Rare Possible Commensal Opportunistic Pathogen human skin, clinical sources (blood, wound, skin - CCUG) and human faeces RajilicStojanovic2014, Lagier2016, Byrd2020 Actinobacteria Actinomycetia Micrococcaceae + FANA Sessile Tetrad No spore 72
Rothia mucilaginosa Stomatococcus mucilaginosus 2 Moderate Possible Commensal Opportunistic Pathogen Found in human breast milk (Jeurink2013). oral flora clinical sources (blood, sputum, urine - CCUG) and human faeces Wang2005, Bik2006, McLaughlin2010, Walker2011, Dubourg2013, Aujoulat2014, RajilicStojanovic2014, Lagier2016, Byrd2020, New2022, Chen2020, Dubinkina2017, Hu2019, Zeller2014, Vachida2019, Li2019b, PerezBrocal2015 Actinobacteria Actinomycetia Micrococcaceae + FANA Sessile Coccus No spore 56-60
Rothia terrae 1 Rare Possible Commensal Non/unknown Pathogen soil, Taiwan Lagier2016 Actinobacteria Actinomycetia Micrococcaceae + FANA Sessile Oval-shaped No spore 56.1
Rubeoparvulum massiliense Rare Possible Commensal Non/unknown Pathogen the faeces of a malnourished child, Senegal Lagier2016 Firmicutes Bacilli Bacillaceae neg FANA Swimming Rod No spore 43.8
Rubinisphaera brasiliensis Planctomyces brasiliensis 1 Non Transient Non/unknown Pathogen human faeces, marine and freshwater King2019 Planctomycetes Planctomycetia Planctomycetaceae neg FANA Swimming Coccus No spore 55.5-57.7
Rubneribacter badeniensis Minor Possible Commensal Non/unknown Pathogen In 14% of Europeans (unseenbio.com). Minor coloniser. human faeces (Danylec2018) Byrd2020 Actinobacteria Coriobacteriia Eggerthellaceae + SANA Sessile Rod No spore 65.1
Rubrobacter xylanophilus 1 Non Non-colonising Non/unknown Pathogen Hydrolyses xylan. High optimum growth temperature suggests it is not a regular gut commensal thermally polluted industrial runoff Cassir2015 Actinobacteria Rubrobacteria Rubrobacteraceae + AER Sessile Pleiomorph rod No spore 67.6
Rudanella lutea 1 Unlikely Transient Non/unknown Pathogen Obligate aerobe; unlikely to be a gut coloniser. human faeces, and air sample RajilicStojanovic2014 Bacteroidetes Cytophagia Cytophagaceae neg SAER Sessile Rod No spore 55
Ruminiclostridium cellobioparum Clostridium cellobioparum 1 Rare Possible Commensal Non/unknown Pathogen human faeces Benno1989, RajilicStojanovic2014, Lagier2016 Firmicutes Clostridia Clostridiaceae vr SANA Swimming Rod - curved Endospore 41
Ruminiclostridium cellulolyticum Clostridium cellulolyticum 1 Unlikely Transient Non/unknown Pathogen decayed grass Byrd2020, New2022, Zeller2014 Firmicutes Clostridia Clostridiaceae + ANA Swimming Rod Endospore 41
Ruminiclostridium herbifermentans Unlikely Transient Non/unknown Pathogen a lab-scale biogas fermenter fed with maize silage New2022 Firmicutes Clostridia Clostridiaceae vr ANA Swimming Rod - curved Endospore 33.2
Ruminiclostridium josui Clostridium josui 1 Rare Possible Commensal Non/unknown Pathogen Strongly degrades and consumes cellulose. compost, Thailand McLaughlin2010, Byrd2020 Firmicutes Clostridia Clostridiaceae + SANA Sessile Rod - curved Endospore 40 neg
Ruminococcus albus 1 Moderate Known Commensal Non/unknown Pathogen human faeces and rumenates Moore1974, Finegold1974, Holdeman1976, Finegold1977, Walker2011, deGoffau2013, RajilicStojanovic2014, Lagier2016, Rothschild2018, Byrd2020, New2022, Hu2019, Zeller2014, Vachida2019, Qin2012, Moore1995, Karlsson2013 Firmicutes Clostridia Oscillospiraceae + SANA Sessile Coccus No spore 43–46
Ruminococcus bicirculans Moderate Known Commensal Non/unknown Pathogen In 94% of Europeans (unseenbio.com). human faeces Lagier2016, Chung2019, Forster2019, King2019, Byrd2020, New2022, Jeong2021, Wang2020a, Urban2020, Minerbi2019 Firmicutes Clostridia Oscillospiraceae + SANA Sessile Coccus No spore 42-43
Ruminococcus bovis Unlikely Transient Non/unknown Pathogen a cow rumen New2022 Firmicutes Clostridia Oscillospiraceae + SANA Sessile Coccus No spore 34.6
Ruminococcus bromii Positive 1 Widespread Known Commensal Non/unknown Pathogen human faeces Finegold1974, Holdeman1976, Finegold1977, Benno1986, Benno1989, Mangin2004, PerisBondia2011, Walker2011, Zupancic2012, Tyakht2013, RajilicStojanovic2014, Salonen2014, Browne2016, Lagier2016, Rothschild2018, Zou2019, Chung2019, Forster2019, Byrd2020, De2020, Yang2020, Chen2020, Dubinkina2017, Hu2019, Jie2017, Zeller2014, Wang2018, Vachida2019, Wang2020a, Urban2020, Qin2012, Minerbi2019, Moore1995, Li2019b, LeChatelier2013, Karlsson2013, PerezBrocal2015 Firmicutes Clostridia Oscillospiraceae + SANA Sessile Coccus No spore 39–40
Ruminococcus callidus Positive 1 Widespread Known Commensal Non/unknown Pathogen human faeces Moore1974, Benno1984, Benno1986, Benno1989, McLaughlin2010, Walker2011, Zupancic2012, deGoffau2013, RajilicStojanovic2014, Salonen2014, Lagier2016, Rothschild2018, Zou2019, Forster2019, Byrd2020, Yang2020, Chen2020, Hu2019, Jeong2021, Vachida2019, Minerbi2019, Moore1995, PerezBrocal2015 Firmicutes Clostridia Oscillospiraceae + SANA Sessile Coccus No spore 43 20(neg)
Ruminococcus champanellensis Positive Moderate Known Commensal Non/unknown Pathogen In 72% of Europeans (unseenbio.com). human faeces RajilicStojanovic2014, Lagier2016, Rothschild2018, Forster2019, King2019, Byrd2020, Yang2020, New2022, Chen2020, Zeller2014, Wang2018, Vachida2019, LeChatelier2013 Firmicutes Clostridia Oscillospiraceae + SANA Sessile Coccus No spore 53.1
Ruminococcus flavefaciens 1 Moderate Known Commensal Non/unknown Pathogen human faeces (Ludwig2009), and rumen Finegold1974, PerisBondia2011, Walker2011, Zupancic2012, RajilicStojanovic2014, Rothschild2018, Almeida2019, Byrd2020, Hu2019, Zeller2014, Vachida2019, Minerbi2019, Moore1995, Karlsson2013, PerezBrocal2015 Firmicutes Clostridia Oscillospiraceae + SANA Sessile Coccus No spore 39–44
Ruminococcus gauvreauii Positive 1 Minor Known Commensal Non/unknown Pathogen In 19% of Europeans (unseenbio.com). Minor coloniser. human faeces PerisBondia2011, Walker2011, RajilicStojanovic2014, Lagier2016, Byrd2020, De2020 Firmicutes Clostridia Oscillospiraceae + SANA Sessile Coccus No spore
Ruminococcus gnavus Positive 1 Widespread Known Commensal Opportunistic Pathogen human faeces and clinical sources (blood, abscess, tissue - CCUG) Benno1986, Benno1989, Mangin2004, McLaughlin2010, Walker2011, Zupancic2012, Tyakht2013, Nielsen2014, RajilicStojanovic2014, Salonen2014, Cassir2015, Browne2016, Lagier2016, Rothschild2018, Zou2019, Almeida2019, Forster2019, Yang2020, New2022, Chen2020, Dubinkina2017, Hu2019, Jie2017, Zeller2014, Wang2018, Vachida2019, Wang2020a, Qin2012, Moore1995, Li2019b, LeChatelier2013, Karlsson2013, PerezBrocal2015 Firmicutes Clostridia Oscillospiraceae + SANA Sessile Coccus Endospore 41 20(+)
Ruminococcus lactaris 1 Widespread Known Commensal Non/unknown Pathogen human faeces Benno1986, Benno1989, Nam2008a, Walker2011, Tyakht2013, Nielsen2014, RajilicStojanovic2014, Salonen2014, Lagier2016, Rothschild2018, Zou2019, Forster2019, Yang2020, Chen2020, Dubinkina2017, Hu2019, Jie2017, Zeller2014, Wang2018, Vachida2019, Wang2020a, Minerbi2019, LeChatelier2013, Karlsson2013 Firmicutes Clostridia Oscillospiraceae + SANA Sessile Coccus No spore 43 20(d)
Ruminococcus phoceensis Rare Possible Commensal Non/unknown Pathogen human faeces (obese) Firmicutes Clostridia Oscillospiraceae + ANA Pleiomorph rod
Ruminococcus torques 1 Widespread Known Commensal Non/unknown Pathogen human faeces Nam2008a, Walker2011, Zupancic2012, Dubourg2013, Tyakht2013, Nielsen2014, RajilicStojanovic2014, Cassir2015, Browne2016, Lagier2016, Rothschild2018, Zou2019, Forster2019, King2019, Yang2020, Chen2020, Dubinkina2017, Hu2019, Jeong2021, Jie2017, Zeller2014, Wang2018, Vachida2019, Wang2020a, Urban2020, Qin2012, Moore1995, Li2019b, LeChatelier2013, Karlsson2013, PerezBrocal2015 Firmicutes Clostridia Oscillospiraceae + SANA Sessile Coccobacillus No spore 43 20(+)
Rummeliibacillus pycnus Bacillus pycnus 1 Unlikely Transient Non/unknown Pathogen Obligate aerobe; unlikely to be a gut coloniser. soil, Japan Lagier2016 Firmicutes Bacilli Planococcaceae + SAER Swimming Rod Endospore 35
Rummeliibacillus stabekisii Rare Possible Commensal Non/unknown Pathogen an aerospace facility, United States Lagier2016, New2022 Firmicutes Bacilli Planococcaceae + AER Swimming Rod Endospore 34.3
Rummeliibacillus suwonensis Rare Possible Commensal Non/unknown Pathogen mountain soil from Korea. Has also been detected in human faeces (Bilen2018e) Lagier2016 Firmicutes Bacilli Planococcaceae + FANA Sessile Rod Endospore 37.8
Ruoffia tabacinasalis Facklamia tabacinasalis 1 Rare Known Commensal Non/unknown Pathogen human faeces, and tobacco Pfleiderer2013, RajilicStojanovic2014, Lagier2016, Yang2020 Firmicutes Bacilli Aerococcaceae + FANA Coccus No spore 40
Ruthenibacterium lactatiformans Moderate Possible Commensal Non/unknown Pathogen In 99% of Europeans (unseenbio.com). human faeces (Shkoporov2016) Zou2019, Byrd2020, New2022, Wang2020a, Minerbi2019 Firmicutes Clostridia Oscillospiraceae neg FANA Sessile Rod No spore 56.5
Saccharibacillus brassicae Unlikely Transient Non/unknown Pathogen Borderline cold mesophile, so unlikely to be a gut coloniser. kimchi cabbage seeds New2022 Firmicutes Bacilli Paenibacillaceae + FANA Swimming Rod Endospore 58.4
Saccharofermentans acetigenes Non Possible Commensal Non/unknown Pathogen Fumarate is a product of fermentation of glucose. sludge treatment, China De2020 Firmicutes Clostridia Oscillospiraceae + SANA Sessile Oval-shaped Endospore 55.6
Salimicrobium jeotgali Non Transient Non/unknown Pathogen Likely to be a non-coloniser of the gut because it is strictly aerobic and has an optimal growth rate at high salt concentrations. anchovy jeotgal Lagier2016 Firmicutes Bacilli Bacillaceae + SAER Swimming Coccus No spore 46.3
Salinicoccus halodurans 1 Unlikely Transient Non/unknown Pathogen Borderline cold mesophile, with optimum growth temp of 28C. Unlikely gut coloniser. saline soil, China New2022 Firmicutes Bacilli Staphylococcaceae + AER Sessile Coccus No spore 45.8
Salinisphaera halophila Non Transient Non/unknown Pathogen Likely a gut non-coloniser because it requires high salt and is strictly aerobic. a brine salt well, China Lagier2016 Proteobacteria Gammaproteobacteria Salinisphaeraceae neg SAER Swimming Short Rod No spore 69.5
Salinivibrio costicola 1 Rare Possible Commensal Non/unknown Pathogen hypersaline environments and salted food Lagier2016 Proteobacteria Gammaproteobacteria Vibrionaceae neg FANA Swimming Rod - curved No spore 49.4-50.5
Salmonella bongori Salmonella enterica subsp. bongori 2 Zoonotic pathogen Rare Possible Commensal Opportunistic Pathogen human faeces (CCUG), cold-blooded animals and the environment Lagier2016, Byrd2020, Zeller2014 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Swimming Rod No spore 51.8
Salmonella enterica Negative 2 Zoonotic pathogen Unlikely Transient Known Pathogen human faeces, clinical (blood, urine - CCUG), and animal sources RajilicStojanovic2014, Lagier2016, Almeida2019, Byrd2020, De2020, New2022, Zeller2014 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Swimming Rod No spore 52-53
Salmonella enterica subsp. arizonae Salmonella arizonae Negative 2 Zoonotic pathogen Non Transient Possible Pathogen mainly cold-blooded animals Lagier2016 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Swimming Rod No spore 50-53
Salmonella enterica subsp. enterica serovar Choleraesuis 2 Zoonotic pathogen Unlikely Possible Commensal Known Pathogen human faeces Tyakht2013 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Swimming Rod No spore 50-53
Salmonella enterica subsp. enterica serovar Enteritidis Negative 2 Zoonotic pathogen Rare Non-commensal Known Pathogen human faeces Lagier2016 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Swimming Rod No spore 50-53
Salmonella enterica subsp. enterica serovar Paratyphi A Salmonella paratyphi Negative 2 Zoonotic pathogen Rare Non-commensal Known Pathogen human faeces Tyakht2013, Lagier2016 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Swimming Rod No spore 50-53
Salmonella enterica subsp. enterica serovar Typhi Negative 3 Vaccine available Rare Non-commensal Dangerous Pathogen human faeces. Only pathogenic in humans, causing typhoid fever Tyakht2013, Lagier2016 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Swimming Rod No spore 50-53
Salmonella enterica subsp. enterica serovar Typhimurium Salmonella typhimurium Negative 2 Zoonotic pathogen Rare Non-commensal Known Pathogen human faeces Tyakht2013, Lagier2016, Dubinkina2017 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Swimming Rod No spore 50-53
Sanguibacter massiliensis Rare Possible Commensal Non/unknown Pathogen human faeces (Bilen2018) Actinobacteria Actinomycetia Sanguibacteraceae + SANA Rod
Sarcina maxima Clostridium maximum 1 Rare Possible Commensal Non/unknown Pathogen human faeces, cereals, soil and horse manure RajilicStojanovic2014 Firmicutes Clostridia Clostridiaceae + ANA Sessile Coccus Endospore 28.6
Sarcina ventriculi Clostridium ventriculi 1 Minor Possible Commensal Rare Opportunist human faeces, clinical specimens (blood) and the environment Finegold1977, Aujoulat2014, RajilicStojanovic2014, Browne2016, Lagier2016, Forster2019, Byrd2020, Yang2020 Firmicutes Clostridia Clostridiaceae + ANA Sessile Coccus Endospore 30.6
Scardovia inopinata Bifidobacterium inopinatum 1 Opportunistic in immunocompromised patients Rare Possible Commensal Opportunistic Infection dental disease and human faeces RajilicStojanovic2014, De2020, New2022, Hu2019, Zeller2014, Vachida2019 Actinobacteria Actinomycetia Bifidobacteriaceae + ANA Sessile Coccus No spore 54
Scardovia wiggsiae Minor Possible Commensal Opportunistic Infection In 15% of Europeans (unseenbio.com). Minor coloniser. the human oral cavity and clinical sources Byrd2020, Hu2019, Vachida2019 Actinobacteria Actinobacteria Bifidobacteriaceae + ANA Sessile Pleiomorph rod No spore 55
Schaalia cardiffensis Actinomyces cardiffensis 2 Rare Unknown Opportunistic Pathogen human faeces RajilicStojanovic2014, New2022, Vachida2019 Actinobacteria Actinomycetia Actinomycetaceae + FANA Sessile Pleiomorph rod No spore
Schaalia hyovaginalis Actinomyces hyovaginalis 2 Animal pathogen Rare Unknown Non/unknown Pathogen porcine genital tract Cassir2015 Actinobacteria Actinomycetia Actinomycetaceae + FANA Sessile Diphtheroidal No spore 63
Schaalia meyeri Actinomyces meyeri 2 Rare Possible Commensal Opportunistic Pathogen clinical sources (brain abcess, cyst, subgingival crevice) New2022 Actinobacteria Actinomycetia Actinomycetaceae + ANA Sessile Rod No spore 67 20(neg)
Schaalia odontolytica Actinomyces odontolyticus 2 Human and animal pathogen Moderate Possible Commensal Opportunistic Pathogen dental disease, clinical sources (blood, cerebrospinal fluid, sputum, abscess - CCUG) and human faeces Bik2006, McLaughlin2010, Walker2011, Dubourg2013, Tyakht2013, RajilicStojanovic2014, Lagier2016, Forster2019, De2020, New2022, Dubinkina2017, Hu2019, Jeong2021, Zeller2014, Vachida2019 Actinobacteria Actinomycetia Actinomycetaceae + FANA Sessile Rod Exospore
