Rare Colonising Gut Bacteria

★ There are 1446 'rarely colonising' bacteria.

Bacteria Phylum O2 Tol Opt Temp Opt pH Pathogenicity Studies Number Studies Notes
Absiella argi Firmicutes SANA 37 7 Non/unknown Pathogen Jeong2021 1
Absiella tortuosum Firmicutes SANA 37-41 7 Known Pathogen Finegold1977, Benno1989, RajilicStojanovic2014, Lagier2016 4
Acetanaerobacterium elongatum Firmicutes SANA 37 6.5-7.0 Non/unknown Pathogen deGoffau2013, McLaughlin2010, RajilicStojanovic2014, Byrd2020 4
Acetatifactor muris Firmicutes SANA 30-37 Non/unknown Pathogen Byrd2020 1
Acetitomaculum ruminis Firmicutes SANA 37-42 6.8 Non/unknown Pathogen Byrd2020, De2020 2 Homoacetogenic. Can consume carbon monoxide.
Acetivibrio cellulolyticus Firmicutes SANA 35 Non/unknown Pathogen Zupancic2012, Zeller2014, Qin2012 3
Acetoanaerobium sticklandii Firmicutes SANA 30-37 Non/unknown Pathogen Benno1986, Benno1986, RajilicStojanovic2014, Lagier2016, New2022, Qin2012 6
Acetobacterium woodii Firmicutes SANA 30 6.8-7 Non/unknown Pathogen De2020, New2022 2 Hydrogen-oxidising, CO2-reducing acetic acid producer. Homoacetogen. Can use CO as an electron donor.
Achromobacter xylosoxidans Proteobacteria SAER Opportunistic Pathogen RajilicStojanovic2014, Lagier2016, Forster2019, Zeller2014 4 Phototrophic.
Acidaminococcus massiliensis Firmicutes ANA Non/unknown Pathogen Lagier2016, Byrd2020 2 In 8% of Europeans (unseenbio.com). A rare coloniser.
Acidaminococcus provencensis Firmicutes SANA Non/unknown Pathogen 0
Acidaminococcus timonensis Firmicutes ANA Non/unknown Pathogen Lagier2016, Byrd2020 2
Acidipropionibacterium acidipropionici Actinobacteria ANA Non/unknown Pathogen RajilicStojanovic2014, Lagier2016 2
Acidipropionibacterium jensenii Actinobacteria ANA Opportunistic Infection Taylor1985, Woodmansey2004, RajilicStojanovic2014, Lagier2016 4
Acidisarcina polymorpha Acidobacteria AER 20-32 4.8-7.0 Non/unknown Pathogen New2022 1
Acidovorax facilis Proteobacteria AER Non/unknown Pathogen McLaughlin2010, Walker2011, RajilicStojanovic2014 3
Acidovorax sp. strain KKS102 Proteobacteria AER Non/unknown Pathogen King2019 1 Biphenyl and polychlorinated biphenyl degrader.
Acidovorax temperans Proteobacteria AER Rare Opportunist McLaughlin2010 1
Acidovorax wautersii Proteobacteria AER Rare Opportunist Yang2020 1
Acinetobacter calcoaceticus Proteobacteria SAER 15-37 Possible Pathogen RajilicStojanovic2014, Lagier2016, De2020 3
Acinetobacter guillouiae Proteobacteria SAER 25-35 Opportunistic Infection Byrd2020 1 Obligate aerobe; has been found in the faeces of non-hospital patients in Leiden (Dijkshoorn2005).
Acinetobacter idrijaensis Proteobacteria None Byrd2020 1 Resistant to mercury, and probably cobalt, cadmium and zinc.
Acinetobacter johnsonii Proteobacteria SAER 15-30 Opportunistic Infection Wang2005, McLaughlin2010, RajilicStojanovic2014, Yang2020, New2022, Zeller2014, Vachida2019, PerezBrocal2015 8 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).
Acinetobacter junii Proteobacteria SAER 15-37 Opportunistic Infection Frank2007, McLaughlin2010, Pandey2012, Tyakht2013, RajilicStojanovic2014, Lagier2016, Forster2019, Yang2020, Hu2019, Zeller2014 10 In 1% of Europeans (unseenbio.com). Rare coloniser.
Acinetobacter radioresistens Proteobacteria AER 27-31 Opportunistic Infection McLaughlin2010, Tyakht2013, RajilicStojanovic2014, Lagier2016 4
Actinobacillus capsulatus Proteobacteria FANA Possible Pathogen Forster2019 1
Actinobacillus pleuropneumoniae Proteobacteria FANA Opportunistic Pathogen Bik2006, RajilicStojanovic2014, Zeller2014 3
Actinobacillus succinogenes Proteobacteria FANA 37-39 Non/unknown Pathogen Tyakht2013 1
Actinomyces ihuae Actinobacteria AER 37 Non/unknown Pathogen Lagier2016 1
Actinomyces johnsonii Actinobacteria FANA Non/unknown Pathogen Lagier2016, Byrd2020, Vachida2019 3
Actinomyces marseillensis Actinobacteria AER 37 Opportunistic Infection 0
Actinomyces massiliensis Actinobacteria ANA 37 Possible Pathogen Byrd2020, Vachida2019 2
Actinomyces mediterranea Actinobacteria Micr Non/unknown Pathogen 0
Actinomyces minihominis Actinobacteria ANA Non/unknown Pathogen 0
Actinomyces oris Actinobacteria FANA Opportunistic Infection RajilicStojanovic2014, Lagier2016, Byrd2020, De2020, New2022, Vachida2019 6
Actinomyces pacaensis Actinobacteria ANA Rare Opportunist New2022 1
Actinomyces polynesiensis Actinobacteria Micr Non/unknown Pathogen Lagier2016 1
Actinomyces provencensis Actinobacteria FANA Non/unknown Pathogen Lagier2016 1
Actinomyces sp. ph3 Actinobacteria None Non/unknown Pathogen Pfleiderer2013, RajilicStojanovic2014, Lagier2016 3
Actinomyces timonensis Actinobacteria ANA 37 Opportunistic Pathogen Vachida2019 1
Actinomyces urogenitalis Actinobacteria FANA Opportunistic Infection Favier2002, RajilicStojanovic2014, Lagier2016, Hu2019, Zeller2014 5
Actinotignum schaalii Actinobacteria FANA Opportunistic Infection 0
Acutalibacter muris Firmicutes SANA Non/unknown Pathogen Byrd2020, New2022 2
Adlercreutzia caecimuris Actinobacteria SANA Non/unknown Pathogen Byrd2020, Vachida2019 2
Adlercreutzia equolifaciens subsp. celatus Actinobacteria SANA Non/unknown Pathogen RajilicStojanovic2014, Yang2020 2
Adlercreutzia hattorii Actinobacteria SANA 37 7.0 Non/unknown Pathogen New2022 1 Doesn't produce equol and is asaccharolytic.
Adlercreutzia mucosicola Actinobacteria SANA 30-40 6.9-7.1 Non/unknown Pathogen Byrd2020 1
Adlercreutzia rubneri Actinobacteria SANA Non/unknown Pathogen 0 Able to metabolise resveratrol (an antioxidant and antimicrobial).
Aerococcus viridans Firmicutes Micr Opportunistic Pathogen Finegold1977, RajilicStojanovic2014, Lagier2016, Yang2020 4
Aeromicrobium massiliense Actinobacteria AER Non/unknown Pathogen Pfleiderer2013, RajilicStojanovic2014, Lagier2016, Forster2019 4
Aeromicrobium tamlense Actinobacteria AER 30 7.1 Non/unknown Pathogen Lagier2016 1
Aeromonas allosaccharophila Proteobacteria FANA Possible Pathogen RajilicStojanovic2014, Lagier2016 2
Aeromonas bestiarum Proteobacteria AER Opportunistic Pathogen RajilicStojanovic2014, Lagier2016 2
Aeromonas dhakensis Proteobacteria FANA 30-37 Opportunistic Infection Lagier2016, Vachida2019 2
Aeromonas enteropelogenes Proteobacteria AER Opportunistic Pathogen RajilicStojanovic2014, Lagier2016, Hu2019, Zeller2014, Vachida2019 5
Aeromonas jandaei Proteobacteria AER Opportunistic Pathogen RajilicStojanovic2014, Lagier2016 2
Aeromonas media Proteobacteria AER Opportunistic Pathogen RajilicStojanovic2014, Lagier2016 2
Aeromonas sobria Proteobacteria FANA 25-30 Opportunistic Pathogen Lagier2016 1
Aeromonas tecta Proteobacteria FANA 30 Non/unknown Pathogen RajilicStojanovic2014, Lagier2016 2
Aeromonas trota Proteobacteria FANA Opportunistic Infection RajilicStojanovic2014 1
Aeromonas veronii Proteobacteria AER 36 Known Pathogen RajilicStojanovic2014, Lagier2016, Almeida2019 3
Aestuariimicrobium kwangyangense Actinobacteria AER 30 7.5-8.5 Non/unknown Pathogen De2020 1
Afipia broomeae Proteobacteria FANA Possible Pathogen Yang2020 1
Africanella massiliensis Firmicutes ANA Non/unknown Pathogen 0
Agathobacter ruminis Firmicutes SANA 35-39 7 Non/unknown Pathogen Byrd2020 1
Aggregatibacter actinomycetemcomitans Proteobacteria FANA Opportunistic Pathogen Forster2019, Byrd2020 2
Agrococcus casei Actinobacteria AER Non/unknown Pathogen Lagier2016 1
Agrococcus jejuensis Actinobacteria AER 30 Non/unknown Pathogen RajilicStojanovic2014 1
Agrococcus jenensis Actinobacteria Micr Non/unknown Pathogen Hoyles2012, Lagier2016, PerezBrocal2015 3
Akkermansia glycaniphila Verrucomicrobia SANA 25-30 6.0 Non/unknown Pathogen Byrd2020, De2020, New2022 3 Can use mucin as a sole C and N source.
Alcaligenes faecalis Proteobacteria AER 30-37 Opportunistic Infection McLaughlin2010, RajilicStojanovic2014, Salonen2014, Lagier2016, Yang2020, Zeller2014 6
Aliagarivorans marinus Proteobacteria FANA 25-30 Non/unknown Pathogen Forster2019 1
Aliarcobacter butzleri Proteobacteria Micr Rare Opportunist Tyakht2013, RajilicStojanovic2014, Lagier2016, Zeller2014, Vachida2019 5
Aliarcobacter cryaerophilus Proteobacteria Micr Possible Pathogen RajilicStojanovic2014, Lagier2016, Byrd2020, Yang2020 4
Aliarcobacter skirrowii Proteobacteria Micr Opportunistic Pathogen Lagier2016 1 Carbohydrates are not fermented or oxidised.
Alicyclobacillus acidocaldarius Firmicutes AER Non/unknown Pathogen New2022, Zeller2014 2
Alistipes communis Bacteroidetes SANA 37 7 Non/unknown Pathogen Lagier2016, New2022, Chen2020, Hu2019, Vachida2019 5
Alistipes dispar Bacteroidetes SANA 37 7 Non/unknown Pathogen New2022 1
Alistipes inops Bacteroidetes SANA Non/unknown Pathogen Forster2019, Yang2020 2
Alistipes marseilloanorexicus Bacteroidetes SANA Non/unknown Pathogen Pfleiderer2013, RajilicStojanovic2014 2
Alistipes massiliensis Bacteroidetes None Non/unknown Pathogen Walker2011, Lagier2016, Minerbi2019, PerezBrocal2015 4
Alistipes megaguti Bacteroidetes ANA Non/unknown Pathogen New2022 1
Alistipes montrealensis Bacteroidetes SANA 37 Non/unknown Pathogen 0
Alistipes onderdonkii subsp. vulgaris Bacteroidetes SANA 37 7 Opportunistic Infection 0
Alistipes provencensis Bacteroidetes ANA Non/unknown Pathogen Lagier2016 1
Alkalihalobacillus gibsonii Firmicutes AER 8.0 Non/unknown Pathogen Lagier2016 1 Tolerates up to 9% salt.
Alkalihalobacillus halodurans Firmicutes AER Non/unknown Pathogen Tyakht2013, RajilicStojanovic2014, Lagier2016 3
Alkaliphilus metalliredigens Firmicutes SANA 35 9.5 Non/unknown Pathogen New2022 1 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.
Allobaculum fili Firmicutes SANA 37 6.5-7.0 Possible Pathogen 0
Allobaculum mucilyticum Firmicutes SANA 37 6.5-7.0 Possible Pathogen 0 Mucin-degrading bacterium
Alloprevotella rava Bacteroidetes SANA 35 7.0 Non/unknown Pathogen Byrd2020, De2020, Vachida2019 3 Probably an oral commensal that passes through the GI tract.
Alteracholeplasma palmae Tenericutes FANA 30 Non/unknown Pathogen Byrd2020, New2022 2 Cholesterol or serum is not required for growth.
Alterileibacterium massiliense Firmicutes SANA 37 Non/unknown Pathogen 0
Amedibacterium intestinale Firmicutes SANA 37 7 Non/unknown Pathogen New2022 1
Aminipila butyrica Firmicutes SANA 30 6.1-6.8 Non/unknown Pathogen New2022 1 Doesn't utilise carbohydrates.
Aminipila terrae Firmicutes SANA 30 7 Non/unknown Pathogen New2022 1 Fermentation products from glucose are glycolic and glyceric acids.
Aminomonas paucivorans Synergistetes SANA 35 7.5 Non/unknown Pathogen New2022, Zeller2014 2 Asaccharolytic but yeast extract is required for growth.
Amycolatopsis alba Actinobacteria AER Non/unknown Pathogen Byrd2020 1 Produces a new glycopeptide antibiotic related to vancomycin.
Amycolatopsis mediterranei Actinobacteria AER Non/unknown Pathogen Zeller2014 1
Amycolatopsis thailandensis Actinobacteria AER 25-37 6-10 Non/unknown Pathogen Byrd2020 1
Anaerobiospirillum succiniciproducens Proteobacteria SANA 37-40 Rare Opportunist Zupancic2012, RajilicStojanovic2014, Lagier2016, Byrd2020 4
Anaerobiospirillum thomasii Proteobacteria SANA 37 Opportunistic Pathogen RajilicStojanovic2014, Lagier2016 2
Anaerobutyricum soehngenii Firmicutes SANA 37 Non/unknown Pathogen 0
Anaerococcus hydrogenalis Firmicutes SANA 37 Opportunistic Pathogen Tyakht2013, RajilicStojanovic2014, Lagier2016, Forster2019, Zeller2014 5
Anaerococcus jeddahensis Firmicutes SANA 37 Non/unknown Pathogen Lagier2016 1
Anaerococcus lactolyticus Firmicutes SANA Opportunistic Pathogen Zeller2014, Vachida2019 2
Anaerococcus marasmi Firmicutes SANA 37 Possible Pathogen 0
Anaerococcus mediterraneensis Firmicutes ANA Possible Pathogen New2022 1
Anaerococcus murdochii Firmicutes SANA Opportunistic Pathogen Lagier2016, Yang2020 2
Anaerococcus obesiensis Firmicutes SANA Non/unknown Pathogen RajilicStojanovic2014, Lagier2016, Byrd2020, New2022, Vachida2019 5
Anaerococcus octavius Firmicutes SANA 37 Opportunistic Infection Dubourg2013, Aujoulat2014, RajilicStojanovic2014, Lagier2016, De2020, Yang2020 6
Anaerococcus provencensis Firmicutes SANA Non/unknown Pathogen Lagier2016 1
Anaerococcus rubeinfantis Firmicutes SANA 37 Possible Pathogen Lagier2016 1
Anaerococcus senegalensis Firmicutes SANA 37 Non/unknown Pathogen RajilicStojanovic2014, Lagier2016, Forster2019 3
Anaerococcus tetradius Firmicutes SANA Opportunistic Pathogen Vachida2019 1
Anaerocolumna aminovalerica Firmicutes SANA 37 Non/unknown Pathogen Finegold1974, Finegold1977, Benno1989, RajilicStojanovic2014, Lagier2016, Byrd2020 6
Anaerocolumna cellulosilytica Firmicutes SANA 35 7.6 Non/unknown Pathogen New2022 1 Slightly alkaliphilic.
Anaerocolumna chitinilytica Firmicutes SANA Non/unknown Pathogen New2022 1
Anaerocolumna sedimenticola Firmicutes SANA 37 7.0 Non/unknown Pathogen New2022 1
Anaerocolumna xylanovorans Firmicutes SANA 37 7 Non/unknown Pathogen deGoffau2013 1
Anaerofilum pentosovorans Firmicutes SANA 25–40 7-7.4 Non/unknown Pathogen RajilicStojanovic2014 1
Anaeromassilibacillus senegalensis Firmicutes ANA Non/unknown Pathogen Lagier2016, Byrd2020 2
Anaerorhabdus furcosa Firmicutes SANA 30-37 Opportunistic Pathogen Moore1974, Benno1989, RajilicStojanovic2014, Lagier2016, Byrd2020 5
Anaerosalibacter bizertensis Firmicutes SANA 40 7.5 Non/unknown Pathogen Lagier2016 1
Anaerosalibacter massiliensis Firmicutes SANA 37 Non/unknown Pathogen Lagier2016 1
Anaerosphaera massiliensis Firmicutes SANA Non/unknown Pathogen 0
Anaerospora hongkongensis Firmicutes SANA Opportunistic Pathogen Lagier2016 1 Relatively inert biochemically.
Anaerostipes butyraticus Firmicutes SANA 37-41 6 Non/unknown Pathogen RajilicStojanovic2014 1
Anaerostipes coli Firmicutes SANA Non/unknown Pathogen RajilicStojanovic2014, Lagier2016 2
Anaerostipes hominis Firmicutes SANA 37 7 Non/unknown Pathogen 0 From a patient with Crohn's disease. Produces butyrate, propionate, oxaloacetate and fumarate from fermentation.
Anaerostipes rhamnosivorans Firmicutes SANA 37 6.5-7 Non/unknown Pathogen Lagier2016, Yang2020, New2022 3
Anaerostipes rhamnosus Firmicutes SANA Non/unknown Pathogen RajilicStojanovic2014 1
Anaerotignum faecicola Firmicutes SANA 40 6.8 Non/unknown Pathogen 0
Anaerotignum neopropionicum Firmicutes SANA 30 Non/unknown Pathogen Byrd2020 1
Anaerotignum propionicum Firmicutes SANA 28-37 7.0-7.4 Non/unknown Pathogen Lagier2016, New2022 2
Anaerotruncus massiliensis Firmicutes ANA 37 7.5 Non/unknown Pathogen Lagier2016, Byrd2020 2 Succinate-producer.