Schaalia radingae Actinomyces radingae 2 Rare Possible Commensal Opportunistic Pathogen clinical sources (abscess, wound, blood - CCUG) and human faeces RajilicStojanovic2014, Lagier2016, Forster2019 Actinobacteria Actinomycetia Actinomycetaceae + FANA Sessile Rod No spore 60
Schaalia turicensis Actinomyces turicensis 2 Rare Possible Commensal Opportunistic Pathogen clinical sources (vagina, urine, abscess - CCUG) and human faeces RajilicStojanovic2014, Lagier2016, Hu2019, Vachida2019 Actinobacteria Actinomycetia Actinomycetaceae + FANA Sessile Rod - curved 57.5
Schleiferilactobacillus harbinensis Lactobacillus harbinensis 1 Unlikely Transient Non/unknown Pathogen human faeces (Bilen2018e), fermented foods and spoilt drinks Lagier2016 Firmicutes Bacilli Lactobacillaceae + FANA Sessile Rod No spore 53.3
Schleiferilactobacillus perolens Lactobacillus perolens 1 Unlikely Transient Non/unknown Pathogen spoilt softdrinks Lagier2016 Firmicutes Bacilli Lactobacillaceae + FANA Sessile Rod No spore 49-53
Schleiferilactobacillus shenzhenensis Lactobacillus shenzhenensis Unlikely Transient Non/unknown Pathogen Firmicutes Bacilli Lactobacillaceae
Schlesneria paludicola 1 Unlikely Transient Non/unknown Pathogen Low optimum growth temp, so unlikely gut coloniser. human faeces, and wetlands RajilicStojanovic2014 Planctomycetes Planctomycetia Planctomycetaceae neg FANA vr Filamentous No spore 54.4-56.5
Schnuerera ultunensis Clostridium ultunense 1 Unlikely Transient Non/unknown Pathogen anaerobic digester sludge New2022 Firmicutes Tissierellia Tissierellaceae + SANA Swimming Rod Endospore 32
Sebaldella termitidis Bacteroides termitidis 1 Unlikely Transient Non/unknown Pathogen posterior intestinal contents of termites New2022 Fusobacteria Fusobacteriia Leptotrichiaceae neg SANA Sessile Rod No spore 32-36
Sediminibacillus massiliensis Rare Possible Commensal Non/unknown Pathogen human faeces (Senghor2017a) Firmicutes Bacilli Bacillaceae + Rod
Sediminispirochaeta smaragdinae Spirochaeta smaragdinae 1 Unlikely Transient Non/unknown Pathogen High salt required for optimum growth, so unlikely gut coloniser. marine sediments Byrd2020, New2022, Qin2012 Spirochaetes Spirochaetia Spirochaetaceae neg SANA Swimming Spirochete No spore 50
Selenomonas artemidis 2 Rare Possible Commensal Opportunistic Infection gingival crevices Zeller2014 Firmicutes Negativicutes Selenomonadaceae neg SANA Swimming Rod No spore 57-58
Selenomonas bovis Rare Possible Commensal Non/unknown Pathogen yak rumen contents Byrd2020, Vachida2019 Firmicutes Negativicutes Selenomonadaceae neg SANA Swimming Rod - curved No spore 62.5-63.9
Selenomonas flueggei 2 Rare Possible Commensal Opportunistic Infection gingival crevices Zeller2014, Vachida2019 Firmicutes Negativicutes Selenomonadaceae neg SANA Swimming Rod - curved No spore 56-58
Selenomonas infelix 2 Rare Possible Commensal Opportunistic Infection gingival crevices Vachida2019 Firmicutes Negativicutes Selenomonadaceae neg SANA Swimming Rod - curved No spore 56-58
Selenomonas noxia 2 Rare Transient Opportunistic Pathogen human faeces and gingival crevices De2020, Yang2020, Zeller2014, Vachida2019 Firmicutes Negativicutes Selenomonadaceae neg SANA Swimming Rod - curved No spore 56-58
Selenomonas ruminantium 1 Minor Possible Commensal Non/unknown Pathogen human faeces, and cattle rumen Benno1986, Zupancic2012, RajilicStojanovic2014, Lagier2016, Almeida2019, Byrd2020, New2022 Firmicutes Negativicutes Selenomonadaceae neg SANA Swimming Rod - curved No spore 54
Selenomonas sputigena 1 Opportunistic in immunocompromised patients Rare Possible Commensal Possible Pathogen oral flora Lagier2016, De2020, New2022, Zeller2014, Vachida2019 Firmicutes Negativicutes Selenomonadaceae neg SANA Swimming Rod - curved No spore 57
Selenomonas timonae Unlikely Transient Rare Opportunist gingivitis patients, France New2022 Firmicutes Negativicutes Selenomonadaceae neg ANA Swimming Rod - curved Endospore
Sellimonas intestinalis Minor Possible Commensal Non/unknown Pathogen In 44% of Europeans (unseenbio.com). Minor coloniser. human faeces (Seo2016) Forster2019, Byrd2020, Yang2020, Minerbi2019 Firmicutes Clostridia Lachnospiraceae + SANA Swimming Diplococci No spore 45.3 4(+)
Senegalia massiliensis Rare Possible Commensal Non/unknown Pathogen human faeces (Traore2020) Lagier2016 Firmicutes Clostridia Clostridiaceae + Micr Swimming Rod No spore 27.4
Senegalimassilia anaerobia Minor Known Commensal Non/unknown Pathogen human faeces RajilicStojanovic2014, Lagier2016, Zou2019, Forster2019, Byrd2020, Yang2020, Minerbi2019 Actinobacteria Coriobacteriia Coriobacteriaceae + ANA Sessile Coccobacillus No spore 60-66.5
Senegalimassilia faecalis Rare Possible Commensal Non/unknown Pathogen human faeces (Han2020) Actinobacteria Coriobacteriia Coriobacteriaceae + SANA Sessile Coccobacillus 61.2
Serratia ficaria 1 Rare Possible Commensal Non/unknown Pathogen human faeces, figs, and wasps RajilicStojanovic2014 Proteobacteria Gammaproteobacteria Yersiniaceae neg FANA Swimming Rod No spore 59.4-59.7
Serratia fonticola 1 Rare Possible Commensal Opportunistic Pathogen human faeces, clinical sources (sputum, blood, wound - CCUG) and drinking water Woodmansey2004, RajilicStojanovic2014, Lagier2016 Proteobacteria Gammaproteobacteria Yersiniaceae neg FANA Swimming Rod No spore 48.8-52.5
Serratia liquefaciens 2 Invertebrate pathogen Rare Possible Commensal Opportunistic Pathogen human faeces, clinical sources (wound, abscess - CCUG) and the environment RajilicStojanovic2014, Lagier2016, Byrd2020, Vachida2019 Proteobacteria Gammaproteobacteria Yersiniaceae neg FANA Swimming Rod No spore 53-54
Serratia marcescens Negative 2 Human and animal pathogen Minor Possible Commensal Known Pathogen human faeces (Alkhalil2017 - high load in several ulcerative colitis patients), clinical sources (blood, sputum, urine - CCUG) and the environment RajilicStojanovic2014, Cassir2015, Lagier2016, Almeida2019, Byrd2020, De2020, New2022, Hu2019, Vachida2019 Proteobacteria Gammaproteobacteria Yersiniaceae neg FANA Swimming Rod No spore 57.5-60
Serratia odorifera 1 Opportunistic in immunocompromised patients Rare Possible Commensal Opportunistic Pathogen Differences in enzyme activities between published reports are labelled 'vr' and might represent strain variability. human faeces (CCUG) and clinical sources (wound, gall, urine - CCUG) Zeller2014 Proteobacteria Gammaproteobacteria Yersiniaceae neg FANA Swimming Rod No spore 54.6
Serratia quinivorans Serratia proteamaculans subsp. quinovora 1 Opportunistic in immunocompromised patients Rare Possible Commensal Opportunistic Infection soil, plant rhizosphere and insect GI tracts Yang2020 Proteobacteria Gammaproteobacteria Yersiniaceae neg FANA Swimming Rod No spore 53-54
Serratia ureilytica 1 Rare Possible Commensal Non/unknown Pathogen river water, India Lagier2016, Byrd2020 Proteobacteria Gammaproteobacteria Yersiniaceae neg FANA Swimming Rod No spore 60
Sharpea azabuensis Rare Possible Commensal Non/unknown Pathogen the faeces of thoroughbred horses Byrd2020 Firmicutes Bacilli Lactobacillaceae + SANA Sessile Rod No spore 36-38
Shewanella algae Shewanella alga 2 Unlikely Transient Opportunistic Pathogen S. algae produces tetrodotoxin, so unlikely to be a gut coloniser without causing severe illness. Can reduce Fe(III) with lactate as a donor. human faeces (CCUG as S. alga), red algae and clinical sources (tissue, blood, trachea - CCUG) Lagier2016, Li2019b Proteobacteria Gammaproteobacteria Shewanellaceae neg FANA Swimming Rod No spore 54
Shewanella carassii Rare Possible Commensal Non/unknown Pathogen human faeces (Fang2017) Proteobacteria Gammaproteobacteria Shewanellaceae neg FANA Swimming Rod No spore 52.7
Shewanella decolorationis 1 Rare Possible Commensal Non/unknown Pathogen A dye-decolourising bacterium. Reduces Fe(III) to Fe(II) using lactate as an electron donor. activated sludge of a waste-water treatment plant, China Byrd2020 Proteobacteria Gammaproteobacteria Shewanellaceae neg FANA Swimming Rod No spore 49.3
Shewanella xiamenensis Rare Possible Commensal Non/unknown Pathogen Reduces Fe(III) to Fe(II) using lactate as an electron donor. coastal sediment, China Lagier2016 Proteobacteria Gammaproteobacteria Shewanellaceae neg FANA Swimming Rod No spore 46
Shigella boydii Negative 2 Rare Unknown Known Pathogen human faeces (including ulcerative colitis patients - Alkhalil2017) Lagier2016, New2022 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Sessile Rod No spore
Shigella dysenteriae Negative 3 Unlikely Transient Dangerous Pathogen human faeces RajilicStojanovic2014, Lagier2016, Zou2019, De2020, New2022 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Sessile Rod No spore 53
Shigella flexneri Negative 2 Human and animal pathogen Minor Unknown Known Pathogen human faeces (Alkhalil2017 - including ulcerative colitis patients) McLaughlin2010, Pandey2012, Zupancic2012, RajilicStojanovic2014, Lagier2016, Zou2019, New2022, Hu2019, Vachida2019 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Sessile Rod No spore 49
Shigella sonnei Negative 2 Human and animal pathogen Minor Possible Commensal Known Pathogen human faeces (Alkhalil2017 - high load in several ulcerative colitis patients) and blood McLaughlin2010, Walker2011, RajilicStojanovic2014, Lagier2016, Forster2019, De2020, New2022, Hu2019, Vachida2019 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Sessile Rod No spore 51
Shuttleworthia satelles 2 Rare Possible Commensal Non/unknown Pathogen the human oral cavity Byrd2020, Zeller2014, Vachida2019 Firmicutes Clostridia Lachnospiraceae + SANA Sessile Rod - curved No spore 51 S(20)
Silanimonas lenta 1 Non Transient Non/unknown Pathogen Obligate aerobe and high salt required for optimum growth, so likely a gut non-coloniser. human faeces, and hot springs RajilicStojanovic2014 Proteobacteria Gammaproteobacteria Lysobacteraceae neg SAER Swimming Rod No spore 50.7
Skermanella aerolata 1 Unlikely Transient Non/unknown Pathogen Obligate aerobe; unlikely to be a gut coloniser. human faeces, and air sample RajilicStojanovic2014 Proteobacteria Alphaproteobacteria Azospirillaceae neg SAER Swimming Rod No spore 65
Slackia equolifaciens Rare Possible Commensal Non/unknown Pathogen human faeces RajilicStojanovic2014, Lagier2016 Actinobacteria Coriobacteriia Eggerthellaceae + SANA Sessile Rod No spore 60.8
Slackia exigua Eubacterium exiguum 2 Rare Possible Commensal Opportunistic Pathogen clinical sources (fistula, blood, dental disease - CCUG) and human faeces RajilicStojanovic2014, Lagier2016, Byrd2020, Zeller2014, Vachida2019 Actinobacteria Coriobacteriia Eggerthellaceae + SANA Sessile Rod No spore 60 20(neg)
Slackia faecicanis 1 Rare Possible Commensal Non/unknown Pathogen dog faeces and has been detected in human faeces (Alkhalil2017) Actinobacteria Coriobacteriia Eggerthellaceae + SANA Rod No spore 61.2 w
Slackia heliotrinireducens Peptostreptococcus heliotrinreducens 1 Rare Possible Commensal Non/unknown Pathogen ovine rumen Byrd2020, De2020, New2022, Zeller2014, Qin2012 Actinobacteria Coriobacteriia Eggerthellaceae + SANA Sessile Coccus No spore 36.1 S
Slackia isoflavoniconvertens Rare Possible Commensal Non/unknown Pathogen Produces equol (an isoflavandiol aestrogen) from daidzein. human faeces RajilicStojanovic2014, Lagier2016 Actinobacteria Coriobacteriia Eggerthellaceae + SANA Sessile Rod No spore 58.5
Slackia piriformis Minor Possible Commensal Non/unknown Pathogen human faeces RajilicStojanovic2014, Lagier2016, Forster2019, Byrd2020, Yang2020, Chen2020, Hu2019, Vachida2019 Actinobacteria Coriobacteriia Eggerthellaceae + SANA Sessile Club rod No spore 58.3 20(w)
Sneathia sanguinegens Leptotrichia sanguinegens 1 Opportunistic in immunocompromised patients Rare Possible Commensal Opportunistic Pathogen human faeces and clinical sources (amniotic fluid, blood, abdomen - CCUG) Aujoulat2014, Byrd2020, Yang2020 Fusobacteria Fusobacteriia Leptotrichiaceae neg ANA Sessile Rod No spore 22-25
Sneathia vaginalis Sneathia amnii Rare Possible Commensal Possible Pathogen Sneathia vaginalis same as 'Sneathia amnii'. Simple metabolism, utilising glycogen, maltose and glucose. human clinical specimens (mid-vaginal wall, amniotic fluid) Byrd2020 Fusobacteria Fusobacteriia Leptotrichiaceae neg ANA Sessile Pleiomorph rod No spore 28
Sodaliphilus pleomorphus Rare Possible Commensal Non/unknown Pathogen Probably uses fructan and amylose. pig faeces New2022 Bacteroidetes Bacteroidia Muribaculaceae neg SANA Rod No spore 54.4
Soleaferrea massiliensis Rare Known Commensal Non/unknown Pathogen human faeces Pfleiderer2013, RajilicStojanovic2014, Lagier2016, Byrd2020 Firmicutes Clostridia Oscillospiraceae + FANA Sessile Rod - curved
Solibacillus silvestris Bacillus silvestris 1 Unlikely Transient Non/unknown Pathogen Obligate aerobe; unlikely to be a gut coloniser. forest soil, Germany Lagier2016, Byrd2020 Firmicutes Bacilli Planococcaceae + SAER Swimming Rod Endospore 39.3
Solibaculum mannosilyticum Rare Possible Commensal Non/unknown Pathogen human faeces Firmicutes Clostridia Oscillospiraceae vr ANA Sessile Rod No spore 50.6 20(+)
Solobacterium moorei Bulleidia moorei 1 Minor Known Commensal Non/unknown Pathogen human faeces and blood Walker2011, RajilicStojanovic2014, Salonen2014, Lagier2016, Zou2019, Byrd2020, Yang2020, Chen2020, Dubinkina2017, Hu2019, Jie2017, Zeller2014, Vachida2019, PerezBrocal2015 Firmicutes Erysipelotrichia Erysipelotrichaceae + SANA Sessile Rod No spore 37-39
Sorangium cellulosum 1 Rare Possible Commensal Non/unknown Pathogen Produces sporangioles and myxospores. Metabolites include epothilone, soraphen, sorangicin, and tartrolon. soil, animal faeces and decaying plant material New2022, Zeller2014 Proteobacteria Deltaproteobacteria Sorangiineae neg Gliding Pleiomorph rod Exospore 69-72
Sphaerotilus natans 1 Unlikely Transient Non/unknown Pathogen Obligate aerobe; unlikely to be a gut coloniser. human faeces and sewage De2020, Yang2020 Proteobacteria Betaproteobacteria Burkholderiales genera incertae sedis neg SAER Swimming Filamentous No spore
Sphingobacterium alimentarium Unlikely Transient Non/unknown Pathogen Obligate aerobe; unlikely to be a gut coloniser. human faeces and raw cow's milk Yang2020 Bacteroidetes Sphingobacteriia Sphingobacteriaceae neg SAER Sessile Rod No spore 39.3
Sphingobacterium faecium 1 Rare Possible Commensal Non/unknown Pathogen human faeces Bacteroidetes Sphingobacteriia Sphingobacteriaceae neg AER Sessile Rod No spore 39.0-40.4
Sphingobacterium mizutaii Flavobacterium mizutaii 1 Opportunistic in immunocompromised patients Unlikely Transient Rare Opportunist Obligate aerobe; unlikely to be a gut coloniser. human faeces and clinical sources (ventricular fluid - CCUG) Yang2020 Bacteroidetes Sphingobacteriia Sphingobacteriaceae neg SAER Sessile Rod No spore 39.3-40.0 40(+)
Sphingobacterium multivorum Flavobacterium multivorum 2 Rare Possible Commensal Opportunistic Pathogen human faeces and clinical sources (sputum, blood, urine - CCUG) RajilicStojanovic2014, Lagier2016 Bacteroidetes Sphingobacteriia Sphingobacteriaceae neg AER Sessile Rod No spore 42.2 20(d)
Sphingobacterium nematocida Unlikely Transient Non/unknown Pathogen Obligate aerobe; unlikely to be a gut coloniser. human faeces and leaf tissue Yang2020 Bacteroidetes Sphingobacteriia Sphingobacteriaceae neg SAER Sessile Rod No spore 40.6
Sphingobacterium siyangense Rare Possible Commensal Non/unknown Pathogen farm soil, China Bacteroidetes Sphingobacteriia Sphingobacteriaceae neg SAER Sessile Rod No spore 38.5
Sphingobacterium spiritivorum Flavobacterium spiritivorum 2 Rare Possible Commensal Opportunistic Pathogen clinical specimens (blood, wound, urine, sputum, bone marrow) Qin2012 Bacteroidetes Sphingobacteriia Sphingobacteriaceae neg FANA Sessile Rod No spore 41.4
Sphingobacterium thalpophilum 2 Unlikely Transient Opportunistic Pathogen clinical sources New2022 Bacteroidetes Sphingobacteriia Sphingobacteriaceae neg AER Sessile Rod No spore 45.0
Sphingobium xenophagum Sphingomonas xenophagum 1 Unlikely Transient Non/unknown Pathogen river water and human faeces Yang2020 Proteobacteria Alphaproteobacteria Sphingomonadaceae neg AER vr Rod No spore 62.9
Sphingomonas adhaesiva 1 Unlikely Transient Non/unknown Pathogen Obligate aerobe; unlikely to be a gut coloniser. human faeces, and a clean surface McLaughlin2010, RajilicStojanovic2014 Proteobacteria Alphaproteobacteria Sphingomonadaceae neg SAER Sessile Rod No spore 67.2
Sphingomonas aerolata 1 Non Transient Non/unknown Pathogen Unlikely gut coloniser because this organism doesn't grow at 37C. an air sample, UK, and an old ice sample from Antarctica Lagier2016 Proteobacteria Alphaproteobacteria Sphingomonadaceae neg AER Swimming Short Rod No spore 65.4
Sphingomonas aestuarii Unlikely Transient Non/unknown Pathogen tidal flats and human faeces Yang2020 Proteobacteria Alphaproteobacteria Sphingomonadaceae neg AER Sessile Rod No spore
Sphingomonas azotifigens 1 Rare Possible Commensal Non/unknown Pathogen the roots of Asian rice, Japan PerezBrocal2015 Proteobacteria Alphaproteobacteria Sphingomonadaceae neg AER Swimming Rod No spore 66.0-68.0
Sphingomonas bisphenolicum Unlikely Transient Non/unknown Pathogen Frank2007 Proteobacteria Alphaproteobacteria Sphingomonadaceae neg AER Swimming Rod No spore
Sphingomonas echinoides Pseudomonas echinoides 1 Unlikely Transient Non/unknown Pathogen human faeces and a laboratory contaminant on a nutrient agar plate Yang2020 Proteobacteria Alphaproteobacteria Sphingomonadaceae neg AER Swimming Rod - curved No spore 65.8
Sphingomonas glacialis Unlikely Transient Non/unknown Pathogen Can't grow at 37C, so unlikely to be a gut coloniser. human faeces and glacier from Austria Yang2020 Proteobacteria Alphaproteobacteria Sphingomonadaceae neg AER Sessile Rod No spore 67.9
Sphingomonas hankookensis Rare Possible Commensal Non/unknown Pathogen wastewater treatment, Korea Yang2020 Proteobacteria Alphaproteobacteria Sphingomonadaceae neg FANA Sessile Rod No spore 67.2
Sphingomonas koreensis 1 Unlikely Transient Non/unknown Pathogen human faeces and mineral water from Korea Yang2020 Proteobacteria Alphaproteobacteria Sphingomonadaceae neg AER Swimming Rod No spore 66
Sphingomonas melonis 1 Plant pathogen Rare Possible Commensal Non/unknown Pathogen fruit disease, Japan Yang2020 Proteobacteria Alphaproteobacteria Sphingomonadaceae neg AER Sessile Rod No spore 65.0
Sphingomonas panni 1 Rare Possible Commensal Non/unknown Pathogen human faeces McLaughlin2010, RajilicStojanovic2014 Proteobacteria Alphaproteobacteria Sphingomonadaceae neg Micr Sessile Rod No spore
Sphingomonas paucimobilis Pseudomonas paucimobilis 2 Rare Possible Commensal Opportunistic Pathogen clinical sources (blood, wound, spinal fluid - CCUG) and human faeces McLaughlin2010, RajilicStojanovic2014, Lagier2016, Byrd2020 Proteobacteria Alphaproteobacteria Sphingomonadaceae neg AER Swimming Rod No spore 62-64
Sphingomonas pseudosanguinis 1 Rare Possible Commensal Non/unknown Pathogen surfaces and human faeces RajilicStojanovic2014, Lagier2016, Yang2020 Proteobacteria Alphaproteobacteria Sphingomonadaceae neg AER Swimming Rod No spore
Sphingomonas sinipercae Unlikely Transient Non/unknown Pathogen Obligate aerobe; unlikely to be a gut coloniser. fish intestines New2022 Proteobacteria Alphaproteobacteria Sphingomonadaceae neg SAER Sessile Rod No spore 65.5
Sphingomonas yabuuchiae 1 Rare Possible Commensal Non/unknown Pathogen an air sample PerezBrocal2015 Proteobacteria Alphaproteobacteria Sphingomonadaceae neg AER Rod No spore 66.1
Sphingopyxis bauzanensis Unlikely Transient Non/unknown Pathogen Can't grow at 37C, so unlikely to be a gut coloniser. human faeces and contaminated soil from Italy Yang2020 Proteobacteria Alphaproteobacteria Sphingomonadaceae neg AER Swimming Rod No spore 64.4
Spiribacter roseus Non Transient Non/unknown Pathogen Strict aerobe and high optimum salt concentration suggests this organism is likely to be a gut non-coloniser. pond water, Spain New2022 Proteobacteria Gammaproteobacteria Ectothiorhodospiraceae neg SAER Sessile Rod - curved No spore 64.2
Spirochaeta coccoides 1 Rare Possible Commensal Non/unknown Pathogen a termite hindgut Qin2012 Spirochaetes Spirochaetia Sphaerochaetaceae neg ANA Sessile Coccus No spore 56.6-57.4
Spirochaeta thermophila 1 Non Transient Non/unknown Pathogen Very high optimum temperature (66-68) suggests this organism is not a gut coloniser. marine hot springs, Russia New2022 Spirochaetes Spirochaetia Spirochaetaceae neg SANA Swimming Helical No spore 52
Spirosoma linguale 1 Unlikely Transient Non/unknown Pathogen human faeces, freshwater, and soil RajilicStojanovic2014 Bacteroidetes Cytophagia Cytophagaceae neg AER Gliding Helical No spore 51-53
Sporobacter termitidis 1 Rare Possible Commensal Non/unknown Pathogen Produces methanethiol. termite gut and detected in human faeces Salonen2014, Byrd2020 Firmicutes Clostridia Oscillospiraceae + SANA Swimming Rod - curved Endospore 57
Sporolactobacillus laevolacticus Bacillus laevolacticus 1 Unlikely Transient Non/unknown Pathogen plant rhizospheres Lagier2016 Firmicutes Bacilli Sporolactobacillaceae + FANA Swimming Rod Endospore 43-45
Sporolactobacillus nakayamae subsp. racemicus 1 Rare Possible Commensal Non/unknown Pathogen soil and alcoholic breverage brewing, Japan Firmicutes Bacilli Sporolactobacillaceae + FANA Swimming Rod Endospore 43-46
Sporomusa termitida 1 Unlikely Transient Non/unknown Pathogen Sporomusa species don't ferment sugars. Homoacetogen. the gut contents of termites New2022 Firmicutes Negativicutes Sporomusaceae neg SANA Swimming Rod - curved Endospore 48.6
Sporosarcina aquimarina 1 Non Transient Non/unknown Pathogen Not likely to be a gut coloniser because this organism doesn't grow well at 37C. seawater, Korea Lagier2016 Firmicutes Bacilli Planococcaceae + FANA Swimming Rod Endospore 40
Sporosarcina koreensis 1 Unlikely Transient Non/unknown Pathogen Obligate aerobe; unlikely to be a gut coloniser. human faeces, blood and soil RajilicStojanovic2014, Lagier2016 Firmicutes Bacilli Planococcaceae + SAER Swimming Rod Endospore 46.5
Sporosarcina luteola Rare Possible Commensal Non/unknown Pathogen soy sauce production equipment, Japan Lagier2016 Firmicutes Bacilli Planococcaceae vr FANA Swimming Rod Endospore 43.6
Sporosarcina siberiensis Unlikely Transient Non/unknown Pathogen Borderline cold mesophile, with optimum growth temp of 28C. Unlikely gut coloniser. human faeces and East Siberian Sea Yang2020 Firmicutes Bacilli Planococcaceae + AER Sessile Rod Unknown 39
Stackebrandtia nassauensis 1 Unlikely Transient Non/unknown Pathogen soil, Bahamas New2022, Zeller2014 Actinobacteria Actinomycetia Glycomycetaceae + AER Sessile Filamentous Exospore 72.4
Staphylococcus arlettae Positive 1 Rare Known Commensal Non/unknown Pathogen animal sources and human faeces RajilicStojanovic2014, Lagier2016 Firmicutes Bacilli Staphylococcaceae + FANA Sessile Coccus No spore 31.0-32.6
Staphylococcus aureus subsp. aureus Staphylococcus aureus 2 Human and animal pathogen Minor Possible Commensal Known Pathogen Found in human breast milk (Jeurink2013). human skin, clinical sources (respiratory tract, wound, urine, cerebrospinal fluid, vagina - CCUG) and human faeces (infant - CCUG) Finegold1974, Finegold1977, Benno1984, Benno1989, Woodmansey2004, Pfleiderer2013, RajilicStojanovic2014, Cassir2015, Almeida2019, Byrd2020, New2022, Dubinkina2017, Zeller2014, Vachida2019 Firmicutes Bacilli Staphylococcaceae + FANA Sessile Coccus No spore 32-36
Staphylococcus auricularis 1 Rare Possible Commensal Non/unknown Pathogen human ear and human faeces RajilicStojanovic2014, Lagier2016 Firmicutes Bacilli Staphylococcaceae + FANA Sessile Tetrad No spore 38-39
Staphylococcus capitis subsp. capitis Staphylococcus capitis 1 Opportunistic in immunocompromised patients Rare Possible Commensal Rare Opportunist Found in human breast milk (Jeurink2013). human skin, head, clinical sources (blood - CCUG) and human faeces Dubourg2013, Pfleiderer2013, RajilicStojanovic2014, Lagier2016, Yang2020, Zeller2014 Firmicutes Bacilli Staphylococcaceae + FANA Sessile Diplococci No spore 31-38.8
Staphylococcus caprae 2 Human and animal pathogen Rare Possible Commensal Opportunistic Pathogen human faeces, goats' milk and clinical specimens (blood, knee aspirate, infection) Pfleiderer2013, RajilicStojanovic2014, Lagier2016 Firmicutes Bacilli Staphylococcaceae + FANA Sessile Coccus No spore 35-37
Staphylococcus carnosus 1 Rare Possible Commensal Non/unknown Pathogen dry sausage Lagier2016, Byrd2020, Zeller2014 Firmicutes Bacilli Staphylococcaceae + FANA Sessile Coccus No spore 35-36
Staphylococcus cohnii subsp. cohnii Staphylococcus cohnii 1 Opportunistic in immunocompromised patients Rare Possible Commensal Opportunistic Infection human skin and human faeces Dubourg2013, Pfleiderer2013, Aujoulat2014, RajilicStojanovic2014, Lagier2016, Yang2020 Firmicutes Bacilli Staphylococcaceae + FANA Sessile Diplococci No spore 36-38
Staphylococcus condimenti 1 Rare Possible Commensal Non/unknown Pathogen soy sauce and human faeces RajilicStojanovic2014, Lagier2016 Firmicutes Bacilli Staphylococcaceae + FANA Sessile Coccus No spore 35.2-36
Staphylococcus devriesei Rare Possible Commensal Non/unknown Pathogen teats of dairy cows and milk Lagier2016 Firmicutes Bacilli Staphylococcaceae + FANA Sessile Coccus No spore 33.3
Staphylococcus epidermidis 2 Human and animal pathogen Widespread Known Commensal Opportunistic Pathogen A significant member of the seeding microbiota that colonises the gut of C-section newborns but also found in breast milk (Jeurink2013). skin, clinical sources (wounds, infections) and human faeces Moore1974, Finegold1974, Holdeman1976, Finegold1977, Benno1984, Taylor1985, Benno1986, Benno1989, Woodmansey2004, McLaughlin2010, Dubourg2013, Pfleiderer2013, Aujoulat2014, RajilicStojanovic2014, Cassir2015, Lagier2016, Zou2019, Almeida2019, Forster2019, Byrd2020, New2022, Zeller2014, PerezBrocal2015 Firmicutes Bacilli Staphylococcaceae + FANA Sessile Diplococci No spore 30-37
Staphylococcus equorum subsp. equorum Staphylococcus equorum 1 Rare Possible Commensal Non/unknown Pathogen skin of horses, seafood, cheese and human faeces RajilicStojanovic2014, Lagier2016, Byrd2020, PerezBrocal2015 Firmicutes Bacilli Staphylococcaceae + AER Sessile Coccus No spore 33.4-34.7
Staphylococcus gallinarum 1 Rare Possible Commensal Non/unknown Pathogen poultry Lagier2016, Yang2020 Firmicutes Bacilli Staphylococcaceae + FANA Sessile Coccus No spore 34.5
Staphylococcus haemolyticus 2 Human and animal pathogen Minor Possible Commensal Opportunistic Pathogen human sources, clinical sources (infections, urine, blood, wound - CCUG) and human faeces MacFarlane2004, Woodmansey2004, Pandey2012, Dubourg2013, Pfleiderer2013, Aujoulat2014, RajilicStojanovic2014, Cassir2015, Lagier2016, De2020, Zeller2014, PerezBrocal2015 Firmicutes Bacilli Staphylococcaceae + FANA Sessile Diplococci No spore 34-36
Staphylococcus hominis subsp. hominis Staphylococcus hominis 2 Minor Possible Commensal Opportunistic Pathogen Found in human breast milk (Jeurink2013). human skin, clinical sources (infections, blood) and human faeces McLaughlin2010, Dubourg2013, Pfleiderer2013, Aujoulat2014, RajilicStojanovic2014, Cassir2015, Lagier2016, Almeida2019, Byrd2020, Yang2020, Zeller2014 Firmicutes Bacilli Staphylococcaceae + FANA Sessile Coccus No spore 30-36
Staphylococcus hyicus 2 Animal pathogen Rare Possible Commensal Possible Pathogen pigs (pathogenic) Lagier2016 Firmicutes Bacilli Staphylococcaceae + FANA Sessile Coccus No spore 32.9
Staphylococcus intermedius 2 Zoonotic pathogen Rare Possible Commensal Possible Pathogen human faeces, and animals Taylor1985, Dubourg2013, RajilicStojanovic2014, Lagier2016 Firmicutes Bacilli Staphylococcaceae + FANA Sessile Diplococci No spore 31-36
Staphylococcus kloosii 1 Rare Possible Commensal Non/unknown Pathogen human faeces, and animals MacFarlane2004, Woodmansey2004, RajilicStojanovic2014, Lagier2016 Firmicutes Bacilli Staphylococcaceae + AER Sessile Coccus No spore 31-32.3
Staphylococcus lugdunensis 2 Rare Known Commensal Opportunistic Pathogen clinical sources (wound, urine, blood, infection - CCUG) and human faeces RajilicStojanovic2014, Lagier2016, Almeida2019 Firmicutes Bacilli Staphylococcaceae + FANA Sessile Coccus No spore 32
Staphylococcus nepalensis 2 Animal pathogen Rare Possible Commensal Opportunistic Pathogen human faeces and goats with pneumonia from the Himalayas Lagier2016, Forster2019 Firmicutes Bacilli Staphylococcaceae + FANA Sessile Coccus No spore 33
Staphylococcus pasteuri 2 Minor Known Commensal Opportunistic Pathogen clinical sources (vomit, blood, wound), animals, food and human faeces McLaughlin2010, Walker2011, Dubourg2013, Pfleiderer2013, RajilicStojanovic2014, Cassir2015, Lagier2016, Byrd2020 Firmicutes Bacilli Staphylococcaceae + FANA Sessile Coccus No spore 35
Staphylococcus petrasii Staphylococcus jettensis Rare Possible Commensal Opportunistic Pathogen clinical sources and ear infections Lagier2016, Byrd2020 Firmicutes Bacilli Staphylococcaceae + FANA Sessile Coccus No spore 34.9
Staphylococcus pettenkoferi 2 Rare Known Commensal Possible Pathogen clinical sources (blood) and human faeces RajilicStojanovic2014, Lagier2016, Yang2020 Firmicutes Bacilli Staphylococcaceae + FANA Sessile Coccus No spore
Staphylococcus pseudintermedius 2 Human and animal pathogen Rare Possible Commensal Opportunistic Pathogen human faeces, clinical sources (wound, blood, infection - CCUG) animal lesions Forster2019, Byrd2020 Firmicutes Bacilli Staphylococcaceae + FANA Sessile Coccus No spore 38