Anaerovorax odorimutans Firmicutes SANA 37 7.2-7.6 Non/unknown Pathogen Salonen2014 1
Ancylobacter polymorphus Proteobacteria AER 28-30 Non/unknown Pathogen RajilicStojanovic2014, Lagier2016 2
Aneurinibacillus aneurinilyticus Firmicutes SAER 35-37 6.5-7 Non/unknown Pathogen RajilicStojanovic2014, Lagier2016, Forster2019 3
Aneurinibacillus migulanus Firmicutes SAER 30-37 Non/unknown Pathogen RajilicStojanovic2014, Lagier2016 2
Angelakisella massiliensis Firmicutes ANA Non/unknown Pathogen Byrd2020, De2020 2
Anoxynatronum sibiricum Firmicutes ANA 35 9.1 Non/unknown Pathogen PerisBondia2011, RajilicStojanovic2014 2
Aquabacterium citratiphilum Proteobacteria Micr Non/unknown Pathogen Aujoulat2014, Yang2020 2
Aquabacterium commune Proteobacteria Micr Non/unknown Pathogen Aujoulat2014, RajilicStojanovic2014 2
Aquabacterium parvum Proteobacteria Micr Non/unknown Pathogen Yang2020 1
Arabia massiliensis Actinobacteria SANA Non/unknown Pathogen Lagier2016, Byrd2020, New2022 3
Arachnia propionica Actinobacteria ANA Opportunistic Infection RajilicStojanovic2014, Lagier2016, New2022, Vachida2019 4
Arcanobacterium haemolyticum Actinobacteria FANA 37 Opportunistic Pathogen RajilicStojanovic2014, Lagier2016 2
Arthrobacter castelli Actinobacteria AER 22–37 Non/unknown Pathogen Dubourg2013, Pfleiderer2013, RajilicStojanovic2014, Lagier2016 4
Asaccharospora irregularis Firmicutes ANA 30-37 Opportunistic Pathogen Finegold1974, PerisBondia2011, RajilicStojanovic2014, Lagier2016, Byrd2020 5
Atlantibacter hermannii Proteobacteria FANA Rare Opportunist Pfleiderer2013, RajilicStojanovic2014, Lagier2016, Byrd2020, Dubinkina2017, Vachida2019 6
Averyella dalhousiensis Proteobacteria FANA Rare Opportunist RajilicStojanovic2014, Lagier2016 2
Azoarcus pumilus Proteobacteria FANA 35-37 8.0 Non/unknown Pathogen New2022 1
Azospirillum lipoferum Proteobacteria FANA 36-38 Non/unknown Pathogen New2022, Zeller2014 2
Bacilliculturomica massiliensis Firmicutes SANA Non/unknown Pathogen 0
Bacillus altitudinis Firmicutes AER Non/unknown Pathogen RajilicStojanovic2014, Lagier2016, Yang2020 3
Bacillus amyloliquefaciens Firmicutes SAER Non/unknown Pathogen RajilicStojanovic2014, Lagier2016 2
Bacillus andreraoultii Firmicutes FANA Non/unknown Pathogen Lagier2016 1
Bacillus aneurinolyticus Firmicutes SAER Non/unknown Pathogen 0 Obligate aerobe, but produces spores.
Bacillus atrophaeus Firmicutes AER Opportunistic Infection RajilicStojanovic2014, Lagier2016 2
Bacillus badius DSM 23T Firmicutes AER 30 7 Non/unknown Pathogen Pfleiderer2013, RajilicStojanovic2014, Lagier2016 3
Bacillus badius DSM 5610 Firmicutes AER 35-40 7-8 Non/unknown Pathogen Pfleiderer2013, RajilicStojanovic2014, Lagier2016 3
Bacillus benzoevorans Firmicutes FANA Non/unknown Pathogen RajilicStojanovic2014, Lagier2016 2
Bacillus caccae Firmicutes AER Non/unknown Pathogen 0
Bacillus circulans Firmicutes FANA Opportunistic Infection Taylor1985, Pfleiderer2013, RajilicStojanovic2014, Lagier2016, Byrd2020 5
Bacillus clausii Firmicutes AER 7 Non/unknown Pathogen Hoyles2012, Dubourg2013, Pfleiderer2013, RajilicStojanovic2014, Lagier2016, Zeller2014 6 May be able to persist in the gut, albeit in low numbers, by residing in niches close to epithelial cells (Ilinskaya2017).
Bacillus cytotoxicus Firmicutes FANA 30-37 Known Pathogen King2019, Zeller2014 2
Bacillus dakarensis Firmicutes AER 37 7.5 Non/unknown Pathogen 0
Bacillus firmus Firmicutes FANA Non/unknown Pathogen RajilicStojanovic2014, Lagier2016 2
Bacillus fordii Firmicutes SAER Non/unknown Pathogen Hoyles2012, RajilicStojanovic2014, Lagier2016 3
Bacillus halotolerans Firmicutes AER 32 7.2 Non/unknown Pathogen RajilicStojanovic2014, Lagier2016 2
Bacillus idriensis Firmicutes AER Opportunistic Pathogen RajilicStojanovic2014, Lagier2016 2
Bacillus infantis Firmicutes AER Opportunistic Pathogen RajilicStojanovic2014, Lagier2016, Byrd2020, Yang2020 4
Bacillus kwashiorkori Firmicutes FANA 37 Non/unknown Pathogen 0
Bacillus marasmi Firmicutes AER Non/unknown Pathogen 0
Bacillus massilioanorexius Firmicutes AER 37 Non/unknown Pathogen RajilicStojanovic2014, Lagier2016, Forster2019 3
Bacillus massilionigeriensis Firmicutes AER 37 Non/unknown Pathogen Lagier2016 1
Bacillus mediterraneensis Firmicutes AER 37 Non/unknown Pathogen Lagier2016 1 May be able to persist in the gut, albeit in low numbers, by residing in niches close to epithelial cells (Ilinskaya2017).
Bacillus mojavensis Firmicutes AER 28-30 Non/unknown Pathogen RajilicStojanovic2014, Lagier2016 2
Bacillus mycoides Firmicutes FANA Opportunistic Pathogen RajilicStojanovic2014, Lagier2016, Zeller2014 3
Bacillus niameyensis Firmicutes FANA 37 Non/unknown Pathogen Lagier2016 1
Bacillus pakistanensis Firmicutes AER 30-35 8.0 Non/unknown Pathogen Lagier2016 1
Bacillus phocaeensis Firmicutes FANA 37 Non/unknown Pathogen Lagier2016 1
Bacillus pseudofirmus Firmicutes AER 9 Non/unknown Pathogen RajilicStojanovic2014, Lagier2016 2
Bacillus pumilus Firmicutes AER Opportunistic Pathogen Hoyles2012, Pfleiderer2013, RajilicStojanovic2014, Lagier2016, Zeller2014 5 May be able to persist in the gut, albeit in low numbers, by residing in niches close to epithelial cells (Ilinskaya2017).
Bacillus rubiinfantis Firmicutes FANA 37 Non/unknown Pathogen Lagier2016 1
Bacillus siralis Firmicutes SANA Rare Opportunist RajilicStojanovic2014, Lagier2016 2
Bacillus smithii Firmicutes FANA Non/unknown Pathogen Lagier2016, Forster2019 2
Bacillus sonorensis Firmicutes FANA Non/unknown Pathogen Hoyles2012, Pfleiderer2013, RajilicStojanovic2014, Lagier2016, Zou2019 5
Bacillus testis Firmicutes FANA Non/unknown Pathogen Lagier2016 1
Bacillus thuringiensis Firmicutes FANA Opportunistic Infection RajilicStojanovic2014, Cassir2015, Lagier2016, Forster2019, Byrd2020, Hu2019 6 May be able to persist in the gut, albeit in low numbers, by residing in niches close to epithelial cells (Ilinskaya2017).
Bacillus timonensis Firmicutes AER 30-37 Non/unknown Pathogen RajilicStojanovic2014, Lagier2016, Forster2019, Byrd2020 4
Bacillus tuaregi Firmicutes AER 37 Non/unknown Pathogen 0
Bacillus vallismortis Firmicutes AER Rare Opportunist Pfleiderer2013, RajilicStojanovic2014, Lagier2016 3
Bacillus velezensis Variant polyfermenticus Firmicutes AER Non/unknown Pathogen Pfleiderer2013, RajilicStojanovic2014, Lagier2016, New2022 4
Bacillus wiedmannii Firmicutes FANA Possible Pathogen Zou2019 1 Psychrotolerant and cytotoxic.
Bacteroides caecimuris Bacteroidetes ANA Non/unknown Pathogen King2019, Byrd2020, New2022, Urban2020 4
Bacteroides coprosuis Bacteroidetes ANA 37 Non/unknown Pathogen Byrd2020, New2022, Zeller2014 3
Bacteroides faecalis Bacteroidetes SANA 37 5 Non/unknown Pathogen 0
Bacteroides faecichinchillae Bacteroidetes SANA 37 Non/unknown Pathogen Byrd2020, Yang2020, Urban2020 3
Bacteroides galacturonicus Bacteroidetes SANA 35-40 8.2-8.5 Opportunistic Infection Walker2011, RajilicStojanovic2014, Lagier2016, Yang2020 4
Bacteroides graminisolvens Bacteroidetes SANA 30-35 7.2 Non/unknown Pathogen RajilicStojanovic2014, Cassir2015, Lagier2016, Byrd2020, Urban2020 5
Bacteroides helcogenes Bacteroidetes SANA 37 Opportunistic Pathogen Zupancic2012, King2019, Byrd2020, New2022, Zeller2014, Urban2020 6
Bacteroides heparinolyticus Bacteroidetes ANA Non/unknown Pathogen Byrd2020, New2022 2 Produces heparinase.