Staphylococcus saccharolyticus Peptococcus saccharolyticus 2 Rare Possible Commensal Opportunistic Pathogen human faeces, clinical sources (blood, bone marrow, infections - CCUG) and skin Benno1984, RajilicStojanovic2014, Lagier2016 Firmicutes Bacilli Staphylococcaceae + ANA Sessile Coccus No spore 33-34
Staphylococcus saprophyticus subsp. saprophyticus Staphylococcus saprophyticus 2 Rare Known Commensal Known Pathogen human skin, clinical sources (UTI, urine - CCUG) and human faeces Pfleiderer2013, Cassir2015, Byrd2020, Yang2020, Dubinkina2017, Zeller2014 Firmicutes Bacilli Staphylococcaceae + FANA Sessile Coccus No spore 31-36
Staphylococcus schleiferi subsp. schleiferi Staphylococcus schleiferi 2 Human and animal pathogen Rare Known Commensal Opportunistic Pathogen clinical sources (wound, blood, catheter) and human faeces RajilicStojanovic2014, Lagier2016, Byrd2020 Firmicutes Bacilli Staphylococcaceae + FANA Sessile Coccus No spore 37
Staphylococcus simiae 2 Animal pathogen Rare Possible Commensal Non/unknown Pathogen faeces of a squirrel monkey Cassir2015 Firmicutes Bacilli Staphylococcaceae + FANA Sessile Coccus No spore 33.8
Staphylococcus simulans 1 Human and animal pathogen; opportunistic in immunocompromised patients Rare Known Commensal Opportunistic Pathogen human skin, primates, human faeces and clinical sources (urine, wound, vagina - CCUG) MacFarlane2004, Woodmansey2004, RajilicStojanovic2014, Lagier2016, De2020 Firmicutes Bacilli Staphylococcaceae + FANA Sessile Diplococci No spore 34-38
Staphylococcus succinus subsp. succinus Staphylococcus succinus 1 Unlikely Transient Non/unknown Pathogen Borderline cold mesophile, with optimum growth temp of 28C. Unlikely gut coloniser. human faeces, and amber RajilicStojanovic2014, Cassir2015, Lagier2016, Byrd2020 Firmicutes Bacilli Staphylococcaceae + AER Sessile Coccus No spore 34.4-35 40(+)
Staphylococcus warneri 1 Human and animal pathogen; opportunistic in immunocompromised patients Minor Known Commensal Opportunistic Pathogen human skin, primates, human faeces and clinical sources (blood, sputum, wound, vagina - CCUG) MacFarlane2004, Woodmansey2004, Dubourg2013, Pfleiderer2013, Aujoulat2014, RajilicStojanovic2014, Cassir2015, Lagier2016, Zou2019, Byrd2020, Zeller2014 Firmicutes Bacilli Staphylococcaceae + FANA Sessile Coccus No spore 34-35
Staphylococcus xylosus 1 Human and animal pathogen; opportunistic in immunocompromised patients Rare Known Commensal Known Pathogen humans, animals, human faeces and clinical sources (blood) RajilicStojanovic2014, Cassir2015, Lagier2016, Forster2019, Byrd2020 Firmicutes Bacilli Staphylococcaceae + FANA Sessile Coccus No spore 30-36
Starkeya novella Thiobacillus novellus 1 Unlikely Transient Non/unknown Pathogen Requires biotin. Strict aerobe suggests it is unlikely to be a gut coloniser. soil Zeller2014 Proteobacteria Alphaproteobacteria Xanthobacteraceae neg SAER Sessile Rod No spore 67.3-68.4
Stenotrophomonas acidaminiphila 1 Unlikely Transient Opportunistic Pathogen Obligate aerobe; unlikely to be a gut coloniser. sludge reactor, clinical sources (trachea, urine, blood - CCUG) and detected in human faeces (Bilen2018e) Lagier2016, PerezBrocal2015 Proteobacteria Gammaproteobacteria Xanthomonadaceae neg SAER Swimming Rod No spore 66.9
Stenotrophomonas bentonitica Unlikely Transient Non/unknown Pathogen Aerobic and optimum growth temperature of 28C suggests this is an unlikely gut coloniser. bentonite formations, Spain Byrd2020 Proteobacteria Gammaproteobacteria Xanthomonadaceae neg AER Sessile Rod No spore 66.5
Stenotrophomonas maltophilia Pseudomonas maltophilia 2 Human and animal pathogen Minor Possible Commensal Opportunistic Pathogen clinical sources (sputum, blood, urine, wound - CCUG) and human faeces McLaughlin2010, Walker2011, RajilicStojanovic2014, Lagier2016, Almeida2019, Forster2019, Yang2020, New2022, Zeller2014, Vachida2019 Proteobacteria Gammaproteobacteria Xanthomonadaceae neg AER Swimming Rod No spore 67
Stenotrophomonas rhizophila 1 Rare Possible Commensal Non/unknown Pathogen Show antifungal activity against C. albicans, Rhizoctonia solani, Sclerotinia sclerotiiorum and Verticillium dahliae. Produces trehalose and glucosylglycerol as osmolytes. rhizosphere, soil and human faeces RajilicStojanovic2014, Lagier2016, Yang2020 Proteobacteria Gammaproteobacteria Xanthomonadaceae neg AER Swimming Rod - curved No spore
Stomatobaculum longum Minor Possible Commensal Rare Opportunist In 27% of Europeans (unseenbio.com). Minor coloniser. human faeces and subgingival dental plaque Byrd2020, Yang2020, Hu2019, Vachida2019 Firmicutes Clostridia Lachnospiraceae vr SANA Sessile Rod No spore 55.0-55.3 neg
Streptobacillus hongkongensis Rare Possible Commensal Opportunistic Pathogen clinical sources (pus) De2020 Fusobacteria Fusobacteriia Leptotrichiaceae neg FANA Sessile Pleiomorph rod No spore 24-26
Streptobacillus moniliformis 2 Zoonotic pathogen Unlikely Transient Non/unknown Pathogen rat nasopharynx Byrd2020, New2022, Zeller2014 Fusobacteria Fusobacteriia Leptotrichiaceae neg FANA Sessile Rod No spore 26.3
Streptococcus acidominimus 2 Human and animal pathogen Unlikely Transient Non/unknown Pathogen cattle and milk New2022 Firmicutes Bacilli Streptococcaceae + FANA Sessile Coccus No spore 39.7
Streptococcus agalactiae 2 Human and animal pathogen Minor Possible Commensal Known Pathogen clinical sources (blood, septicemia, urine, vagina - CCUG) and human faeces Finegold1974, RajilicStojanovic2014, Lagier2016, Almeida2019, Forster2019, Byrd2020, De2020, New2022, Dubinkina2017, Zeller2014, Vachida2019 Firmicutes Bacilli Streptococcaceae + FANA Sessile Coccus No spore 34 40(d)
Streptococcus alactolyticus 1 Rare Transient Non/unknown Pathogen human faeces, faeces of pigs and chickens RajilicStojanovic2014, Lagier2016, PerezBrocal2015 Firmicutes Bacilli Streptococcaceae + FANA Sessile Coccus No spore 39.9-41.3
Streptococcus anginosus 2 Widespread Possible Commensal Opportunistic Pathogen oral flora, clinical sources (plaque, appendix, vagina, urine - CCUG) and human faeces Wang2005, McLaughlin2010, Walker2011, Zupancic2012, Tyakht2013, Aujoulat2014, RajilicStojanovic2014, Lagier2016, Rothschild2018, Almeida2019, Forster2019, De2020, Yang2020, New2022, Byrd2020, New2022, Chen2020, Dubinkina2017, Hu2019, Jie2017, Zeller2014, Vachida2019, Li2019b, PerezBrocal2015 Firmicutes Bacilli Streptococcaceae + ANA Sessile Coccus No spore 38-40
Streptococcus anginosus subsp. whileyi Rare Possible Commensal Opportunistic Pathogen sore throats and other clinical sources (blood, abscess, abdominal infections) Zou2019 Firmicutes Bacilli Streptococcaceae + FANA Sessile Coccus No spore 38.5
Streptococcus australis 1 Minor Possible Commensal Rare Opportunist Found in human breast milk (Jeurink2013). oral flora, human faeces and clinical specimens (saliva, blood, sputum) McLaughlin2010, RajilicStojanovic2014, Lagier2016, Rothschild2018, Forster2019, Byrd2020, Yang2020, New2022, Chen2020, Hu2019, Zeller2014, Vachida2019 Firmicutes Bacilli Streptococcaceae + FANA Sessile Coccus No spore 43.5
Streptococcus caballi Rare Possible Commensal Non/unknown Pathogen Homoacetogen. the rectum of a horse with laminitis Forster2019 Firmicutes Bacilli Streptococcaceae + FANA Sessile Oval-shaped No spore 46.8 40(+)
Streptococcus canis 2 Zoonotic pathogen Unlikely Transient Non/unknown Pathogen cows and cats New2022 Firmicutes Bacilli Streptococcaceae + FANA Sessile Coccus No spore 39-40 40(neg)
Streptococcus castoreus 1 Opportunistic in immunocompromised patients Rare Possible Commensal Opportunistic Infection a European beaver Lagier2016, Forster2019 Firmicutes Bacilli Streptococcaceae + FANA Sessile Coccus No spore 37.4
Streptococcus constellatus subsp. constellatus Streptococcus constellatus 2 Minor Possible Commensal Opportunistic Pathogen oral flora, respiratory system, vagina, clinical sources (appendix, blood, abscess) and human faeces Finegold1977, Bik2006, Walker2011, RajilicStojanovic2014, Lagier2016, New2022, Vachida2019 Firmicutes Bacilli Streptococcaceae + FANA Sessile Diplococci No spore 37-38
Streptococcus cristatus Streptococcus oligofermentans 1 Opportunistic in immunocompromised patients Minor Possible Commensal Rare Opportunist oral flora, throat, clinical sources (dental disease, blood) and human faeces Bik2006, McLaughlin2010, RajilicStojanovic2014, Lagier2016, Byrd2020, De2020, Yang2020, New2022, Dubinkina2017, Hu2019, Zeller2014, Vachida2019 Firmicutes Bacilli Streptococcaceae + FANA Sessile Coccus No spore 42.6-43.2
Streptococcus danieliae Rare Possible Commensal Non/unknown Pathogen mouse caecal contents De2020 Firmicutes Bacilli Streptococcaceae + FANA Sessile Coccobacillus No spore 45.1
Streptococcus didelphis 2 Animal pathogen Rare Possible Commensal Opportunistic Pathogen Initial catalase activity is lost in subsequent cultures. opossums Forster2019, De2020 Firmicutes Bacilli Streptococcaceae + FANA Sessile Coccus No spore
Streptococcus downei 1 Rare Possible Commensal Non/unknown Pathogen dental plaque of monkeys Yang2020, Zeller2014, Vachida2019 Firmicutes Bacilli Streptococcaceae + FANA Sessile Coccus No spore 41-42 40(d)
Streptococcus dysgalactiae Negative 2 Animal pathogen Rare Transient Opportunistic Pathogen human faeces, respiratory, genital, and clinical sources (blood) RajilicStojanovic2014, Lagier2016, Byrd2020, New2022, Zeller2014, Vachida2019 Firmicutes Bacilli Streptococcaceae + FANA Sessile Oval-shaped No spore 38.1-40.2
Streptococcus dysgalactiae subsp. equisimilis 2 Human and animal pathogen Unlikely Transient Non/unknown Pathogen human respiratory tracts and vaginas Finegold1977 Firmicutes Bacilli Streptococcaceae + FANA Sessile Coccus No spore 38.1-40.2
Streptococcus equi subsp. equi Streptococcus equi Negative 2 Human and animal pathogen Rare Transient Known Pathogen human faeces, clinical sources, and animal disease RajilicStojanovic2014, Byrd2020, De2020, New2022 Firmicutes Bacilli Streptococcaceae + FANA Sessile Coccus No spore 40.7 10(neg)
Streptococcus equinus Streptococcus bovis Unknown 2 Human and animal pathogen Moderate Known Commensal Known Pathogen human faeces (especially in children as S. bovis), clinical sources (blood, urine) and animal faeces Finegold1977, Benno1984, MacFarlane2004, McLaughlin2010, Tyakht2013, RajilicStojanovic2014, Salonen2014, Cassir2015, Lagier2016, Almeida2019, Forster2019, Byrd2020, De2020, New2022, Dubinkina2017, Jie2017, Zeller2014 Firmicutes Bacilli Streptococcaceae + FANA Sessile Coccus No spore 36.2-38.6 40(+)
Streptococcus ferus 1 Rare Possible Commensal Non/unknown Pathogen pigs and rats De2020 Firmicutes Bacilli Streptococcaceae + FANA Sessile Coccobacillus No spore 43 +
Streptococcus gallolyticus subsp. gallolyticus Streptococcus gallolyticus Negative 2 Human and animal pathogen Minor Possible Commensal Opportunistic Pathogen Found in human breast milk (Jeurink2013). human faeces, clinical sources (blood, cerebrospinal fluid - CCUG), and animal faeces RajilicStojanovic2014, Cassir2015, Lagier2016, Byrd2020, Yang2020, New2022, Hu2019, Zeller2014, Vachida2019 Firmicutes Bacilli Streptococcaceae + FANA Sessile Coccus No spore 37-38
Streptococcus gordonii Unknown 2 Minor Possible Commensal Opportunistic Infection dental disease, clinical sources (blood, sputum, infection - CCUG) and human faeces Bik2006, McLaughlin2010, Pfleiderer2013, RajilicStojanovic2014, Lagier2016, Zou2019, Forster2019, Byrd2020, De2020, Yang2020, New2022, Hu2019, Zeller2014, Vachida2019 Firmicutes Bacilli Streptococcaceae + FANA Sessile Coccus No spore 40-43
Streptococcus gwangjuense Unlikely Transient Rare Opportunist pericoronitis lesion, Korea New2022 Firmicutes Bacilli Streptococcaceae + FANA Sessile Coccus No spore 40.2
Streptococcus henryi Rare Possible Commensal Non/unknown Pathogen caecum of a horse with laminitis Forster2019 Firmicutes Bacilli Streptococcaceae + FANA Sessile Oval-shaped No spore 40(+)
Streptococcus hyovaginalis 1 Rare Possible Commensal Non/unknown Pathogen the vagina of a pig Forster2019, Byrd2020 Firmicutes Bacilli Streptococcaceae + FANA Sessile Coccus No spore 40
Streptococcus ilei Unlikely Transient Rare Opportunist ileostomy effluent of a colorectal cancer patient New2022 Firmicutes Bacilli Streptococcaceae + FANA Sessile Coccus No spore 42.1
Streptococcus infantarius 2 Minor Possible Commensal Rare Opportunist human faeces, food, and clinical sources (blood - CCUG) Tyakht2013, RajilicStojanovic2014, Cassir2015, Lagier2016, Byrd2020, New2022, Hu2019, Zeller2014, Vachida2019, Wang2020a Firmicutes Bacilli Streptococcaceae + FANA Sessile Coccus No spore
Streptococcus infantarius subsp. infantarius 2 Minor Transient Rare Opportunist In 15% of Europeans (unseenbio.com). Minor coloniser. human faeces (CCUG; transient), food and clinical sources (blood) Lagier2016, Dubinkina2017, Jie2017 Firmicutes Bacilli Streptococcaceae + FANA Sessile Coccus No spore
Streptococcus infantis Unknown 1 Opportunistic in immunocompromised patients Minor Possible Commensal Opportunistic Infection oral flora, pharynx, blood and human faeces Bik2006, Walker2011, RajilicStojanovic2014, Lagier2016, Zou2019, Forster2019, Byrd2020, Yang2020, Hu2019, Jie2017, Zeller2014, Vachida2019, PerezBrocal2015 Firmicutes Bacilli Streptococcaceae + FANA Sessile Coccus No spore 39.9-40.4
Streptococcus intermedius 2 Human and animal pathogen Moderate Possible Commensal Opportunistic Pathogen human faeces, clinical sources (blood, wound, vagina, abscess - CCUG) and oral cavity Holdeman1976, Finegold1977, Benno1984, Benno1986, Benno1989, MacFarlane2004, Woodmansey2004, Walker2011, RajilicStojanovic2014, Salonen2014, Lagier2016, Byrd2020, Yang2020, New2022, Vachida2019 Firmicutes Bacilli Streptococcaceae + FANA Sessile Coccus No spore 37-38
Streptococcus koreensis Unlikely Transient Rare Opportunist subgingival dental plaque from patients with periodontitis New2022 Firmicutes Bacilli Streptococcaceae + FANA Sessile Coccus No spore 42.1
Streptococcus lactarius Rare Possible Commensal Non/unknown Pathogen Found in human breast milk (Jeurink2013). Probably a rare or transient gut inhabitant but has not been reported to have been isolated from faeces. breast milk from healthy test subjects Firmicutes Bacilli Streptococcaceae + FANA Sessile Coccus No spore
Streptococcus lutetiensis Streptococcus infantarius subsp. coli Unknown 2 Minor Possible Commensal Opportunistic Pathogen human faeces (CCUG), and clinical sources (blood, tissue - CCUG) Dubourg2013, RajilicStojanovic2014, Cassir2015, Lagier2016, Zou2019, Forster2019, Byrd2020, Yang2020, New2022, Hu2019, Vachida2019, Li2019b, PerezBrocal2015 Firmicutes Bacilli Streptococcaceae + FANA Sessile Coccus No spore
Streptococcus macedonicus Rare Transient Non/unknown Pathogen Greek Kasseri cheese Byrd2020, New2022, Hu2019, Vachida2019 Firmicutes Bacilli Streptococcaceae + FANA Sessile Coccus No spore 38 neg
Streptococcus merionis Rare Possible Commensal Non/unknown Pathogen the oropharynge of a Mongolian jird Forster2019 Firmicutes Bacilli Streptococcaceae + FANA Sessile Coccus No spore
Streptococcus mitis 2 Moderate Known Commensal Opportunistic Pathogen Homoacetogen. Found in human breast milk (Jeurink2013). oral flora, clinical sources (blood, sputum, infection, urine, fistula - CCUG) and human faeces Finegold1974, Finegold1977, Benno1984, MacFarlane2004, Wang2005, Bik2006, McLaughlin2010, Walker2011, Dubourg2013, Pfleiderer2013, RajilicStojanovic2014, Salonen2014, Cassir2015, Lagier2016, Almeida2019, Forster2019, King2019, Byrd2020, De2020, New2022, Zeller2014, Vachida2019 Firmicutes Bacilli Streptococcaceae + FANA Sessile Coccus No spore 39-41
Streptococcus mutans Unknown 2 Moderate Possible Commensal Opportunistic Pathogen human faeces, clinical sources (blood, eye, pleural fluid - CCUG) and oral cavity Finegold1977, MacFarlane2004, Woodmansey2004, Hoyles2012, RajilicStojanovic2014, Lagier2016, Rothschild2018, Zou2019, Almeida2019, Forster2019, Byrd2020, De2020, Yang2020, New2022, Chen2020, Dubinkina2017, Zeller2014, Vachida2019, Karlsson2013 Firmicutes Bacilli Streptococcaceae + FANA Sessile Coccus No spore 36-38
Streptococcus oralis Negative 2 Minor Possible Commensal Opportunistic Pathogen dental disease, clinical sources (blood, infection, sputum, wound - CCUG) and human faeces Wang2005, Walker2011, Pfleiderer2013, Aujoulat2014, RajilicStojanovic2014, Lagier2016, Forster2019, Byrd2020, Yang2020, New2022, Dubinkina2017, Zeller2014 Firmicutes Bacilli Streptococcaceae + FANA Sessile Coccus No spore 38-42
Streptococcus oralis subsp. tigurinus Streptococcus tigurinus Rare Possible Commensal Opportunistic Pathogen clinical sources (blood) Lagier2016, Hu2019, Vachida2019 Firmicutes Bacilli Streptococcaceae + FANA Sessile Coccus No spore 40.0
Streptococcus orisratti 1 Rare Possible Commensal Non/unknown Pathogen the tooth surface of laboratory rats Byrd2020 Firmicutes Bacilli Streptococcaceae + FANA Sessile Coccus No spore 39.6-43.5 40(+)
Streptococcus ovis 2 Animal pathogen Rare Possible Commensal Opportunistic Pathogen sheep clinical specimens Forster2019, Byrd2020 Firmicutes Bacilli Streptococcaceae + FANA Sessile Coccus No spore 38
Streptococcus pantholopis Rare Possible Commensal Non/unknown Pathogen the faeces of a Tibetan antelope De2020 Firmicutes Bacilli Streptococcaceae + FANA Sessile Coccus No spore 42
Streptococcus parasanguinis Negative 2 Widespread Known Commensal Opportunistic Pathogen Found in human breast milk (Jeurink2013). clinical sources (blood, abscess, cerebrospinal fluid - CCUG) and human faeces Mangin2004, MacFarlane2004, Woodmansey2004, Wang2005, Bik2006, McLaughlin2010, Walker2011, Pandey2012, Zupancic2012, Dubourg2013, Pfleiderer2013, Aujoulat2014, Nielsen2014, RajilicStojanovic2014, Lagier2016, Rothschild2018, Zou2019, Almeida2019, Forster2019, King2019, Byrd2020, De2020, Yang2020, New2022, Chen2020, Dubinkina2017, Hu2019, Jeong2021, Jie2017, Zeller2014, Vachida2019 Firmicutes Bacilli Streptococcaceae + FANA Sessile Coccus No spore 40.6-42.7 40(d)
Streptococcus parasuis Rare Possible Commensal Non/unknown Pathogen healthy pigs De2020 Firmicutes Bacilli Streptococcaceae + FANA Sessile Coccus No spore 39.8
Streptococcus parauberis Negative 2 Animal pathogen Rare Possible Commensal Known Pathogen human faeces, raw milk, and cows Dubourg2013, RajilicStojanovic2014, Byrd2020, Zeller2014 Firmicutes Bacilli Streptococcaceae + FANA Sessile Coccus No spore 34.8-36.5
Streptococcus pasteurianus Streptococcus gallolyticus subsp. pasteurianus Negative 2 Human and animal pathogen Minor Possible Commensal Opportunistic Pathogen human faeces, clinical sources (pharynx, blood, urine - CCUG) and tooth surfaces Zou2019, King2019, Byrd2020, New2022, Hu2019, Jie2017, Vachida2019, Wang2020a Firmicutes Bacilli Streptococcaceae + FANA Sessile Coccus No spore
Streptococcus periodonticum Unlikely Transient Rare Opportunist subgingival dental plaque from patients with periodontitis, Korea New2022 Firmicutes Bacilli Streptococcaceae + FANA Sessile Coccus No spore 38.9
Streptococcus peroris Unknown 1 Opportunistic in immunocompromised patients Rare Transient Opportunistic Infection dental, clinical sources (pharynx) and human faeces RajilicStojanovic2014, Lagier2016, Yang2020, Dubinkina2017, Zeller2014, Vachida2019 Firmicutes Bacilli Streptococcaceae + FANA Sessile Coccus No spore 39.8-40.5
Streptococcus pluranimalium 2 Animal pathogen Unlikely Transient Non/unknown Pathogen subclinical mastitis in a cow New2022 Firmicutes Bacilli Streptococcaceae + FANA Sessile Coccus No spore 38.5
Streptococcus plurextorum Rare Possible Commensal Possible Pathogen pigs with pneumonia Forster2019 Firmicutes Bacilli Streptococcaceae + FANA Sessile Coccus No spore 42.1
Streptococcus pneumoniae Negative 2 Human and animal pathogen Minor Possible Commensal Known Pathogen nasopharynx, clinical sources (blood, sputum, cerebrospinal fluid - CCUG) and human faeces McLaughlin2010, Pfleiderer2013, RajilicStojanovic2014, Lagier2016, Byrd2020, De2020, Yang2020, New2022, Zeller2014 Firmicutes Bacilli Streptococcaceae + FANA Sessile Coccus No spore 38.5-42
Streptococcus porci Rare Possible Commensal Possible Pathogen the heart of a pig with pericarditis Forster2019 Firmicutes Bacilli Streptococcaceae + FANA Sessile Coccus No spore 41.5
Streptococcus pseudopneumoniae 2 Minor Transient Possible Pathogen respiratory, clinical sources (sputum, respiratory tract - CCUG) and human faeces RajilicStojanovic2014, Lagier2016, Byrd2020, New2022, Hu2019, Zeller2014, Vachida2019 Firmicutes Bacilli Streptococcaceae + FANA Sessile Coccus No spore
Streptococcus pseudoporcinus 2 Rare Possible Commensal Opportunistic Pathogen the genitourinary tract of women Lagier2016, New2022, Zeller2014 Firmicutes Bacilli Streptococcaceae + FANA Sessile Oval-shaped No spore
Streptococcus pyogenes 2 Minor Transient Known Pathogen human faeces, skin flora, clinical sources (sputum, urine, throat, infection - CCUG) Finegold1974, RajilicStojanovic2014, Lagier2016, Forster2019, Byrd2020, New2022, Zeller2014 Firmicutes Bacilli Streptococcaceae + FANA Sessile Coccus No spore 34.5-38.5
Streptococcus rubneri Rare Possible Commensal Possible Pathogen the throat Zou2019 Firmicutes Bacilli Streptococcaceae + FANA Sessile Coccus No spore 40.9
Streptococcus salivarius Streptococcus salivarius subsp. salivarius 2 Widespread Known Commensal Opportunistic Pathogen Found in human breast milk (Jeurink2013). human faeces (mainly adults), clinical sources (sputum, blood - CCUG) and oral cavity Finegold1974, Finegold1977, Benno1984, Benno1986, Benno1989, Favier2002, Mangin2004, MacFarlane2004, Woodmansey2004, Wang2005, Bik2006, McLaughlin2010, Walker2011, Pandey2012, Zupancic2012, Dubourg2013, Pfleiderer2013, Aujoulat2014, Nielsen2014, RajilicStojanovic2014, Lagier2016, Rothschild2018, Zou2019, Almeida2019, Forster2019, King2019, Byrd2020, New2022, Chen2020, Dubinkina2017, Hu2019, Jeong2021, Jie2017, Zeller2014, Wang2018, Vachida2019, Wang2020a, Urban2020 Firmicutes Bacilli Streptococcaceae + FANA Sessile Coccus No spore 39-42 40(d)
Streptococcus sanguinis 2 Moderate Known Commensal Opportunistic Pathogen This organism also produces D-lactate, which could be linked to cronic fatigue syndrome (Sheedy2009). dental disease, clinical sources (infection, blood - CCUG) and human faeces Finegold1974, Finegold1977, Benno1984, Benno1986, Benno1989, Bik2006, McLaughlin2010, Walker2011, Dubourg2013, Aujoulat2014, RajilicStojanovic2014, Lagier2016, Byrd2020, De2020, Yang2020, New2022, Hu2019, Zeller2014, Vachida2019 Firmicutes Bacilli Streptococcaceae + FANA Sessile Coccus No spore 43-46 40(d)
Streptococcus sinensis 2 Rare Possible Commensal Opportunistic Pathogen the blood of a patient with infective endocarditis Byrd2020, De2020 Firmicutes Bacilli Streptococcaceae + FANA Sessile Coccus No spore 53 40(+)
Streptococcus sobrinus 2 Minor Possible Commensal Opportunistic Pathogen Most strains produce hydrogen peroxide. surfaces of teeth Lagier2016, Forster2019, Byrd2020, New2022, Vachida2019, Wang2020a, Li2019b Firmicutes Bacilli Streptococcaceae + FANA Sessile Coccus No spore 44-46
Streptococcus suis Negative 2 Zoonotic pathogen Rare Possible Commensal Opportunistic Pathogen pig disease, clinical sources, human faeces Lagier2016, King2019, Byrd2020, Yang2020, New2022, Zeller2014 Firmicutes Bacilli Streptococcaceae + FANA Sessile Coccobacillus No spore 38-42 40(d)
Streptococcus thermophilus 1 Widespread Known Commensal Non/unknown Pathogen Produces GABA (Sahab2020). human faeces , and dairy fermentation Favier2002, McLaughlin2010, Zupancic2012, Tyakht2013, Aujoulat2014, Nielsen2014, RajilicStojanovic2014, Cassir2015, Lagier2016, Rothschild2018, Almeida2019, King2019, Byrd2020, Byrd2020, New2022, Chen2020, Dubinkina2017, Hu2019, Jie2017, Zeller2014, Wang2018, Vachida2019, Wang2020a Firmicutes Bacilli Streptococcaceae + FANA Sessile Oval-shaped No spore 37-40
Streptococcus thoraltensis Unknown 1 Rare Transient Non/unknown Pathogen animal sources and human faeces RajilicStojanovic2014, Lagier2016, Forster2019 Firmicutes Bacilli Streptococcaceae + FANA Sessile Coccus No spore 40 neg
Streptococcus timonensis Minor Possible Commensal Non/unknown Pathogen In 16% of Europeans (unseenbio.com). Minor coloniser. stomach samples, France Lagier2016, Byrd2020 Firmicutes Bacilli Streptococcaceae + FANA Sessile Coccus No spore 38.6
Streptococcus uberis 2 Human and animal pathogen Rare Transient Known Pathogen human faeces, cows, and milk Finegold1974, RajilicStojanovic2014, Cassir2015, Lagier2016, Byrd2020 Firmicutes Bacilli Streptococcaceae + FANA Sessile Coccus No spore 36-37.5 40(d)
Streptococcus vestibularis Unknown 1 Moderate Possible Commensal Rare Opportunist Found in human breast milk (Jeurink2013). oral cavity, clinical sources (blood, ear - CCUG) and human faeces Pandey2012, RajilicStojanovic2014, Lagier2016, Rothschild2018, Byrd2020, De2020, Yang2020, New2022, Chen2020, Dubinkina2017, Hu2019, Jie2017, Zeller2014, Vachida2019, Karlsson2013 Firmicutes Bacilli Streptococcaceae + FANA Sessile Coccus No spore 38-40 10(+)
Streptococcus viridans Rare Possible Commensal Non/unknown Pathogen oral cavity and human faeces RajilicStojanovic2014, Lagier2016 Firmicutes Bacilli Streptococcaceae + FANA Sessile Coccus No spore
Streptomyces albus 1 Unlikely Transient Possible Pathogen human faeces, clinical specimens and the environment Forster2019, Zeller2014 Actinobacteria Actinomycetia Streptomycetaceae + AER Sessile Filamentous Exospore
Streptomyces flavogriseus 1 Unlikely Transient Non/unknown Pathogen Streptomyces, being aerobic and having lower optimum growth temperatures are unlikely to be gut colonisers. soils from numerous locations Zeller2014 Actinobacteria Actinomycetia Streptomycetaceae + AER Sessile Filamentous Exospore
Streptomyces hygroscopicus 1 Unlikely Transient Non/unknown Pathogen Streptomyces, being aerobic and having lower optimum growth temperatures are unlikely to be gut colonisers. Zeller2014 Actinobacteria Actinomycetia Streptomycetaceae + AER Sessile Filamentous Exospore 70.2-71.9
Streptomyces koyangensis 1 Rare Possible Commensal Non/unknown Pathogen Produces 4-phenyl-3-butenoic acid, which inhibits several plant-pathogenic fungi. soil, Korea Lagier2016 Actinobacteria Actinomycetia Streptomycetaceae + AER Sessile Filamentous Exospore 67.8
Streptomyces lividans Unlikely Transient Non/unknown Pathogen Streptomyces, being aerobic and having lower optimum growth temperatures are unlikely to be gut colonisers. Zeller2014 Actinobacteria Actinomycetia Streptomycetaceae + AER Sessile Filamentous Exospore
Streptomyces massiliensis Unlikely Transient Non/unknown Pathogen Obligate aerobe; unlikely to be a gut coloniser. human faeces, and saline soil Pfleiderer2013, RajilicStojanovic2014, Lagier2016 Actinobacteria Actinomycetia Streptomycetaceae + SAER Sessile Filamentous
Streptomyces misionensis 1 Rare Possible Commensal Non/unknown Pathogen soil, decaying vegetation and human faeces RajilicStojanovic2014, Lagier2016 Actinobacteria Actinomycetia Streptomycetaceae + AER Sessile Filamentous Exospore
Streptomyces specialis Unlikely Transient Non/unknown Pathogen Streptomyces, being aerobic and having lower optimum growth temperatures are unlikely to be gut colonisers. soil Actinobacteria Actinomycetia Streptomycetaceae + AER Sessile Filamentous Exospore
Streptomyces thermoviolaceus 1 Rare Possible Commensal Non/unknown Pathogen human faeces (Hoyles2012) and blood Hoyles2012, RajilicStojanovic2014, Lagier2016 Actinobacteria Actinomycetia Streptomycetaceae + AER Sessile Filamentous Exospore
Streptomyces thermovulgaris 1 Unlikely Possible Commensal Non/unknown Pathogen human faeces, and bovine faeces Dubourg2013, RajilicStojanovic2014, Lagier2016 Actinobacteria Actinomycetia Streptomycetaceae + AER Sessile Filamentous Exospore
Streptomyces violaceusniger 1 Unlikely Transient Non/unknown Pathogen Streptomyces, being aerobic and having lower optimum growth temperatures are unlikely to be gut colonisers. sources unknown Zeller2014 Actinobacteria Streptomycetaceae + AER Sessile Filamentous Exospore 71.2
Streptosporangium roseum 1 Unlikely Transient Non/unknown Pathogen garden soil Zeller2014 Actinobacteria Actinomycetia Streptosporangiaceae + AER Sessile Filamentous Exospore 70
Subdoligranulum formicile Gemmiger formicilis 1 Rare Known Commensal Non/unknown Pathogen human faeces (Gossling1975) Firmicutes Clostridia Oscillospiraceae neg SANA Sessile Coccus No spore
Subdoligranulum variabile 1 Moderate Known Commensal Non/unknown Pathogen human faeces Nam2008a, McLaughlin2010, Walker2011, Tyakht2013, RajilicStojanovic2014, Salonen2014, Lagier2016, Yang2020, Dubinkina2017, Hu2019, Zeller2014, Vachida2019, Qin2012, Minerbi2019, LeChatelier2013, Karlsson2013 Firmicutes Clostridia Oscillospiraceae neg SANA Sessile No spore 52
Succinatimonas hippei Minor Possible Commensal Non/unknown Pathogen human faeces Tyakht2013, RajilicStojanovic2014, Lagier2016, Forster2019, Byrd2020, Yang2020, Dubinkina2017, Hu2019, Jie2017, Zeller2014, Vachida2019 Proteobacteria Gammaproteobacteria Succinivibrionaceae neg SANA Sessile Rod No spore 40.3 20(neg)
Succinivibrio dextrinosolvens 1 Opportunistic in immunocompromised patients Rare Possible Commensal Possible Pathogen human faeces , cattle rumen, and clinical sources RajilicStojanovic2014, Byrd2020, De2020, New2022 Proteobacteria Gammaproteobacteria Succinivibrionaceae neg SANA Swimming Helical No spore 39-44
Sulfurospirillum deleyianum 1 Rare Possible Commensal Non/unknown Pathogen Can reduce elemental sulfur but not sulfate. anoxic mud, Germany De2020 Proteobacteria Epsilonproteobacteria Campylobacteraceae neg Micr Swimming Vibrio No spore 40.6
Sutcliffiella cohnii Bacillus cohnii Positive 1 Unlikely Transient Non/unknown Pathogen Poor growth at pH7 so unlikely to be a gut coloniser. soil and faeces (Logan2011Bergey) Firmicutes Bacilli Bacillaceae + AER Rod Endospore 33.5-35