Bacteroides ihuae Bacteroidetes ANA 30 7 Non/unknown Pathogen Byrd2020, Urban2020 2
Bacteroides luhongzhouii Bacteroidetes SANA Non/unknown Pathogen 0
Bacteroides luti Bacteroidetes SANA 37-40 6.5-7.0 Non/unknown Pathogen Byrd2020, Urban2020 2
Bacteroides propionicifaciens Bacteroidetes SANA 30 7.9 Non/unknown Pathogen De2020 1
Bacteroides reticulotermitis Bacteroidetes SANA Non/unknown Pathogen Byrd2020, Urban2020 2
Bacteroides sp. Strain D8 Bacteroidetes SANA Non/unknown Pathogen 0
Bacteroides timonensis Bacteroidetes SANA 37 Non/unknown Pathogen Pfleiderer2013, RajilicStojanovic2014, Lagier2016, Byrd2020, Urban2020 5
Bacteroides zhangwenhongi Bacteroidetes SANA Non/unknown Pathogen 0
Bacteroides zoogleoformans Bacteroidetes SANA 30-37 Rare Opportunist Byrd2020, New2022 2 Haemin is required for growth.
Barnesiella viscericola Bacteroidetes SANA Non/unknown Pathogen King2019, Byrd2020, New2022, PerezBrocal2015 4
Bavariicoccus seileri Firmicutes ANA Non/unknown Pathogen Forster2019, Byrd2020, De2020 3
Beduinella massiliensis Firmicutes SANA Non/unknown Pathogen 0
Beduini massiliensis Firmicutes SANA 37 7 Non/unknown Pathogen Lagier2016 1
Beduinibacterium massiliense Firmicutes SANA Non/unknown Pathogen 0
Belnapia soli Proteobacteria AER 30 7 Non/unknown Pathogen Yang2020 1
Berryella intestinalis Actinobacteria None Non/unknown Pathogen New2022 1 Doesn't utilise carbohydrates.
Bhargavaea beijingensis Firmicutes SAER 30 7-8 Non/unknown Pathogen RajilicStojanovic2014, Lagier2016 2
Bifidobacterium aerophilum Actinobacteria FANA 40 6.0 Non/unknown Pathogen De2020 1
Bifidobacterium animalis subsp. lactis Actinobacteria ANA 39-42 Non/unknown Pathogen Lagier2016, King2019, Dubinkina2017, Jie2017, Wang2018, LeChatelier2013 6 Tolerates up to 10% oxygen.
Bifidobacterium asteroides Actinobacteria FANA 35-36 6.5-7.0 Non/unknown Pathogen New2022 1 CO2 required for growth.
Bifidobacterium avesanii Actinobacteria FANA 6 Non/unknown Pathogen De2020 1
Bifidobacterium biavatii Actinobacteria FANA Non/unknown Pathogen Byrd2020, De2020 2
Bifidobacterium boum Actinobacteria ANA 39 6.5-7.0 Non/unknown Pathogen Woodmansey2004, RajilicStojanovic2014, Lagier2016, Byrd2020 4
Bifidobacterium callitrichidarum Actinobacteria Micr 45 6.5 Non/unknown Pathogen Byrd2020 1
Bifidobacterium catenulatum subsp. kashiwanohense Actinobacteria SANA 7.2-8.0 Non/unknown Pathogen RajilicStojanovic2014, Lagier2016, King2019 3
Bifidobacterium choerinum Actinobacteria ANA 37-41 6.5-7.0 Non/unknown Pathogen Byrd2020, New2022 2 Doesn't require CO2 for growth.
Bifidobacterium coryneforme Actinobacteria ANA Non/unknown Pathogen Woodmansey2004, RajilicStojanovic2014, Lagier2016 3
Bifidobacterium cuniculi Actinobacteria SANA 36-38 6.7-7.1 Non/unknown Pathogen Byrd2020 1
Bifidobacterium eulemuris Actinobacteria Micr 37-42 6.5-7.0 Non/unknown Pathogen Byrd2020, New2022 2
Bifidobacterium faecale Actinobacteria SANA 37 7 Non/unknown Pathogen Zou2019, Yang2020 2
Bifidobacterium gallicum Actinobacteria ANA 37-39 6.0-7.0 Non/unknown Pathogen Tyakht2013, RajilicStojanovic2014, Lagier2016, Forster2019, Byrd2020, Zeller2014 6
Bifidobacterium imperatoris Actinobacteria FANA Non/unknown Pathogen Byrd2020, New2022 2
Bifidobacterium indicum Actinobacteria ANA Non/unknown Pathogen Lagier2016 1
Bifidobacterium lemurum Actinobacteria Micr 37-42 6.5-7.0 Non/unknown Pathogen Byrd2020, New2022 2
Bifidobacterium longum subsp. suis Actinobacteria ANA 37-41 6.5-7.0 Non/unknown Pathogen Woodmansey2004 1 Riboflavin required for growth.
Bifidobacterium merycicum Actinobacteria SANA 38-42 6.5-6.9 Non/unknown Pathogen Byrd2020 1
Bifidobacterium minimum Actinobacteria ANA Non/unknown Pathogen Byrd2020 1
Bifidobacterium moukalabense Actinobacteria SANA 37 Non/unknown Pathogen Byrd2020 1
Bifidobacterium myosotis Actinobacteria ANA 40 7 Non/unknown Pathogen Byrd2020 1
Bifidobacterium pseudolongum subsp. globosum Actinobacteria ANA 39-40 6.5-7.0 Non/unknown Pathogen Moore1974, Lagier2016 2
Bifidobacterium pullorum subsp. gallinarum Actinobacteria SANA Non/unknown Pathogen Byrd2020, De2020, New2022 3
Bifidobacterium pullorum subsp. saeculare Actinobacteria ANA 36-38 6.8-7.3 Non/unknown Pathogen Lagier2016, De2020 2
Bifidobacterium ramosum Actinobacteria FANA 40 6 Non/unknown Pathogen De2020 1
Bifidobacterium reuteri Actinobacteria FANA Non/unknown Pathogen Byrd2020 1
Bifidobacterium saguini Actinobacteria FANA 37-42 Non/unknown Pathogen Byrd2020, New2022 2
Bifidobacterium stellenboschense Actinobacteria FANA Non/unknown Pathogen Byrd2020 1
Bifidobacterium subtile Actinobacteria ANA 34-36 Non/unknown Pathogen Byrd2020, New2022 2 Non-proteolytic.
Bifidobacterium thermacidophilum Actinobacteria ANA 37-41 7.0-7.2 Non/unknown Pathogen Finegold1974, RajilicStojanovic2014, Lagier2016, Byrd2020 4
Bifidobacterium thermophilum Actinobacteria Micr Non/unknown Pathogen RajilicStojanovic2014, Lagier2016, King2019, New2022 4
Bifissio spartinae Bacteroidetes None Non/unknown Pathogen McLaughlin2010, Walker2011, RajilicStojanovic2014 3
Blastococcus massiliensis Actinobacteria Micr 37 Non/unknown Pathogen Pfleiderer2013, RajilicStojanovic2014, Lagier2016 3
Blautia brookingsii Firmicutes SANA 37 6.8 Non/unknown Pathogen 0
Blautia caecimuris Firmicutes SANA Non/unknown Pathogen Jeong2021 1
Blautia faecicola Firmicutes SANA Non/unknown Pathogen 0
Blautia faecis Firmicutes SANA Non/unknown Pathogen RajilicStojanovic2014, Lagier2016, Zou2019, Forster2019, Minerbi2019 5
Blautia glucerasea Firmicutes SANA 37 7 Non/unknown Pathogen RajilicStojanovic2014, Minerbi2019 2 Ferments pectin and fructo-oligosaccharides
Blautia hominis Firmicutes SANA 37 Non/unknown Pathogen Byrd2020 1
Blautia intestinalis Firmicutes SANA 37 6-8 Non/unknown Pathogen 0
Blautia liquoris Firmicutes SANA 37 8.0 Non/unknown Pathogen New2022 1
Blautia marasmi Firmicutes SANA Non/unknown Pathogen 0
Blautia phocaeensis Firmicutes SANA Non/unknown Pathogen Lagier2016 1
Blautia provencensis Firmicutes SANA Non/unknown Pathogen 0
Blautia pseudococcoides Firmicutes SANA 37 Non/unknown Pathogen Wang2020a 1
Blautia schinkii Firmicutes SANA 39 6.5-7.0 Non/unknown Pathogen Byrd2020 1 Walker2011 found a related species in human faeces, but is likely an uncharacterised species. Homoacetogen.
Bosea massiliensis Proteobacteria AER Non/unknown Pathogen Yang2020 1
Brachybacterium conglomeratum Actinobacteria FANA Non/unknown Pathogen PerezBrocal2015 1
Brachybacterium massiliense Actinobacteria AER 37 Non/unknown Pathogen Lagier2016 1
Brachybacterium muris Actinobacteria Micr 25-37 Non/unknown Pathogen Hu2019 1
Brachybacterium paraconglomeratum Actinobacteria FANA Non/unknown Pathogen RajilicStojanovic2014, Lagier2016, Yang2020 3
Brachyspira aalborgi Spirochaetes ANA 37-39 Opportunistic Pathogen RajilicStojanovic2014, Lagier2016 2
Brachyspira hyodysenteriae Spirochaetes Micr 36-42 Non/unknown Pathogen Cassir2015, Byrd2020, New2022, Zeller2014 4 Cholesterol is required and is reduced to cholestanol.
Bradyrhizobium denitrificans Proteobacteria AER Opportunistic Pathogen Bik2006, RajilicStojanovic2014 2
Bradyrhizobium elkanii Proteobacteria AER Non/unknown Pathogen McLaughlin2010, Walker2011, RajilicStojanovic2014 3
Bradyrhizobium japonicum Proteobacteria AER Non/unknown Pathogen RajilicStojanovic2014, Zeller2014 2
Bradyrhizobium neotropicale Proteobacteria AER 28-32 5.0-7.0 Non/unknown Pathogen Yang2020 1
Brassicibacter mesophilus Firmicutes SANA 37 7.5 Non/unknown Pathogen Lagier2016 1
Brenneria populi Li et al. 2015 Proteobacteria FANA 30 6.5 Non/unknown Pathogen De2020 1
Brevibacillus borstelensis Firmicutes SAER 30 7.0 Possible Pathogen Pfleiderer2013, RajilicStojanovic2014, Lagier2016 3
Brevibacillus brevis Firmicutes SAER 7.0 Opportunistic Infection Taylor1985, RajilicStojanovic2014, Lagier2016 3
Brevibacillus choshinensis Firmicutes AER 7.0 Non/unknown Pathogen Lagier2016, New2022 2
Brevibacillus laterosporus Firmicutes FANA 30 Opportunistic Infection Lagier2016 1
Brevibacillus massiliensis Firmicutes SAER 37 7.0 Non/unknown Pathogen RajilicStojanovic2014, Lagier2016 2
Brevibacterium casei Actinobacteria AER 30-37 Rare Opportunist RajilicStojanovic2014, Lagier2016 2
Brevibacterium celere Actinobacteria AER 8.5-9.0 Non/unknown Pathogen Lagier2016 1
Brevibacterium epidermidis Actinobacteria AER 30-37 Rare Opportunist RajilicStojanovic2014, Lagier2016 2
Brevibacterium ihuae Actinobacteria FANA 28 Non/unknown Pathogen 0
Brevibacterium luteolum Actinobacteria AER 30-37 Rare Opportunist Lagier2016, De2020 2 Produces methanethiol.
Brevibacterium paucivorans Actinobacteria FANA Rare Opportunist Lagier2016 1
Brevibacterium pityocampae Actinobacteria AER Non/unknown Pathogen RajilicStojanovic2014, Lagier2016 2
Brevibacterium ravenspurgense Actinobacteria AER 30-37 Opportunistic Pathogen Dubourg2013, RajilicStojanovic2014, Lagier2016 3
Brevibacterium samyangense Actinobacteria AER Non/unknown Pathogen Yang2020 1
Brevibacterium sanguinis Actinobacteria AER Rare Opportunist Yang2020 1
Brevibacterium senegalense Actinobacteria AER 30-37 Non/unknown Pathogen RajilicStojanovic2014, Lagier2016, Forster2019 3
Brevundimonas aurantiaca Proteobacteria AER Non/unknown Pathogen Yang2020 1
Brevundimonas bacteroides Proteobacteria AER Non/unknown Pathogen Bik2006, RajilicStojanovic2014 2
Brevundimonas bullata Proteobacteria AER 30 6.0-8.0 Non/unknown Pathogen Yang2020 1
Brevundimonas diminuta Proteobacteria AER 30-37 Opportunistic Pathogen Walker2011, RajilicStojanovic2014, Lagier2016, Yang2020, Zeller2014, PerezBrocal2015 6
Brevundimonas intermedia Proteobacteria AER Non/unknown Pathogen McLaughlin2010 1 Grows a stalk (prostheca). Requires biotin.
Brevundimonas nasdae Proteobacteria AER Non/unknown Pathogen McLaughlin2010, Walker2011 2
Brevundimonas terrae Proteobacteria AER 30 7.5-8.0 Non/unknown Pathogen RajilicStojanovic2014 1
Brevundimonas vesicularis Proteobacteria AER 30-37 Opportunistic Pathogen Bik2006, McLaughlin2010, RajilicStojanovic2014 3
Brucella cytisi Proteobacteria AER Non/unknown Pathogen Yang2020 1
Bulleidia extructa Firmicutes SANA 30-37 Opportunistic Pathogen RajilicStojanovic2014, De2020, Dubinkina2017, Zeller2014, Vachida2019 5
Burkholderia arboris Proteobacteria AER Opportunistic Pathogen Yang2020 1
Burkholderia cepacia Proteobacteria AER Opportunistic Pathogen RajilicStojanovic2014, Lagier2016, Byrd2020 3
Burkholderia multivorans Proteobacteria AER Opportunistic Pathogen Zeller2014 1
Burkholderia vietnamiensis Proteobacteria AER Opportunistic Infection Zeller2014 1
Buttiauxella agrestis Proteobacteria ANA Non/unknown Pathogen Lagier2016 1
Butyribacter intestini Firmicutes SANA 37 Non/unknown Pathogen 0
Butyricicoccus faecihominis Firmicutes SANA Non/unknown Pathogen Zou2019, De2020, Minerbi2019 3
Butyricicoccus porcorum Firmicutes SANA 39 6.0 Non/unknown Pathogen Byrd2020 1
Butyricimonas faecalis Bacteroidetes SANA 37 Non/unknown Pathogen New2022, Wang2020a 2
Butyricimonas faecihominis Bacteroidetes SANA 37 Non/unknown Pathogen Lagier2016, Yang2020 2
Butyricimonas paravirosa Bacteroidetes SANA 37 Non/unknown Pathogen Lagier2016, Yang2020, Minerbi2019 3
Butyricimonas phoceensis Bacteroidetes ANA 37 Non/unknown Pathogen Lagier2016 1
Butyrivibrio proteoclasticus Firmicutes SANA Non/unknown Pathogen Byrd2020, New2022, Zeller2014, Qin2012 4
Caballeronia novacaledonica Proteobacteria FANA 28 5-6 Non/unknown Pathogen Byrd2020 1 Able to utilise telurite.
Caecibacter massiliensis Firmicutes None Byrd2020 1 Isolation and characterisation not yet published.
Campylobacter curvus Proteobacteria Micr Opportunistic Pathogen RajilicStojanovic2014, Lagier2016, Almeida2019, Zeller2014, Vachida2019 5
Campylobacter faecalis Proteobacteria Micr Non/unknown Pathogen RajilicStojanovic2014, De2020 2
Campylobacter fetus subsp. fetus Proteobacteria Micr Possible Pathogen RajilicStojanovic2014, Lagier2016, New2022 3
Campylobacter jejuni subsp. doylei Proteobacteria Micr 35-37 Possible Pathogen 0
Campylobacter lanienae Proteobacteria Micr Possible Pathogen 0
Campylobacter lari subsp. concheus Proteobacteria Micr Opportunistic Pathogen 0
Campylobacter lari subsp. lari Proteobacteria Micr Opportunistic Pathogen RajilicStojanovic2014, Lagier2016, Byrd2020, New2022 4
Campylobacter mucosalis Proteobacteria Micr Non/unknown Pathogen Lagier2016 1
Campylobacter peloridis Proteobacteria Micr Possible Pathogen Lagier2016 1
Campylobacter rectus Proteobacteria ANA Opportunistic Pathogen RajilicStojanovic2014, Lagier2016, Byrd2020, New2022, Zeller2014 5
Campylobacter showae Proteobacteria Micr Opportunistic Infection Bik2006, RajilicStojanovic2014, Lagier2016, Yang2020, Zeller2014, Vachida2019 6
Campylobacter troglodytis Proteobacteria None Possible Pathogen 0
Campylobacter upsaliensis Proteobacteria Micr Rare Opportunist Tyakht2013, RajilicStojanovic2014, Lagier2016, Forster2019, Vachida2019 5
Candidatus Dorea massiliensis Firmicutes FANA 37 Non/unknown Pathogen Pfleiderer2013, RajilicStojanovic2014, Lagier2016, Minerbi2019 4
Candidatus Stoquefichus massiliensis Firmicutes ANA 37 Non/unknown Pathogen Pfleiderer2013, RajilicStojanovic2014, Lagier2016, Byrd2020 4
Capnocytophaga granulosa Bacteroidetes ANA Opportunistic Pathogen Bik2006, RajilicStojanovic2014, Lagier2016, Yang2020 4
Capnocytophaga leadbetteri Bacteroidetes FANA Opportunistic Pathogen Byrd2020 1 All strains cleave human IgA1 in the hinge region.
Capnocytophaga ochracea Bacteroidetes FANA 35-37 Opportunistic Pathogen RajilicStojanovic2014, Lagier2016, De2020 3
Capnocytophaga sputigena Bacteroidetes ANA 35-37 Opportunistic Pathogen RajilicStojanovic2014, Lagier2016, De2020, Zeller2014 4
Caproicibacter fermentans Firmicutes SANA 37 7 Non/unknown Pathogen New2022 1 Produces caproate.
Cardiobacterium hominis Proteobacteria FANA 30-37 7.0-7.2 Opportunistic Pathogen Yang2020, New2022, Zeller2014 3
Cardiobacterium valvarum Proteobacteria AER Opportunistic Pathogen Vachida2019 1 In 1% of Europeans (unseenbio.com). Rare coloniser.
Carnobacterium inhibens Firmicutes FANA Opportunistic Infection Yang2020 1
Casaltella massiliensis Firmicutes None Non/unknown Pathogen Lagier2016 1
Catenibacillus scindens Firmicutes ANA Non/unknown Pathogen 0
Catonella morbi Firmicutes SANA Opportunistic Pathogen Byrd2020, Zeller2014, Vachida2019 3
Cedecea davisae Proteobacteria FANA 37 Opportunistic Pathogen RajilicStojanovic2014, Lagier2016, Forster2019, Byrd2020, Vachida2019 5
Cedecea lapagei Proteobacteria FANA Possible Pathogen Lagier2016 1
Cedecea neteri Proteobacteria FANA Opportunistic Pathogen Lagier2016 1
Cellulomonas composti Actinobacteria FANA 30 6.8-7.5 Non/unknown Pathogen RajilicStojanovic2014, Lagier2016 2 Able to digest cellulose
Cellulomonas denverensis Actinobacteria AER Rare Opportunist RajilicStojanovic2014, Lagier2016 2
Cellulomonas fimi Actinobacteria AER 30 Non/unknown Pathogen Zeller2014 1
Cellulomonas flavigena Actinobacteria AER Non/unknown Pathogen Lagier2016, Zeller2014 2 Can digest cellulose
Cellulomonas hominis Actinobacteria None Opportunistic Pathogen Lagier2016 1 Doesn't degrade cellulose
Cellulomonas massiliensis Actinobacteria AER 37 Non/unknown Pathogen RajilicStojanovic2014, Lagier2016, Forster2019 3
Cellulomonas parahominis Actinobacteria AER Non/unknown Pathogen RajilicStojanovic2014, Lagier2016 2
Cellulomonas timonensis Actinobacteria FANA 37 7 Non/unknown Pathogen Lagier2016 1
Cellulosilyticum lentocellum Firmicutes SANA 40 7.5-7.7 Non/unknown Pathogen RajilicStojanovic2014, Byrd2020, New2022, Zeller2014, Vachida2019, Qin2012 6 Cellulolytic.