Sutterella faecalis Rare Possible Commensal Non/unknown Pathogen Asaccharolytic. human faeces New2022 Proteobacteria Betaproteobacteria Sutterellaceae neg SANA Sessile Coccobacillus No spore 58.3
Sutterella massiliensis Rare Possible Commensal Non/unknown Pathogen human faeces (Bilen2018e) Lagier2016, Minerbi2019 Proteobacteria Betaproteobacteria Sutterellaceae neg SANA Sessile Rod No spore
Sutterella megalosphaeroides Rare Possible Commensal Non/unknown Pathogen human faeces (Sakamoto2018b) New2022 Proteobacteria Betaproteobacteria Sutterellaceae neg SANA Sessile Coccus No spore 62.8 20(w)
Sutterella parvirubra 1 Minor Possible Commensal Non/unknown Pathogen human faeces RajilicStojanovic2014, Lagier2016, Zou2019, Forster2019, Byrd2020, Yang2020, Vachida2019 Proteobacteria Betaproteobacteria Sutterellaceae neg Micr Sessile Coccobacillus No spore 64.1-64.5
Sutterella seckii Rare Possible Commensal Non/unknown Pathogen human faeces (Dione2018a) Proteobacteria Betaproteobacteria Sutterellaceae neg No spore
Sutterella stercoricanis 1 Rare Possible Commensal Non/unknown Pathogen human faeces, and dog faeces McLaughlin2010, Walker2011, RajilicStojanovic2014 Proteobacteria Betaproteobacteria Sutterellaceae neg Micr Rod No spore 60
Sutterella timonensis Rare Possible Commensal Non/unknown Pathogen human faeces (Bilen2018e) Proteobacteria Betaproteobacteria Sutterellaceae neg SANA Swimming Rod No spore
Sutterella wadsworthensis 2 Widespread Known Commensal Possible Pathogen human faeces (CCUG) and clinical sources (blood, fistula, appendix tissue - CCUG) Wang2005, McLaughlin2010, Walker2011, Tyakht2013, Nielsen2014, RajilicStojanovic2014, Salonen2014, Chung2016, Lagier2016, Rothschild2018, Zou2019, Almeida2019, Chung2019, Forster2019, Byrd2020, Yang2020, New2022, Chen2020, Dubinkina2017, Hu2019, Jeong2021, Jie2017, Zeller2014, Wang2018, Vachida2019, Wang2020a, Minerbi2019 Proteobacteria Betaproteobacteria Sutterellaceae neg Micr Rod No spore 20(+)
Symbiobacterium thermophilum 1 Unlikely Transient Non/unknown Pathogen Isolated as a co-culture with Bacillus or other bacteria. High minimum growth temperature (45C) so unlikely to be a gut coloniser. compost, Japan New2022, Zeller2014 Firmicutes Clostridia Symbiobacteriaceae neg Micr Sessile Rod No spore 65.1
Symbiobacterium toebii Unlikely Transient Non/unknown Pathogen A high minimum growth temperature (45C) suggests this is an unlikely gut coloniser. Symbiotic (obligate commensal) with Geobacillus sp. farmland compost, Korea Firmicutes Clostridia Symbiobacteriaceae neg Micr Sessile Rod No spore 65
Syntrophobotulus glycolicus 1 Unlikely Transient Non/unknown Pathogen Glyoxylate is fermentatively oxidised. Borderline cold mesophile, with optimum growth temp of 28C. Unlikely gut coloniser. sewage sludge and anoxic freshwater sediments New2022 Firmicutes Clostridia Peptococcaceae neg SANA Sessile Rod - curved Endospore 46.7
Syntrophococcus sucromutans 1 Rare Possible Commensal Non/unknown Pathogen One of the following electron acceptor systems allowed growth (organic products in parentheses): Methanobrevibacter simithii (CH4), formate (acetate), 3,4,5- trimethoxybenzoate and syringate (acetate and gallate), vanillate (acetate and protocatechuate), vanillin (acetate, protocatechuic aldehyde and protocatechuate), ferulate (acetate, caffeate and hydrocaffeate), caffeate (hydrocaffeate) mesophilic, anaerobic, microbial ecosystems where complex organic matter is degraded Firmicutes Clostridia Lachnospiraceae neg SANA Sessile Coccus No spore 52
Syntrophomonas zehnderi 1 Rare Possible Commensal Non/unknown Pathogen Grows in co-culture with hydrogenophilic archaea. Consumes mainly saturated fatty acids C4:0-C18:0. an oleate-degrading culture enriched from anaerobic sludge sampled from an EGSB reactor, Netherlands Byrd2020 Firmicutes Clostridia Syntrophomonadaceae vr FANA Swimming Rod - curved Endospore
Tannerella forsythia Bacteroides forsythus 2 Minor Possible Commensal Opportunistic Pathogen human faeces, and oral cavity MacFarlane2004, Woodmansey2004, Bik2006, McLaughlin2010, RajilicStojanovic2014, Lagier2016, King2019, Byrd2020, De2020, New2022, Zeller2014, Vachida2019 Bacteroidetes Bacteroidia Tannerellaceae neg SANA Sessile Rod No spore 46 20(neg)
Tannerella serpentiformis Tannerella sp. HOT-286 Unlikely Transient Non/unknown Pathogen the human mouth New2022 Bacteroidetes Bacteroidia Tannerellaceae neg SANA Sessile Filamentous No spore 56.5
Taonella mepensis Unlikely Transient Non/unknown Pathogen Obligate aerobe; unlikely to be a gut coloniser. human faeces and activated sludge Yang2020 Proteobacteria Alphaproteobacteria Rhodospirillaceae neg SAER Swimming Rod No spore 65.1
Tatumella ptyseos 2 Rare Possible Commensal Possible Pathogen clinical sources (sputum, throat - CCUG) and human faeces RajilicStojanovic2014, Lagier2016 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA vr Rod No spore 53-54
Tepidanaerobacter acetatoxydans Rare Possible Commensal Non/unknown Pathogen Byrd2020, New2022 Firmicutes Clostridia Tepidanaerobacteraceae vr ANA Swimming Rod Endospore 38.4
Tepiditoga spiralis Unlikely Transient Non/unknown Pathogen High optimum growth temperature so unlikely to be a gut coloniser. a hydrothermal vent chimney, western Pacific Ocean New2022 Thermotogae Thermotogae Petrotogaceae neg SANA Swimming Rod - curved 25.8
Terrahaemophilus aromaticivorans Rare Possible Commensal Non/unknown Pathogen human faeces, oral cavity and petroleum sludge Walker2011, Chung2019 Proteobacteria Gammaproteobacteria Pasteurellaceae neg No spore
Terribacillus aidingensis Rare Possible Commensal Non/unknown Pathogen a salt lake, China Lagier2016 Firmicutes Bacilli Bacillaceae + Swimming Rod Endospore 44.6-45.0
Terribacillus halophilus 1 Unlikely Transient Non/unknown Pathogen Obligate aerobe; unlikely to be a gut coloniser. field soil, Japan Lagier2016 Firmicutes Bacilli Bacillaceae + SAER Sessile Rod Endospore 45.8
Terrisporobacter glycolicus Clostridium glycolicum 2 Minor Known Commensal Opportunistic Pathogen human faeces, wastewater and clinical sources (wounds, abscesses and peritoneal fluid) Finegold1974, Finegold1977, Benno1986, Zupancic2012, Pfleiderer2013, Aujoulat2014, RajilicStojanovic2014, Lagier2016, Forster2019, Byrd2020, Vachida2019 Firmicutes Clostridia Clostridiaceae + SANA Swimming Rod Endospore 29.1 20(neg)
Terrisporobacter mayombei Clostridium mayombei 1 Rare Transient Non/unknown Pathogen human faeces and termite gut Lagier2016, Forster2019, Minerbi2019 Firmicutes Clostridia Peptostreptococcaceae + SANA Swimming Rod Endospore 25.6
Terrisporobacter othiniensis Rare Possible Commensal Opportunistic Pathogen Full characterisation not yet published. a blood culture from a patient (sepsis) Byrd2020 Firmicutes Clostridia Peptostreptococcaceae + ANA Rod 28.5
Terrisporobacter petrolearius Rare Possible Commensal Non/unknown Pathogen Uses sulfite as an electron acceptor. an oilfield, China Minerbi2019 Firmicutes Clostridia Peptostreptococcaceae + SANA Swimming Rod Endospore 27.1
Tessaracoccus massiliensis Rare Possible Commensal Non/unknown Pathogen human faeces (Seck2016) Lagier2016, Byrd2020 Actinobacteria Actinomycetia Propionibacteriaceae + FANA Sessile Rod No spore 67.8
Tetragenococcus halophilus Pediococcus halophilus 1 Unlikely Transient Non/unknown Pathogen High salt required for optimum growth, so unlikely gut coloniser. human faeces, soy sauce and pickling brines Byrd2020, Yang2020, Zeller2014 Firmicutes Bacilli Enterococcaceae + FANA Sessile Tetrad No spore 34-36
Tetragenococcus koreensis 1 Rare Possible Commensal Non/unknown Pathogen fermented food (kimchi), Korea Lagier2016 Firmicutes Bacilli Enterococcaceae + FANA Sessile Coccus No spore 34-36
Tetragenococcus solitarius Enterococcus solitarius 1 Opportunistic in immunocompromised patients Rare Possible Commensal Opportunistic Infection human faeces Woodmansey2004, RajilicStojanovic2014, Lagier2016 Firmicutes Bacilli Enterococcaceae + FANA Sessile Oval-shaped No spore 38
Thalassobacillus devorans 1 Non Transient Non/unknown Pathogen Obligate aerobe and high salt required for optimum growth, so likely a gut non-coloniser. human faeces and hypersaline phenol enrichment (Spain) Lagier2016, Forster2019 Firmicutes Bacilli Bacillaceae + SAER Swimming Rod Endospore 42.4
Thauera terpenica 1 Rare Possible Commensal Non/unknown Pathogen human faeces and forest ditch Yang2020 Proteobacteria Betaproteobacteria Zoogloeaceae neg FANA Swimming Rod No spore 63.9-64.2
Thermaerobacter marianensis 1 Non Transient Non/unknown Pathogen Very high minimum growth temperature (50C) and strictly aerobic nature suggests this is a gut non-coloniser. the Mariana Trench New2022, Zeller2014 Firmicutes Clostridia Eubacteriales Family XVII. Incertae Sedis vr SAER Sessile Rod No spore 72.5
Thermoanaerobacterium thermosaccharolyticum Clostridium thermosaccharolyticum 1 Rare Possible Commensal Non/unknown Pathogen hot springs, soil, ponds, manure and grape processing facilities Qin2012 Firmicutes Clostridia Thermoanaerobacterales Family III. Incertae Sedis neg SANA Swimming Rod Endospore 29-32
Thermobacillus composti 1 Unlikely Transient Non/unknown Pathogen High optimum growth temperature so unlikely to be a gut coloniser. a composting reactor New2022 Firmicutes Bacilli Paenibacillaceae neg AER Sessile Rod Endospore 60
Thermobispora bispora Microbispora bispora 1 Unlikely Transient Non/unknown Pathogen Aerobic and high growth temperature optima of 50-65C suggests this is an unlikely gut coloniser. decaying manure Zeller2014 Actinobacteria Actinomycetia Streptosporangiaceae + AER Sessile Filamentous Exospore 70
Thermoclostridium stercorarium Clostridium stercorarium Unlikely Transient Non/unknown Pathogen High optimum growth temperature so unlikely to be a gut coloniser. compost and has been detected in human faeces Salonen2014, New2022 Firmicutes Clostridia Oscillospiraceae neg SANA Swimming Rod Endospore 39-41
Thermolithobacter ferrireducens 1 Non Transient Non/unknown Pathogen Reduces Fe(III). Non-coloniser due to very high minimum growth temperature. hot spring outflow, Yellowstone National Park, USA Firmicutes Thermolithobacteria Thermolithobacteraceae + SANA Swimming Short Rod No spore 52-53
Thermomonas carbonis Unlikely Transient Non/unknown Pathogen Borderline cold mesophile, with optimum growth temp of 28C. Unlikely gut coloniser. human faeces and soil from a coal mine in China Yang2020 Proteobacteria Gammaproteobacteria Xanthomonadaceae neg AER Sessile Rod No spore 67
Thermomonospora curvata 1 Unlikely Transient Non/unknown Pathogen Strictly aerobic and preferred higher growth temperatures suggests this is unlikely to be a gut coloniser. overheated substrates such as composts, manures Zeller2014 Actinobacteria Actinomycetia Thermomonosporaceae + SAER Filamentous Exospore
Thermophilibacter immobilis Unlikely Transient Non/unknown Pathogen Produces skatole and p-cresol. the mud in a fermentation cellar, China New2022 Actinobacteria Coriobacteriia Atopobiaceae + SANA Sessile Oval-shaped No spore 65.2
Thermophilibacter mediterraneus Olsenella mediterranea Rare Possible Mutualist Non/unknown Pathogen Full characterisation not yet published. the human colon Byrd2020 Actinobacteria Coriobacteriia Atopobiaceae + SANA Coccus No spore
Thermophilibacter provencensis Olsenella provencensis Minor Possible Commensal Non/unknown Pathogen In 19% of Europeans (unseenbio.com). Minor coloniser. a colonoscopy patient, France Lagier2016, Byrd2020 Actinobacteria Coriobacteriia Atopobiaceae + SANA Coccus No spore
Thermus scotoductus 1 Unlikely Transient Non/unknown Pathogen Grows poorly at 37C, so unlikely to be a gut coloniser. human faeces and hot water pipe from Iceland Yang2020, Vachida2019 Deinococcus-Thermus Deinococci Thermaceae neg FANA Sessile Rod No spore 64.5
Thiomonas islandica Unlikely Transient Non/unknown Pathogen Aerobic and high growth temperature optimum (45C) suggests this is an unlikely gut coloniser. a hot spring, Iceland Proteobacteria Betaproteobacteria Burkholderiales genera incertae sedis neg AER Swimming Rod No spore 65.2
Thomasclavelia saccharogumia Clostridium saccharogumia 1 Rare Known Commensal Non/unknown Pathogen human faeces RajilicStojanovic2014, Lagier2016, Yang2020, PerezBrocal2015 Firmicutes Clostridia Clostridiaceae + SANA Sessile Helical No spore 29.4-31.7
Thomasclavelia spiroformis Clostridium spiroforme 1 Opportunistic in immunocompromised patients Moderate Known Commensal Opportunistic Infection human faeces (Alkhalil2017) Benno1986, Walker2011, Zupancic2012, Tyakht2013, Nielsen2014, RajilicStojanovic2014, Lagier2016, Zou2019, Chen2020, Dubinkina2017, Hu2019, Jie2017, Zeller2014, Wang2018, Vachida2019, Wang2020a Firmicutes Clostridia Clostridiaceae + SANA Sessile Helical Endospore 27 20(neg)
Tidjanibacter inops Moderate Isolation and characterisation not yet published. In 83% of Europeans (unseenbio.com). A moderate coloniser. Byrd2020 Bacteroidetes Bacteroidia Rikenellaceae No spore
Tidjanibacter massiliensis Rare Possible Commensal Non/unknown Pathogen human faeces (Bilen2018e) and human colon Lagier2016 Bacteroidetes Bacteroidia Rikenellaceae neg ANA Swimming Rod No spore
Timonella senegalensis Positive Rare Known Commensal Non/unknown Pathogen human faeces RajilicStojanovic2014, Lagier2016, Forster2019 Actinobacteria Actinomycetia Jonesiaceae + FANA Swimming Rod No spore 61.4
Tissierella praeacuta Bacteroides praeacutus 2 Human and animal pathogen Rare Known Commensal Opportunistic Pathogen human faeces, and clinical sources (gangrenous lesions, abscesses and blood) Benno1984, Walker2011, RajilicStojanovic2014, Lagier2016, Byrd2020 Firmicutes Tissierellia Tissierellaceae + SANA Swimming Rod No spore 28
Trabulsiella guamensis 1 Rare Possible Commensal Non/unknown Pathogen human faeces, and environmental samples RajilicStojanovic2014, Lagier2016, Byrd2020 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Swimming Rod No spore
Tractidigestivibacter scatoligenes Olsenella scatoligenes Rare Possible Commensal Non/unknown Pathogen Produces skatole. pig and human faeces Zou2019, Byrd2020, Yang2020 Actinobacteria Coriobacteriia Atopobiaceae + SANA Sessile Coccobacillus No spore 62.1
Traorella massiliensis Rare Possible Mutualist Non/unknown Pathogen human left colon Byrd2020 Firmicutes Erysipelotrichia Erysipelotrichaceae neg SANA Swimming Rod No spore 36
Treponema berlinense 1 Rare Possible Commensal Non/unknown Pathogen human faeces, and pig faeces RajilicStojanovic2014, De2020 Spirochaetes Spirochaetia Treponemataceae neg SANA Swimming Spirochete No spore
Treponema brennaborense 2 Animal pathogen Unlikely Transient Non/unknown Pathogen a cow suffering from digital dermatitis New2022, Zeller2014, Qin2012 Spirochaetes Spirochaetia Treponemataceae neg ANA Swimming Spirochete No spore
Treponema denticola 2 Human and animal pathogen Rare Possible Commensal Possible Pathogen oral cavities between teeth and gums Zeller2014, Vachida2019, Qin2012 Spirochaetes Spirochaetia Treponemataceae neg ANA Swimming Spirochete No spore 37-39
Treponema medium 2 Unlikely Transient Rare Opportunist subgingival dental plaque New2022, Vachida2019 Spirochaetes Spirochaetia Treponemataceae neg ANA Swimming Spirochete No spore 51
Treponema parvum 2 Unlikely Transient Rare Opportunist a deep periodontal lesion Zupancic2012 Spirochaetes Spirochaetia Treponemataceae neg SANA Swimming Spirochete No spore
Treponema pectinovorum 2 Rare Possible Commensal Possible Pathogen a patient with peridontal disease De2020 Spirochaetes Spirochaetia Treponemataceae neg SANA Swimming Helical No spore 39
Treponema pedis Unlikely Transient Possible Pathogen bovine digital dermatitis legions New2022 Spirochaetes Spirochaetia Treponemataceae neg ANA Swimming Spirochete No spore
Treponema peruense Rare Known Commensal Non/unknown Pathogen the faeces of an Amazonian, Peru New2022 Spirochaetes Spirochaetia Treponemataceae neg SANA Swimming Helical No spore 41
Treponema phagedenis 1 Unlikely Transient Non/unknown Pathogen bovine digital dermatitis legions Byrd2020, New2022 Spirochaetes Spirochaetia Treponemataceae neg SANA Swimming Spirochete No spore 39.9-40.1
Treponema primitia 1 Unlikely Transient Non/unknown Pathogen termite intestinal contents New2022, Qin2012 Spirochaetes Spirochaetia Treponemataceae neg ANA Swimming Spirochete No spore 50.9
Treponema ruminis Unlikely Transient Non/unknown Pathogen bovine rumen New2022 Spirochaetes Spirochaetia Treponemataceae neg ANA Swimming Spirochete No spore
Treponema socranskii 2 Unlikely Transient Non/unknown Pathogen gingival crevices New2022, Vachida2019, PerezBrocal2015 Spirochaetes Spirochaetia Treponemataceae neg ANA Swimming Spirochete No spore 50.2
Treponema succinifaciens 1 Rare Possible Commensal Non/unknown Pathogen human faeces and pig intestine King2019, Yang2020, New2022, Zeller2014, Vachida2019 Spirochaetes Spirochaetia Treponemataceae neg SANA Swimming Spirochete No spore 36
Treponema vincentii 2 Rare Possible Commensal Possible Pathogen the oral cavity Vachida2019 Spirochaetes Spirochaetia Treponemataceae neg ANA Swimming Spirochete No spore
Tropheryma whipplei 2 Unlikely Transient Known Pathogen human faeces, intracellular parasite and human gut RajilicStojanovic2014, Lagier2016, Byrd2020, Dubinkina2017, Zeller2014, Vachida2019 Actinobacteria Actinomycetia Tropherymataceae neg Sessile Rod 59.4
Trueperella bernardiae Arcanobacterium bernardiae 2 Rare Possible Commensal Opportunistic Pathogen clinical sources (wound, blood, abscess, ear infection - CCUG) and human faeces RajilicStojanovic2014, Lagier2016, Byrd2020 Actinobacteria Actinomycetia Actinomycetaceae + FANA Sessile Coccobacillus No spore 63-66
Trueperella pyogenes Arcanobacterium pyogenes > Actinomyces pyogenes Rare Possible Commensal Possible Pathogen clinical sources (blood, abscess - CCUG) and human faeces RajilicStojanovic2014, Cassir2015, Lagier2016, Byrd2020, New2022 Actinobacteria Actinomycetia Actinomycetaceae + FANA Sessile Coccobacillus No spore
Tsukamurella pulmonis Tsukamurella spongiae 2 Unlikely Transient Opportunistic Pathogen human faeces and clinical sources (sputum, blood, wound, eye - CCUG) Yang2020 Actinobacteria Actinomycetia Tsukamurellaceae + AER Sessile Rod No spore 70.4
Tumebacillus avium Unlikely Transient Non/unknown Pathogen the gut of a vulture, Korea New2022 Firmicutes Bacilli Alicyclobacillaceae + FANA Swimming Rod Endospore 56.0
Tumebacillus permanentifrigoris 1 Unlikely Transient Non/unknown Pathogen human faeces, permafrost RajilicStojanovic2014 Firmicutes Bacilli Alicyclobacillaceae + AER Sessile Rod Endospore 53.1
Turicibacter sanguinis Positive 1 Opportunistic in immunocompromised patients Moderate Known Commensal Opportunistic Pathogen clinical sources (abscess, blood, appendix - CCUG) and human faeces (gut) McLaughlin2010, Walker2011, Pfleiderer2013, Tyakht2013, RajilicStojanovic2014, Browne2016, Lagier2016, Forster2019, Byrd2020, Yang2020, New2022, Chen2020, Dubinkina2017, Hu2019, Jie2017, Zeller2014, Vachida2019, Wang2020a, Qin2012, Minerbi2019 Firmicutes Erysipelotrichia Erysipelotrichaceae + SANA Rod No spore 36.9
Turicimonas muris Rare Possible Commensal Non/unknown Pathogen In 1% of Europeans (unseenbio.com). Rare coloniser. Byrd2020, New2022, Minerbi2019 Proteobacteria Betaproteobacteria Sutterellaceae neg FANA Rod No spore 44.0
Tyzzerella nexilis Clostridium nexile Positive 1 Widespread Known Commensal Non/unknown Pathogen human faeces Moore1974, Finegold1977, Mangin2004, Frank2007, McLaughlin2010, Walker2011, Zupancic2012, Tyakht2013, Nielsen2014, RajilicStojanovic2014, Salonen2014, Lagier2016, Rothschild2018, Zou2019, Byrd2020, Chen2020, Dubinkina2017, Hu2019, Jie2017, Vachida2019, Qin2012, LeChatelier2013, Karlsson2013 Firmicutes Clostridia Clostridiaceae + SANA Sessile Oval-shaped Rare 40-41 20(neg)
Ureaplasma parvum 2 Rare Possible Commensal Possible Pathogen human faeces, urogenital flora, and clinical sources RajilicStojanovic2014 Tenericutes Mollicutes Mycoplasmataceae unk FANA Sessile Coccus No spore 25.5
Ureaplasma urealyticum 2 Human and animal pathogen Rare Possible Commensal Known Pathogen human faeces, urogenital flora, and clinical sources RajilicStojanovic2014, Lagier2016, Zeller2014 Tenericutes Mollicutes Mycoplasmataceae unk FANA Sessile Coccus No spore 25.5-27.8
Ureibacillus massiliensis Bacillus massiliensis 1 Opportunistic in immunocompromised patients Rare Possible Commensal Opportunistic Pathogen clinical sources (cerebrospinal fluid) and human faeces RajilicStojanovic2014, Lagier2016 Firmicutes Bacilli Caryophanaceae neg AER Swimming Rod Endospore
Ureibacillus suwonensis 1 Unlikely Transient Non/unknown Pathogen Obligate aerobe; unlikely to be a gut coloniser. compost and human faeces RajilicStojanovic2014, Lagier2016 Firmicutes Bacilli Caryophanaceae neg SAER Swimming Rod Endospore 41.5
Ureibacillus thermosphaericus Bacillus thermosphaericus 1 Non Transient Opportunistic Pathogen Obligate aerobe and high salt required for optimum growth, so likely a gut non-coloniser. human faeces (Hoyles2012), clinical sources (cerebrospinal fluid, blood - CCUG), air sample, and landfill waste Hoyles2012, RajilicStojanovic2014, Lagier2016, Byrd2020 Firmicutes Bacilli Caryophanaceae neg SAER Swimming Endospore 36-37
Urinicoccus timonensis Rare Possible Commensal Non/unknown Pathogen human faeces Firmicutes Tissierellia Peptoniphilaceae + SANA Coccus 41.1
Urmitella timonensis Rare Possible Commensal Non/unknown Pathogen human faeces (child with marasmus - Pham2017a) Lagier2016 Firmicutes Tissierellia Tissierellaceae + ANA Rod
Uruburuella suis 2 Animal pathogen Rare Possible Commensal Opportunistic Pathogen human faeces and clinical sources from pigs Yang2020 Proteobacteria Betaproteobacteria Neisseriaceae neg FANA Sessile Coccobacillus No spore 55
Vaginimicrobium propionicum Unlikely Transient Non/unknown Pathogen a healthy vagina, France New2022 Actinobacteria Actinomycetia Propionibacteriaceae + Micr Sessile Pleiomorph rod No spore 50.6
Vagococcus carniphilus Rare Possible Commensal Non/unknown Pathogen ground beef Lagier2016 Firmicutes Bacilli Enterococcaceae + FANA Swimming Coccus No spore 34.0 40(+)
Vagococcus fluvialis 2 Human and animal pathogen Rare Possible Commensal Opportunistic Pathogen chicken faeces (CCUG) and human faeces (Bilen2018e) Lagier2016 Firmicutes Bacilli Enterococcaceae + FANA Swimming Oval-shaped No spore 33.6
Vagococcus lutrae 1 Rare Possible Commensal Non/unknown Pathogen common otter and has been detected in human faeces (Bilen2018e) Lagier2016 Firmicutes Bacilli Enterococcaceae + FANA Swimming Coccus No spore
Vagococcus penaei Rare Possible Commensal Non/unknown Pathogen microbiota of spoilt shrimp Lagier2016, Zou2019 Firmicutes Bacilli Enterococcaceae + FANA Sessile Coccus No spore 35.4
Vagococcus teuberi Rare Possible Commensal Non/unknown Pathogen fermented milk, Malia Lagier2016 Firmicutes Bacilli Enterococcaceae + FANA Sessile Diplococci No spore 34.1
Vampirovibrio chlorellavorus 1 Unlikely Transient Non/unknown Pathogen freshwater and human faeces. Predator of algae Yang2020 Cyanobacteria Candidatus Melainabacteria neg Swimming Pleiomorphic No spore 51.4
Varibaculum cambriense Varibaculum cambriensis 2 Rare Possible Commensal Opportunistic Pathogen clinical sources (abscess, fistula, IUCD - CCUG) and human faeces RajilicStojanovic2014, Lagier2016, Forster2019, Byrd2020, Vachida2019 Actinobacteria Actinomycetia Actinomycetaceae + SANA Sessile Rod 51.7
Varibaculum timonense Rare Possible Mutualist Non/unknown Pathogen human stool samples Actinobacteria Actinomycetia Actinomycetaceae + SANA Sessile Rod - curved No spore 33.2
Variovorax boronicumulans 1 Rare Possible Commensal Non/unknown Pathogen human faeces, and soil RajilicStojanovic2014 Proteobacteria Betaproteobacteria Comamonadaceae neg Swimming Rod No spore 71.2
Variovorax ginsengisoli Unlikely Transient Non/unknown Pathogen human faeces and soil from Korea McLaughlin2010, Walker2011 Proteobacteria Betaproteobacteria Comamonadaceae neg FANA Swimming Rod No spore 66
Variovorax paradoxus Alcaligenes paradoxus 1 Unlikely Transient Non/unknown Pathogen Obligate aerobe; unlikely to be a gut coloniser. human faeces and soil Yang2020, Zeller2014, PerezBrocal2015 Proteobacteria Betaproteobacteria Comamonadaceae neg SAER Swimming Rod No spore 67
Veillonella atypica Veillonella parvula subsp. atypica 1 Opportunistic in immunocompromised patients Widespread Known Commensal Rare Opportunist saliva and human faeces Mangin2004, MacFarlane2004, Woodmansey2004, Wang2005, Bik2006, DalBello2006, McLaughlin2010, Walker2011, Nielsen2014, RajilicStojanovic2014, Lagier2016, Rothschild2018, Zou2019, Almeida2019, Forster2019, Byrd2020, De2020, New2022, Chen2020, Dubinkina2017, Hu2019, Jeong2021, Jie2017, Zeller2014, Vachida2019, Wang2020a Firmicutes Negativicutes Veillonellaceae neg SANA Sessile No spore 36-40
Veillonella denticariosi 1 Opportunistic in immunocompromised patients Rare Possible Commensal Opportunistic Infection carious dentine Lagier2016, Byrd2020 Firmicutes Negativicutes Veillonellaceae neg SANA Sessile Coccus No spore
Veillonella dispar Veillonella alcalescens subsp. dispar Negative 1 Opportunistic in immunocompromised patients Moderate Possible Commensal Opportunistic Pathogen oral flora, clinical sources (endocarditis and infections) and human faeces Favier2002, DalBello2006, McLaughlin2010, Walker2011, Aujoulat2014, RajilicStojanovic2014, Lagier2016, Zou2019, Forster2019, Byrd2020, Byrd2020, New2022, Chen2020, Dubinkina2017, Hu2019, Jeong2021, Jie2017, Zeller2014, Vachida2019, PerezBrocal2015 Firmicutes Negativicutes Veillonellaceae neg SANA Sessile No spore 38-40
Veillonella infantium Rare Possible Commensal Non/unknown Pathogen the tongue biofilm of a Thai child Byrd2020 Firmicutes Negativicutes Veillonellaceae neg ANA Sessile Coccus No spore 38.6
Veillonella magna Rare Possible Commensal Non/unknown Pathogen Putrescine is required for growth. a pig mucosal jejunum, Germany De2020 Firmicutes Negativicutes Veillonellaceae neg Micr Sessile Coccus No spore
Veillonella montpellierensis Negative 1 Opportunistic in immunocompromised patients Rare Transient Opportunistic Pathogen human gastric fluid (CCUG), oral cavity, and clinical sources (endocarditis, blood - CCUG) Byrd2020 Firmicutes Negativicutes Veillonellaceae neg SANA Sessile Coccus No spore
Veillonella nakazawae Rare Transient Rare Opportunist child oral cavities, Japan New2022 Firmicutes Negativicutes Veillonellaceae neg SANA Sessile Coccus No spore 38.6
Veillonella parvula 2 Widespread Known Commensal Known Pathogen human faeces, human gut, oral cavity, and clinical sources (osteomyelitis, endocarditis, blood, bacteremia, wound) Finegold1974, Finegold1977, Benno1984, Taylor1985, Benno1986, Benno1989, MacFarlane2004, McLaughlin2010, Dubourg2013, Aujoulat2014, Nielsen2014, RajilicStojanovic2014, Lagier2016, Rothschild2018, Zou2019, Almeida2019, Chung2019, Forster2019, King2019, Byrd2020, New2022, Chen2020, Dubinkina2017, Hu2019, Jeong2021, Zeller2014, Wang2018, Vachida2019, Wang2020a, Li2019b Firmicutes Negativicutes Veillonellaceae neg SANA Sessile No spore 37-40
Veillonella ratti Veillonella alcalescens subsp. ratti 1 Rare Transient Non/unknown Pathogen human faeces, and rat mouth McLaughlin2010, RajilicStojanovic2014, Vachida2019 Firmicutes Negativicutes Veillonellaceae neg SANA Sessile No spore 41-43
Veillonella rodentium 1 Unlikely Transient Non/unknown Pathogen the mouths of hampsters Byrd2020, New2022 Firmicutes Negativicutes Veillonellaceae neg ANA Sessile Coccus No spore 42-43
Veillonella rogosae 1 Minor Transient Non/unknown Pathogen In 43% of Europeans (unseenbio.com). Minor coloniser. human faeces, and oral cavity RajilicStojanovic2014, Byrd2020 Firmicutes Negativicutes Veillonellaceae neg SANA Sessile Coccus No spore
Veillonella tobetsuensis Minor Possible Commensal Non/unknown Pathogen In 28% of Europeans (unseenbio.com). Minor coloniser. human tongue biofilms Byrd2020 Firmicutes Negativicutes Veillonellaceae neg SANA Sessile Coccus No spore
Vescimonas coprocola Rare Known Commensal Non/unknown Pathogen human faeces Firmicutes Clostridia Oscillospiraceae neg SANA Sessile Rod No spore 56.4
Vescimonas fastidiosa Rare Known Commensal Non/unknown Pathogen human faeces Firmicutes Clostridia Oscillospiraceae neg SANA Sessile Rod No spore 58.2
Vibrio alginolyticus 1 Rare Possible Commensal Possible Pathogen human faeces (CCUG) and clinical specimens (ear, wound - CCUG) Lagier2016 Proteobacteria Gammaproteobacteria Vibrionaceae neg FANA Swimming Rod No spore 45-47
Vibrio cholerae Negative 2 Zoonotic pathogen Unlikely Possible Commensal Dangerous Pathogen human faeces (CCUG), clinical sources (ear infections - CCUG) and causes severe diarrhoea Lagier2016, Almeida2019, De2020, Zeller2014 Proteobacteria Gammaproteobacteria Veillonellaceae neg FANA Swimming No spore 47-49
Vibrio cincinnatiensis 2 Rare Possible Commensal Opportunistic Pathogen human faeces (CCUG) and clinical sources (enteritis, blood, cerebrospinal fluid - CCUG) Lagier2016, Forster2019 Proteobacteria Gammaproteobacteria Vibrionaceae neg FANA Swimming Rod No spore 45
Vibrio fluvialis 2 Zoonotic pathogen Rare Possible Commensal Opportunistic Pathogen Data combined for biovars I and II, plus other strains. human faeces and clinical sources (wound, diarrhoea - CCUG) RajilicStojanovic2014, Lagier2016 Proteobacteria Gammaproteobacteria Vibrionaceae neg FANA Swimming Rod No spore 49.3-50.6
Vibrio furnissii 2 Zoonotic pathogen Rare Possible Commensal Opportunistic Pathogen human faeces and aquatic environments RajilicStojanovic2014, Lagier2016, Yang2020 Proteobacteria Gammaproteobacteria Vibrionaceae neg FANA Swimming Rod - curved No spore 50.4