Cellulosilyticum ruminicola Firmicutes SANA 38 6.7 Non/unknown Pathogen 0
Cellulosimicrobium cellulans Actinobacteria FANA Possible Pathogen Pfleiderer2013, RajilicStojanovic2014, Lagier2016 3 Cellulolytic.
Centipeda periodontii Firmicutes SANA 35 Opportunistic Infection Zeller2014, Vachida2019 2
Cetobacterium somerae Fusobacteria Micr Non/unknown Pathogen RajilicStojanovic2014, Lagier2016, Forster2019, Vachida2019 4
Christensenella massiliensis Firmicutes SANA 37 7 Non/unknown Pathogen Lagier2016, Byrd2020, De2020 3
Chryseobacterium hominis Bacteroidetes AER 30 Possible Pathogen Pfleiderer2013, RajilicStojanovic2014, Lagier2016 3
Chryseobacterium indologenes Bacteroidetes FANA Known Pathogen Lagier2016 1
Chryseobacterium oranimense Bacteroidetes AER 30-33 6-8 Non/unknown Pathogen 0
Chryseobacterium taklimakanense Bacteroidetes FANA 30 7-8 Non/unknown Pathogen Lagier2016 1
Chryseomicrobium amylolyticum Firmicutes AER 30-37 7-8 Non/unknown Pathogen Yang2020 1
Citrobacter amalonaticus Proteobacteria FANA Opportunistic Pathogen RajilicStojanovic2014, Lagier2016, Byrd2020, De2020 4
Citrobacter braakii Proteobacteria FANA Opportunistic Pathogen RajilicStojanovic2014, Lagier2016, Forster2019, Byrd2020 4
Citrobacter europaeus Proteobacteria FANA Non/unknown Pathogen Byrd2020 1
Citrobacter gillenii Proteobacteria FANA Possible Pathogen RajilicStojanovic2014, Lagier2016, Yang2020 3
Citrobacter murliniae Proteobacteria FANA Opportunistic Pathogen Pandey2012, RajilicStojanovic2014, Lagier2016 3
Citrobacter pasteurii Proteobacteria FANA Non/unknown Pathogen Forster2019, Byrd2020 2
Citrobacter portucalensis Proteobacteria FANA Non/unknown Pathogen Byrd2020, New2022, Jie2017 3 In 9% of Europeans (unseenbio.com). Rare coloniser.
Citrobacter rodentium Proteobacteria FANA Possible Pathogen Byrd2020, Zeller2014 2
Citrobacter sedlakii Proteobacteria FANA Possible Pathogen RajilicStojanovic2014, Lagier2016, Byrd2020 3
Citrobacter werkmanii Proteobacteria FANA Possible Pathogen RajilicStojanovic2014, Lagier2016, Byrd2020, Yang2020, Wang2020a 5
Citrobacter youngae Proteobacteria FANA Opportunistic Pathogen Tyakht2013, RajilicStojanovic2014, Lagier2016, Dubinkina2017, Zeller2014 5
Citroniella saccharovorans Firmicutes SANA 30 6.5-7.3 Non/unknown Pathogen 0
Cloacibacillus porcorum Synergistetes SANA 39 6.5 Possible Pathogen Lagier2016, Byrd2020, Yang2020, New2022, Jeong2021, Wang2020a 6 Ferments mucin to formate, acetate and propionate.
Cloacibacterium normanense Bacteroidetes FANA 30 7 Non/unknown Pathogen RajilicStojanovic2014, Cassir2015, Byrd2020 3
Clostridioides mangenotii Firmicutes SANA 30-37 8.5 Known Pathogen Lagier2016 1 Produces 5-aminovalerate and 2-aminobutyrate.
Clostridium acetobutylicum Firmicutes SANA 37 6.0-7.0 Non/unknown Pathogen Taylor1985, RajilicStojanovic2014, Lagier2016, New2022, Qin2012 5
Clostridium amazonense Firmicutes SANA 37 7 Non/unknown Pathogen 0
Clostridium amazonitimonense Firmicutes SANA 37 Non/unknown Pathogen Lagier2016 1
Clostridium aminobutyricum Firmicutes SANA 31-37 Non/unknown Pathogen 0
Clostridium aminophilum Firmicutes SANA Non/unknown Pathogen 0 Asaccharolytic. Sodium is essential for growth
Clostridium amylolyticum Firmicutes SANA 37 7.0 Non/unknown Pathogen Lagier2016 1
Clostridium anorexicamassiliense Firmicutes SANA 37 Non/unknown Pathogen Pfleiderer2013, RajilicStojanovic2014 2
Clostridium argentinense Firmicutes ANA Opportunistic Pathogen New2022 1 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.
Clostridium aurantibutyricum Firmicutes SANA 37 Non/unknown Pathogen 0
Clostridium autoethanogenum Firmicutes SANA 37 Non/unknown Pathogen New2022 1 Ferments CO, H2 and CO2 to ethanol and acetate.
Clostridium boliviensis Firmicutes ANA Non/unknown Pathogen Forster2019 1 Unpublished thus far.
Clostridium bornimense Firmicutes ANA 35 7 Non/unknown Pathogen Byrd2020, New2022 2
Clostridium budayi Firmicutes SANA Non/unknown Pathogen Finegold1977, RajilicStojanovic2014, Lagier2016 3
Clostridium cadaveris Firmicutes SANA 30-37 Opportunistic Pathogen Finegold1977, RajilicStojanovic2014, Lagier2016, Byrd2020 4
Clostridium cagae Firmicutes SANA 37 Non/unknown Pathogen 0
Clostridium carboxidivorans Firmicutes SANA 38 6.2 Non/unknown Pathogen Lagier2016, New2022, Qin2012 3 Consumes H2/CO2 or CO autotrophically. Cellulolytic. Homoacetogen.
Clostridium carnis Firmicutes SANA 37 Opportunistic Pathogen 0
Clostridium cellulovorans Firmicutes SANA 37 7 Non/unknown Pathogen Byrd2020, New2022 2 Can't utilise starch or proteolyse protein.
Clostridium chartatabidum Firmicutes SANA 39 Non/unknown Pathogen Walker2011, RajilicStojanovic2014, Yang2020 3 Cellulolytic.
Clostridium chauvoei Firmicutes SANA 37 Opportunistic Pathogen RajilicStojanovic2014, Byrd2020, New2022 3
Clostridium cocleatum Firmicutes ANA 37-45 Opportunistic Infection Benno1984, Benno1986, Woodmansey2004, Walker2011, RajilicStojanovic2014, PerezBrocal2015 6
Clostridium colicanis Firmicutes ANA 37-40 Non/unknown Pathogen 0
Clostridium colinum Firmicutes ANA 35-42 Possible Pathogen Salonen2014, PerezBrocal2015 2
Clostridium combesii Firmicutes SANA 35-37 Rare Opportunist Finegold1977 1
Clostridium culturomicium Firmicutes SANA 37 Non/unknown Pathogen 0
Clostridium dakarense Firmicutes SANA 37 Non/unknown Pathogen Lagier2016 1
Clostridium diolis Firmicutes SANA 37 7.0 Non/unknown Pathogen Lagier2016 1 Produces 1,3-propanediol from glycerol.
Clostridium fallax Firmicutes SANA 37 Opportunistic Pathogen Finegold1974, RajilicStojanovic2014, Lagier2016, Byrd2020 4 Found in human breast milk (Jeurink2013).
Clostridium felsineum Firmicutes SANA 37 Non/unknown Pathogen Finegold1974, RajilicStojanovic2014, Salonen2014, Byrd2020 4
Clostridium fessum Firmicutes SANA 37 5.6 Non/unknown Pathogen 0
Clostridium haemolyticum Firmicutes SANA 37 Opportunistic Pathogen 0
Clostridium herbivorans Firmicutes SANA 39-42 6.8-7.2 Non/unknown Pathogen Nam2008a, Walker2011, RajilicStojanovic2014 3
Clostridium ihumii Firmicutes SANA 37 Non/unknown Pathogen Lagier2016, Byrd2020 2
Clostridium intestinale Firmicutes FANA 37 Non/unknown Pathogen Byrd2020, New2022 2
Clostridium jeddahense Firmicutes SANA 37 Non/unknown Pathogen Lagier2016, Byrd2020 2
Clostridium jeddahitimonense Firmicutes SANA 37 Non/unknown Pathogen 0
Clostridium magnum Firmicutes SANA 30-32 7.0 Non/unknown Pathogen De2020 1 Homoacetogen.