Vibrio metoecus Rare Possible Commensal Opportunistic Pathogen Close relative of V. cholerae. human faeces, brackish ponds and clinical sources (blood) Lagier2016, De2020 Proteobacteria Gammaproteobacteria Vibrionaceae neg FANA Swimming Rod - curved No spore 47.7
Vibrio metschnikovii 2 Zoonotic pathogen Rare Possible Commensal Rare Opportunist brackish waters, fowl and (rarely) clinical sources (blood) Lagier2016 Proteobacteria Gammaproteobacteria Vibrionaceae neg FANA vr Rod - curved No spore 44-46
Vibrio mimicus 2 Zoonotic pathogen Rare Possible Commensal Opportunistic Pathogen human faeces, and clinical sources (diarrhoea, ear infections - CCUG) RajilicStojanovic2014, Lagier2016, Zeller2014 Proteobacteria Gammaproteobacteria Vibrionaceae neg FANA Swimming Rod No spore
Vibrio natriegens Pseudomonas natriegens 1 Rare Possible Commensal Non/unknown Pathogen human faeces and salt marsh mud Yang2020 Proteobacteria Gammaproteobacteria Vibrionaceae neg FANA Swimming Rod No spore 45.1-47
Vibrio neptunius 1 Unlikely Transient Non/unknown Pathogen Borderline cold mesophile, with optimum growth temp of 28C. Unlikely gut coloniser. the larvae of bivalves, Brazil De2020 Proteobacteria Gammaproteobacteria Vibrionaceae neg FANA Swimming Rod - curved No spore 46.0
Vibrio parahaemolyticus 1 Rare Possible Commensal Opportunistic Pathogen human faeces and clinical sources (diarrhoea, blood, wound - CCUG) RajilicStojanovic2014, Lagier2016, De2020 Proteobacteria Gammaproteobacteria Vibrionaceae neg FANA Swimming Rod No spore 46-47
Vibrio proteolyticus Aeromonas hydrophila subsp. proteolytica 1 Rare Possible Commensal Non/unknown Pathogen the alimentary canal of marine isopods De2020 Proteobacteria Gammaproteobacteria Vibrionaceae neg FANA Swimming Rod No spore 50.5
Vibrio rumoiensis 1 Unlikely Transient Non/unknown Pathogen Low growth temperatures of 2-34C suggest it is an unlikely gut coloniser. the waste stream of a fish processing facility, Japan Li2019b, PerezBrocal2015 Proteobacteria Gammaproteobacteria Vibrionaceae neg FANA Sessile Rod No spore 43.2
Vibrio vulnificus Beneckea vulnifica 2 Zoonotic pathogen Rare Possible Commensal Known Pathogen Includes all biogroups (1-3). Can cause food poisoning. Colonises the mucus layer at the expense of Phocaeicola vulgatus, killing the latter. eels and clinical sources (wounds, septicaemia, bacteraemia) Lagier2016 Proteobacteria Gammaproteobacteria Vibrionaceae neg FANA Swimming Rod - curved No spore 46-48
Victivallis vadensis 1 Minor Possible Commensal Non/unknown Pathogen human faeces, blood, digester, and termites Walker2011, Zupancic2012, RajilicStojanovic2014, Lagier2016, Jie2017, Zeller2014, Wang2020a, Minerbi2019, LeChatelier2013 Lentisphaerae Lentisphaeria Victivallaceae neg SANA Sessile Coccus No spore 59.2
Virgibacillus dakarensis Positive Rare Known Commensal Non/unknown Pathogen human faeces (Senghor2017) that are salty Firmicutes Bacilli Bacillaceae + AER Swimming Rod Endospore
Virgibacillus dokdonensis 1 Rare Possible Commensal Non/unknown Pathogen an island, Korea Lagier2016 Firmicutes Bacilli Bacillaceae vr FANA Swimming Rod Endospore 36.7
Virgibacillus doumboii Rare Possible Commensal Non/unknown Pathogen human faeces (healthy) Firmicutes Bacilli Bacillaceae + SAER Swimming Rod No spore 39.8
Virgibacillus halodenitrificans Bacillus halodenitrificans 1 Rare Possible Commensal Non/unknown Pathogen a solar evaporation pond, France Lagier2016 Firmicutes Bacilli Bacillaceae vr FANA Swimming Rod Endospore 38-39
Virgibacillus ihumii Rare Possible Commensal Non/unknown Pathogen Halophilic human faeces (healthy) Firmicutes Bacilli Bacillaceae + SAER Swimming Rod No spore 41.1
Virgibacillus massiliensis Positive Rare Known Commensal Non/unknown Pathogen human faeces (Senghor2017) that are salty Lagier2016 Firmicutes Bacilli Bacillaceae + SAER Swimming Rod Endospore 36.9
Virgibacillus ndiopensis Positive Rare Known Commensal Non/unknown Pathogen human faeces (Senghor2017) that are salty Firmicutes Bacilli Bacillaceae + AER Swimming Rod Endospore 36.4
Virgibacillus pantothenticus Bacillus pantothenticus 1 Rare Possible Commensal Non/unknown Pathogen soil Lagier2016 Firmicutes Bacilli Bacillaceae + FANA Swimming Rod Endospore 36.9
Virgibacillus profundi Unlikely Transient Non/unknown Pathogen Low optimum temperatures (15-25C) and inability to grow at 37C makes this an unlikely gut coloniser. marine sediments Byrd2020 Firmicutes Bacilli Bacillaceae vr FANA Swimming Rod Endospore 37.3
Virgibacillus proomii 1 Rare Possible Commensal Non/unknown Pathogen human faeces (Hoyles2012), soil and clinical sources (infant bile) Hoyles2012, RajilicStojanovic2014, Lagier2016 Firmicutes Bacilli Bacillaceae + FANA Swimming Rod Endospore 37
Virgibacillus salexigens Bacillus salexigens 1 Unlikely Transient Non/unknown Pathogen Obligate aerobe; unlikely to be a gut coloniser. human faeces and hypersaline soil in Spain Forster2019 Firmicutes Bacilli Bacillaceae + SAER Swimming Rod Endospore 36.3-39.5
Virgibacillus senegalensis Non Transient Non/unknown Pathogen Likely gut non-coloniser because its optimum growth is with high salt and is an obligate aerobe. the faeces of a healthy volunteer, Senegal Lagier2016 Firmicutes Bacilli Bacillaceae + SAER Swimming Rod Endospore 42.9
Virgibacillus siamensis Unlikely Transient Non/unknown Pathogen Unlikely gut coloniser because its optimum growth is with high salt. fermented fish, Thailand Lagier2016 Firmicutes Bacilli Bacillaceae + FANA Swimming Rod Endospore 38.0
Vitreoscilla massiliensis Rare Possible Commensal Non/unknown Pathogen human faeces (Ndongo2018) Lagier2016, Byrd2020 Proteobacteria Betaproteobacteria Neisseriaceae neg Micr Sessile Rod No spore
Vitreoscilla stercoraria 1 Rare Possible Commensal Non/unknown Pathogen cow faeces De2020 Proteobacteria Betaproteobacteria Neisseriaceae neg AER Gliding Rod No spore 50-51
Weeksella virosa 1 Opportunistic in immunocompromised patients Rare Possible Commensal Opportunistic Pathogen clinical specimens (UTI, rectal swab, vagina) Lagier2016 Firmicutes Bacilli Leuconostocaceae neg AER Sessile Rod No spore 37.3
Weissella cibaria 1 Human and animal pathogen; opportunistic in immunocompromised patients Minor Known Commensal Known Pathogen Found in human breast milk (Jeurink2013). human faeces, fermented food, and clinical specimens (gall, urine - CCUG) RajilicStojanovic2014, Lagier2016, Zou2019, Byrd2020, Hu2019, Jie2017, Zeller2014, Vachida2019, Wang2020a Firmicutes Bacilli Leuconostocaceae + FANA Sessile Rod No spore 44-45
Weissella confusa Lactobacillus confusus 1 Human and animal pathogen; opportunistic in immunocompromised patients Minor Possible Commensal Known Pathogen Found in human breast milk (Jeurink2013). human faeces, fermented food, and clinical sources (gall, blood, drainage - CCUG) Bik2006, RajilicStojanovic2014, Lagier2016, Zou2019, Byrd2020, Yang2020, Hu2019, Vachida2019, PerezBrocal2015 Firmicutes Bacilli Leuconostocaceae + FANA Sessile Rod No spore 45-47
Weissella paramesenteroides Leuconostoc paramesenteroides 1 Minor Known Commensal Non/unknown Pathogen human faeces Tyakht2013, RajilicStojanovic2014, Lagier2016, Forster2019, Yang2020, Zeller2014, Vachida2019 Firmicutes Bacilli Leuconostocaceae + FANA Sessile Coccus No spore 37-38
Weissella viridescens Lactobacillus viridescens 1 Minor Possible Commensal Rare Opportunist In 48% of Europeans (unseenbio.com). Minor coloniser. human faeces (Sanz2007 - coeliac children), clinical specimens (blood), discolored cured meat products and pasteurized milk Lagier2016, Byrd2020, Yang2020 Firmicutes Bacilli Lactobacillaceae + FANA Sessile Rod No spore 41-44
Weizmannia coagulans Bacillus coagulans Positive 1 Opportunistic in immunocompromised patients Rare Known Commensal Opportunistic Infection human faeces, soil and spoilt food Zou2019, PerezBrocal2015 Firmicutes Bacilli Bacillaceae + FANA Swimming Rod Endospore 45.4-50.3
Winkia neuii Actinomyces neuii Rare Possible Commensal Opportunistic Pathogen human faeces and clinical sources (blood, wound, abscess, vagina, urine - CCUG) Lagier2016, Almeida2019, Forster2019 Actinobacteria Actinomycetia Actinomycetaceae + FANA Sessile Diphtheroidal No spore 55-58
Wolinella succinogenes Vibrio succinogenes 1 Rare Possible Commensal Non/unknown Pathogen Hydrogen and formate are used as energy sources; carbohydrates are not fermented and don't support growth. Has acquired the genes necessary for N2 fixation, probably by lateral gene transfer from cyanobacteria. bovine rumen Tyakht2013 Proteobacteria Epsilonproteobacteria Helicobacteraceae neg ANA Swimming Helical No spore 46-49
Xanthomonas massiliensis Unlikely Transient Non/unknown Pathogen human faeces (Ndongo2017) Lagier2016 Proteobacteria Gammaproteobacteria Xanthomonadaceae neg AER Swimming Rod No spore
Xylanimonas cellulosilytica 1 Rare Possible Commensal Non/unknown Pathogen a decayed tree, Spain Zeller2014 Actinobacteria Actinomycetia Promicromonosporaceae + FANA Sessile Coccus No spore 73
Yangia pacifica Salipiger pacificus 1 Non Transient Non/unknown Pathogen Obligate aerobe and high salt required for optimum growth, so likely a gut non-coloniser. coastal sediment, China New2022 Proteobacteria Alphaproteobacteria Roseobacteraceae neg SAER Swimming Rod No spore 63.3
Yersinia aldovae Yersinia enterocolitica-Like Group X2 1 Rare Possible Commensal Non/unknown Pathogen human faeces (CCUG) and aquatic ecosystems Proteobacteria Gammaproteobacteria Yersiniaceae neg FANA Swimming Rod No spore 48
Yersinia aleksiciae 2 Rare Possible Commensal Opportunistic Pathogen human faeces, dairy products, and animals RajilicStojanovic2014, Lagier2016 Proteobacteria Gammaproteobacteria Yersiniaceae neg FANA Swimming Coccobacillus No spore 48.1
Yersinia alsatica Rare Known Commensal Non/unknown Pathogen human faeces, France Proteobacteria Gammaproteobacteria Yersiniaceae neg FANA Swimming Rod - curved No spore 47.6
Yersinia artesiana Rare Known Commensal Non/unknown Pathogen human faeces, France Proteobacteria Gammaproteobacteria Yersiniaceae neg FANA Sessile Rod - curved No spore 47.8
Yersinia bercovieri Yersinia enterocolitica Biogroup 3B 1 Rare Possible Commensal Non/unknown Pathogen human faeces, vegetables, and water sources RajilicStojanovic2014, Lagier2016, Byrd2020 Proteobacteria Gammaproteobacteria Yersiniaceae neg FANA Swimming Coccobacillus No spore 50
Yersinia enterocolitica subsp. enterocolitica Yersinia enterocolitica 2 Zoonotic pathogen Unlikely Possible Commensal Known Pathogen Pathogenic; unlikely to be a coloniser in a healthy microbiome. human faeces, and clinical sources RajilicStojanovic2014, Cassir2015, Lagier2016, Byrd2020, Zeller2014 Proteobacteria Gammaproteobacteria Yersiniaceae neg FANA Swimming Coccobacillus No spore 48.5
Yersinia frederiksenii 2 Zoonotic pathogen Rare Possible Commensal Opportunistic Pathogen human faeces, and water sources RajilicStojanovic2014, Lagier2016, Byrd2020 Proteobacteria Gammaproteobacteria Yersiniaceae neg FANA Swimming Coccobacillus No spore 48
Yersinia intermedia 2 Zoonotic pathogen Rare Possible Commensal Opportunistic Pathogen Unlikely to be pathogenic. Most clinical isolates are clusters and seem unrelated to the illnesses of the patients. In 2% of healthy Europeans (unseenbio.com) aquatic systems, rarely terrestrially or in humans. Found in human faeces and clinical sources (blood) and food. Cassir2015, Lagier2016, Byrd2020 Proteobacteria Gammaproteobacteria Yersiniaceae neg FANA Swimming Rod No spore 48.5
Yersinia kristensenii subsp. kristensenii 2 Zoonotic pathogen Rare Transient Opportunistic Pathogen Although the bacterium can be found in faeces, it requires cold enrichment to grow. This suggests it won't be a significant coloniser of the gut. soil, food, clinical sources (rare) and human faeces RajilicStojanovic2014, Lagier2016 Proteobacteria Gammaproteobacteria Yersiniaceae neg FANA Swimming Rod No spore 48.5
Yersinia kristensenii subsp. rochesterensis Negative Rare Possible Commensal Non/unknown Pathogen human faeces Proteobacteria Gammaproteobacteria Yersiniaceae neg FANA Swimming Coccobacillus No spore 48.5
Yersinia massiliensis Rare Possible Commensal Non/unknown Pathogen water, milk, vegetatables and human faeces (CCUG) Byrd2020 Proteobacteria Gammaproteobacteria Yersiniaceae neg FANA vr Coccobacillus No spore
Yersinia mollaretii Yersinia enterocolitica biogroup 3A 1 Rare Possible Commensal Non/unknown Pathogen human faeces (CCUG), drinking water, vegetables Lagier2016 Proteobacteria Gammaproteobacteria Yersiniaceae neg FANA vr Coccobacillus No spore 50-51
Yersinia occitanica Rare Known Commensal Non/unknown Pathogen human faeces, France Proteobacteria Gammaproteobacteria Yersiniaceae neg FANA vr Short Rod No spore 47.8
Yersinia pestis 4 Can be passed from animals to humans Non Transient Known Pathogen Highly dangerous pathogen. Not a long term coloniser of the human gut. rodents and their fleas Byrd2020, New2022 Proteobacteria Gammaproteobacteria Yersiniaceae neg FANA Sessile Coccobacillus No spore 46
Yersinia proxima Rare Known Commensal Non/unknown Pathogen human faeces, France Proteobacteria Gammaproteobacteria Yersiniaceae neg FANA Swimming Rod - curved No spore 47
Yersinia pseudotuberculosis Pasteurella lymphangitidis Negative 2 Zoonotic pathogen Unlikely Transient Possible Pathogen clinical sources (blood, lymph node - CCUG) and human faeces RajilicStojanovic2014, Lagier2016 Proteobacteria Gammaproteobacteria Yersiniaceae neg FANA vr Coccobacillus No spore 46.5
Yersinia rohdei 1 Opportunistic in immunocompromised patients Rare Possible Commensal Opportunistic Infection human faeces RajilicStojanovic2014, Lagier2016 Proteobacteria Gammaproteobacteria Yersiniaceae neg FANA vr Coccobacillus No spore 49.1
Yersinia vastinensis Rare Known Commensal Non/unknown Pathogen human faeces, France Proteobacteria Gammaproteobacteria Yersiniaceae neg FANA vr Rod - curved No spore 46.9
Yokenella regensburgei Koserella trabulsii Negative 2 Rare Possible Commensal Possible Pathogen human faeces (ulceritive colitis - Alkhalil2017), insects, and clinical sources (wound) RajilicStojanovic2014, Lagier2016, Dubinkina2017 Proteobacteria Gammaproteobacteria Enterobacteriaceae neg FANA Swimming Rod No spore 58-59.3
Yonghaparkia alkaliphila 1 Non Transient Non/unknown Pathogen Obligate aerobe, no spore formation and doesn't grow at 38C, so probably a gut non-coloniser. human faeces, and alkaline soil McLaughlin2010, RajilicStojanovic2014 Actinobacteria Actinomycetia Microbacteriaceae + SAER Sessile Rod No spore 71.1-71.6
Zunongwangia profunda Wangia profunda 1 Non Transient Non/unknown Pathogen Strictly aerobic and low optimum growth conditions suggests this not a gut coloniser. deep-sea sediment, Japan Qin2012 Bacteroidetes Flavobacteriia Flavobacteriaceae neg SAER Sessile Rod No spore 35.8

Click on table headings to sort. Table abbreviations: OxTol - oxygen tolerance; Motil - motility; Morph - morphology; Spore - endo/exospore; DnaGC - %GC content in DNA; Bile - growth with bile;