Clostridium malenominatum Firmicutes SANA 37 Opportunistic Pathogen Finegold1974, Taylor1985, MacFarlane2004, Woodmansey2004, RajilicStojanovic2014, Lagier2016 6
Clostridium manihotivorum Firmicutes ANA 37 7 Non/unknown Pathogen New2022 1
Clostridium massiliamazoniense Firmicutes SANA Non/unknown Pathogen Pfleiderer2013, Lagier2016 2
Clostridium massiliodielmoense Firmicutes SANA Non/unknown Pathogen Lagier2016, Byrd2020 2
Clostridium mediterraneense Firmicutes SANA Non/unknown Pathogen Lagier2016, Byrd2020 2
Clostridium merdae Firmicutes SANA Non/unknown Pathogen 0
Clostridium metallolevans Firmicutes SANA 37 Non/unknown Pathogen Zupancic2012 1 Produces volatile metalloids from As, Sb, Se, Te, Bi and Hg. Butyraldehyde is also a product of fermentation.
Clostridium methoxybenzovorans Firmicutes SANA 37 7.4 Non/unknown Pathogen RajilicStojanovic2014 1 Methoxyaryl demethylation occurs. Homoacetogen. Able to use the following electron donors: methanol, sugars, lactate, methoxylated aromatics.
Clostridium minihomine Firmicutes SANA Non/unknown Pathogen Byrd2020 1
Clostridium moniliforme Firmicutes SANA Opportunistic Infection Finegold1974, Finegold1977, RajilicStojanovic2014, Lagier2016 4
Clostridium niameyense Firmicutes SANA 37 Non/unknown Pathogen Lagier2016, Byrd2020 2
Clostridium nigeriense Firmicutes FANA 37 6 Non/unknown Pathogen Lagier2016, Byrd2020 2
Clostridium nitritogenes Firmicutes SANA Opportunistic Infection Finegold1974, RajilicStojanovic2014, Lagier2016 3
Clostridium novyi A Firmicutes SANA 45 Opportunistic Pathogen Woodmansey2004, Lagier2016, New2022 3
Clostridium oceanicum Firmicutes ANA 30-37 Non/unknown Pathogen 0
Clostridium pasteurianum Firmicutes ANA 37 Non/unknown Pathogen New2022 1
Clostridium phoceensis Firmicutes SANA 45 Non/unknown Pathogen Lagier2016, Minerbi2019 2
Clostridium polyendosporum Firmicutes SANA 25-35 6.5-7.5 Non/unknown Pathogen Forster2019 1
Clostridium polynesiense Firmicutes SANA 37 Non/unknown Pathogen Lagier2016 1
Clostridium polysaccharolyticum Firmicutes SANA 30-38 6.8 Non/unknown Pathogen Walker2011, Byrd2020, De2020 3 Cellulolytic.
Clostridium populeti Firmicutes SANA 35 7 Non/unknown Pathogen Nam2008a, RajilicStojanovic2014, Byrd2020 3 Cellulolytic.
Clostridium punense Firmicutes SANA 37 Non/unknown Pathogen 0
Clostridium rectalis Firmicutes SANA 37 Non/unknown Pathogen 0
Clostridium roseum Firmicutes SANA 37 Non/unknown Pathogen 0
Clostridium saccharoperbutylacetonicum Firmicutes SANA 25-35 5.6-6.7 Non/unknown Pathogen RajilicStojanovic2014, Cassir2015, Byrd2020, New2022 4
Clostridium sardiniense Firmicutes SANA 25-37 Possible Pathogen Woodmansey2004, RajilicStojanovic2014, Lagier2016, Zou2019, Yang2020 5
Clostridium scatologenes Firmicutes SANA 30-37 6.3 Opportunistic Infection 0 Homoacetogen. Able to use the following donors: ethanol, butanol, glycerol, sugars, methoxylated aromatics.
Clostridium senegalense Firmicutes SANA 37 Non/unknown Pathogen RajilicStojanovic2014, Lagier2016, Byrd2020 3
Clostridium septicum Firmicutes SANA 37-40 Opportunistic Pathogen Finegold1974, Finegold1977, RajilicStojanovic2014, Lagier2016, Byrd2020, New2022 6
Clostridium subterminale Firmicutes SANA 37 Opportunistic Infection Taylor1985, McLaughlin2010, RajilicStojanovic2014, Lagier2016 4
Clostridium sulfidigenes Firmicutes SANA 34 6.6 Non/unknown Pathogen Lagier2016 1
Clostridium thermobutyricum Firmicutes ANA 55 6.8-7.1 Non/unknown Pathogen Byrd2020 1
Clostridium thiosulfatireducens Firmicutes ANA 37 7.4 Non/unknown Pathogen Lagier2016 1
Clostridium transplantifaecale Firmicutes ANA 37 Non/unknown Pathogen 0 Virtually all 50 carbohydrates tested (API50) were positive; this result is rather surprising.
Clostridium tyrobutyricum Firmicutes SANA 30-37 Non/unknown Pathogen Taylor1985, Benno1986, RajilicStojanovic2014, Lagier2016, Byrd2020, New2022 6
Clostridium vincentii Firmicutes SANA 12 6.5 Non/unknown Pathogen RajilicStojanovic2014, Byrd2020 2 Can't grow at 31C or above. In 1% of Europeans (unseenbio.com).
Clostridium viride Firmicutes SANA Non/unknown Pathogen Walker2011, Zupancic2012, RajilicStojanovic2014 3
Colibacter massiliensis Firmicutes SANA Non/unknown Pathogen 0
Colidextribacter massiliensis Firmicutes SANA Non/unknown Pathogen De2020, Minerbi2019 2
Collinsella ihumii Actinobacteria SANA 37 Non/unknown Pathogen Lagier2016, Byrd2020, De2020 3
Collinsella massiliensis Actinobacteria SANA 37 Non/unknown Pathogen Lagier2016 1
Collinsella phocaeensis Actinobacteria SANA Non/unknown Pathogen Byrd2020, De2020 2
Collinsella provencensis Actinobacteria ANA Non/unknown Pathogen Byrd2020 1
Collinsella vaginalis Actinobacteria SANA Non/unknown Pathogen Byrd2020 1
Comamonas denitrificans Proteobacteria FANA 30 7.5 Non/unknown Pathogen Yang2020 1
Comamonas kerstersii Proteobacteria AER 35-40 Opportunistic Pathogen RajilicStojanovic2014, Lagier2016, Byrd2020, Yang2020 4
Comamonas testosteroni Proteobacteria FANA Rare Opportunist Bik2006, McLaughlin2010, RajilicStojanovic2014, De2020, Zeller2014 5 Metabolises testosterone.
Comamonas thiooxydans Proteobacteria AER Non/unknown Pathogen Pandey2012, Yang2020 2 Utilises thiosulfate as an electron acceptor.
Companilactobacillus alimentarius Firmicutes Micr 35 Non/unknown Pathogen MacFarlane2004, RajilicStojanovic2014, Lagier2016, Byrd2020 4
Companilactobacillus farciminis Firmicutes Micr 35 Non/unknown Pathogen Yang2020, Hu2019, Zeller2014 3 In 1% of Europeans (unseenbio.com). Rare coloniser.
Conexibacter woesei Actinobacteria AER 7-7.5 Non/unknown Pathogen Frank2007, Zeller2014 2
Congobacterium massiliense Firmicutes None Non/unknown Pathogen 0
Coprobacter secundus subsp. similis Bacteroidetes SANA 37 7.0 Non/unknown Pathogen New2022 1
Coprococcus phoceensis Firmicutes SANA 37 7 Non/unknown Pathogen 0
Corynebacterium accolens Actinobacteria FANA 37 7.2 Opportunistic Pathogen Lagier2016, De2020, Zeller2014, Vachida2019 4
Corynebacterium afermentans Actinobacteria AER Opportunistic Pathogen Pfleiderer2013, RajilicStojanovic2014, Lagier2016 3 Nonlipophilic.
Corynebacterium ammoniagenes Actinobacteria FANA 30 Opportunistic Infection Tyakht2013, RajilicStojanovic2014, Lagier2016, Forster2019, Zeller2014 5
Corynebacterium amycolatum Actinobacteria FANA Opportunistic Pathogen Hoyles2012, Pfleiderer2013, RajilicStojanovic2014, Lagier2016, Forster2019, Zeller2014 6 Nonlipophilic.
Corynebacterium appendicis Actinobacteria FANA Opportunistic Pathogen RajilicStojanovic2014, Lagier2016 2 Lipophilic.
Corynebacterium argentoratense Actinobacteria FANA Possible Pathogen Byrd2020 1
Corynebacterium aurimucosum Actinobacteria FANA Opportunistic Pathogen RajilicStojanovic2014, Lagier2016, Zeller2014 3
Corynebacterium bouchesdurhonense Actinobacteria FANA Non/unknown Pathogen Lagier2016 1
Corynebacterium bovis Actinobacteria AER Opportunistic Pathogen De2020 1 Lipophilic irregular rods.
Corynebacterium casei Actinobacteria FANA Non/unknown Pathogen Byrd2020 1
Corynebacterium coyleae Actinobacteria FANA Opportunistic Pathogen RajilicStojanovic2014, Lagier2016 2 Nonlipophilic.
Corynebacterium cystitidis Actinobacteria FANA Opportunistic Pathogen De2020 1
Corynebacterium doosanense Actinobacteria AER Non/unknown Pathogen Lagier2016, De2020 2
Corynebacterium efficiens Actinobacteria FANA 30-40 Non/unknown Pathogen Lagier2016, Zeller2014 2 Produces large amounts of L-glutamic acid under aerobic conditions.
Corynebacterium falsenii Actinobacteria FANA Opportunistic Pathogen De2020 1 Nonlipophilic.
Corynebacterium flavescens Actinobacteria FANA Possible Pathogen Lagier2016, Byrd2020 2
Corynebacterium freneyi Actinobacteria FANA Opportunistic Pathogen RajilicStojanovic2014, Lagier2016 2 Nonlipophilic.
Corynebacterium genitalium Actinobacteria FANA Opportunistic Infection Zeller2014 1
Corynebacterium glaucum Actinobacteria FANA Non/unknown Pathogen Bik2006, RajilicStojanovic2014, Lagier2016, De2020 4
Corynebacterium glucuronolyticum Actinobacteria FANA Opportunistic Pathogen Dubourg2013, RajilicStojanovic2014, Lagier2016 3 Nonlipophilic.
Corynebacterium glutamicum Actinobacteria FANA 25-37 Non/unknown Pathogen Zeller2014 1 Produces large amounts of L-glutamate under aerobic conditions.
Corynebacterium ihumii Actinobacteria FANA 37 Non/unknown Pathogen Lagier2016 1
Corynebacterium jeddahense Actinobacteria FANA 37 Non/unknown Pathogen Lagier2016 1
Corynebacterium jeikeium Actinobacteria AER Opportunistic Pathogen Zeller2014 1
Corynebacterium lipophiloflavum Actinobacteria FANA Opportunistic Pathogen Lagier2016 1 Slightly lipophilic.
Corynebacterium lujinxingii Actinobacteria FANA 35-37 7.0-8.0 Non/unknown Pathogen 0
Corynebacterium minutissimum Actinobacteria FANA Opportunistic Pathogen RajilicStojanovic2014, Lagier2016 2
Corynebacterium mucifaciens Actinobacteria FANA Rare Opportunist Bik2006, Pfleiderer2013, RajilicStojanovic2014, Lagier2016 4 Nonlipophilic.
Corynebacterium neomassiliense Actinobacteria AER 37 6 Non/unknown Pathogen 0
Corynebacterium otitidis Actinobacteria FANA Opportunistic Infection Lagier2016, De2020 2
Corynebacterium pacaense Actinobacteria AER Non/unknown Pathogen Lagier2016 1
Corynebacterium propinquum Actinobacteria FANA Rare Opportunist RajilicStojanovic2014, Lagier2016, Byrd2020, Vachida2019 4
Corynebacterium provencense Actinobacteria FANA Non/unknown Pathogen Lagier2016, Byrd2020 2
Corynebacterium pseudodiphtheriticum Actinobacteria FANA 37 Rare Opportunist RajilicStojanovic2014, Lagier2016, Forster2019 3
Corynebacterium pseudogenitalium Actinobacteria FANA Rare Opportunist Lagier2016, Vachida2019 2
Corynebacterium pyruviciproducens Actinobacteria FANA 37 Opportunistic Infection Lagier2016, Byrd2020 2 Lipophilic.
Corynebacterium riegelii Actinobacteria FANA Opportunistic Infection Lagier2016 1
Corynebacterium sanguinis Actinobacteria FANA Opportunistic Pathogen RajilicStojanovic2014 1
Corynebacterium simulans Actinobacteria FANA Possible Pathogen RajilicStojanovic2014, Lagier2016, De2020 3
Corynebacterium singulare Actinobacteria FANA Non/unknown Pathogen 0
Corynebacterium stationis Actinobacteria FANA Rare Opportunist Lagier2016 1 Nonlipophilic.
Corynebacterium striatum Actinobacteria FANA Known Pathogen RajilicStojanovic2014, Lagier2016, Zeller2014 3 Nonlipophilic.
Corynebacterium suicordis Actinobacteria FANA Possible Pathogen Lagier2016 1 Nonlipophilic.
Corynebacterium sundsvallense Actinobacteria AER Opportunistic Pathogen RajilicStojanovic2014, Lagier2016 2
Corynebacterium tuberculostearicum Actinobacteria FANA Opportunistic Pathogen Pfleiderer2013, Aujoulat2014, RajilicStojanovic2014, Lagier2016, Yang2020, Zeller2014 6 Lipophilic.
Corynebacterium ulcerans Actinobacteria FANA Known Pathogen RajilicStojanovic2014 1
Corynebacterium urealyticum Actinobacteria AER Opportunistic Pathogen Lagier2016, Zeller2014 2 Lipophilic.
Corynebacterium ureicelerivorans Actinobacteria FANA Rare Opportunist Pfleiderer2013, RajilicStojanovic2014, Lagier2016 3
Corynebacterium urinapleomorphum Actinobacteria FANA 37 7 Non/unknown Pathogen Byrd2020 1
Corynebacterium wankanglinii Actinobacteria FANA 35-37 7.0-8.0 Non/unknown Pathogen 0
Corynebacterium xerosis Actinobacteria FANA Opportunistic Pathogen RajilicStojanovic2014, Lagier2016 2 Nonlipophilic.
Criibacterium bergeronii Firmicutes ANA 42 7.0-7.5 Possible Pathogen Byrd2020 1
Cronobacter muytjensii Proteobacteria FANA Non/unknown Pathogen 0
Cronobacter turicensis Proteobacteria FANA Opportunistic Infection 0
Cruoricaptor ignavus Bacteroidetes Micr 35 7.8-8 Opportunistic Pathogen New2022 1
Culturomica massiliensis Bacteroidetes SANA 37 Non/unknown Pathogen Lagier2016, Minerbi2019 2
Cutibacterium acnes subsp. defendens Actinobacteria ANA 30-37 Opportunistic Infection King2019 1
Cutibacterium avidum Actinobacteria ANA Opportunistic Pathogen RajilicStojanovic2014, Cassir2015, Lagier2016, Almeida2019, Forster2019 5
Cytophaga hutchinsonii Bacteroidetes AER 30 7 Non/unknown Pathogen Yang2020 1
Dakarella massiliensis Proteobacteria SANA Possible Pathogen Lagier2016, Byrd2020, Minerbi2019 3
Dakotella fusiforme Firmicutes FANA 37 7.0 Non/unknown Pathogen 0
Delftia acidovorans Proteobacteria SAER Rare Opportunist Bik2006, McLaughlin2010, Walker2011, RajilicStojanovic2014 4
Delftia tsuruhatensis Proteobacteria AER 35 7.0 Non/unknown Pathogen Lagier2016 1
Dellaglioa algida Firmicutes FANA Non/unknown Pathogen Byrd2020 1
Denitrobacterium detoxificans Actinobacteria ANA Non/unknown Pathogen Byrd2020, New2022 2
Dermabacter hominis Actinobacteria FANA Opportunistic Pathogen Dubourg2013, Pfleiderer2013, RajilicStojanovic2014, Cassir2015, Lagier2016, Forster2019 6
Dermacoccus nishinomiyaensis Actinobacteria AER Rare Opportunist RajilicStojanovic2014, Lagier2016 2
Desemzia incerta Firmicutes Micr Non/unknown Pathogen Lagier2016, Yang2020 2
Desnuesiella massiliensis Firmicutes FANA 37 Non/unknown Pathogen Lagier2016 1
Desulfococcus multivorans Proteobacteria SANA 35 Non/unknown Pathogen Byrd2020 1
Desulfoscipio gibsoniae Firmicutes SANA 35-37 6.9-7.2 Non/unknown Pathogen 0
Desulfosporosinus youngiae Firmicutes None 32-35 7.0-7.3 Non/unknown Pathogen New2022 1 Fe(III) and arsenate are not electron acceptors and do not support growth
Desulfovibrio diazotrophicus Proteobacteria SANA 37 5.9 Non/unknown Pathogen 0 Able to respire sulfate using hydrogen, CO or alcohols. Can fix N2.
Desulfovibrio intestinalis Proteobacteria ANA 37 Non/unknown Pathogen 0
Desulfovibrio legallii Proteobacteria SANA 35 7.3-7.5 Non/unknown Pathogen Zou2019, Byrd2020, Yang2020, Minerbi2019 4
Desulfovibrio longreachensis Proteobacteria ANA 37 7-7.4 Non/unknown Pathogen 0
Desulfovibrio vulgaris Proteobacteria SANA 30-36 Non/unknown Pathogen Lagier2016, New2022, Zeller2014 3 Uses sulfate, sulfite and thiosulfate as electron acceptors
Devosia chinhatensis Proteobacteria AER Non/unknown Pathogen Yang2020 1
Dialister hominis Firmicutes SANA 37 Non/unknown Pathogen New2022 1
Dialister massiliensis Firmicutes ANA 37 Non/unknown Pathogen New2022, Wang2020a 2
Dialister micraerophilus Firmicutes Micr Non/unknown Pathogen Zeller2014, Vachida2019 2
Dialister propionicifaciens Firmicutes ANA Opportunistic Pathogen 0
Dietzia cinnamea Actinobacteria AER Opportunistic Pathogen RajilicStojanovic2014, Lagier2016 2
Dietzia maris Actinobacteria AER Rare Opportunist RajilicStojanovic2014, Lagier2016, Byrd2020 3
Dietzia natronolimnaea Actinobacteria None 30 9 Non/unknown Pathogen RajilicStojanovic2014, Lagier2016 2
Dorea hylemonae Firmicutes None Byrd2020 1 Isolation and characterisation not yet published.
Dorea phocaeensis Firmicutes SANA Non/unknown Pathogen 0
Dorea scindens Firmicutes None Byrd2020 1 Isolation and characterisation not yet published.
Drancourtella massiliensis Firmicutes SANA 37 Non/unknown Pathogen Lagier2016 1
Dubosiella newyorkensis Firmicutes SANA 37 Non/unknown Pathogen De2020 1
Duncaniella muris Bacteroidetes SANA Non/unknown Pathogen Byrd2020 1
Dysgonomonas capnocytophagoides Bacteroidetes FANA Opportunistic Pathogen Forster2019, Byrd2020 2
Dysgonomonas gadei Bacteroidetes FANA Opportunistic Pathogen RajilicStojanovic2014, Lagier2016, Forster2019, Byrd2020, Vachida2019 5
Dysgonomonas massiliensis Bacteroidetes FANA 37 Non/unknown Pathogen 0
Dysgonomonas mossii Bacteroidetes ANA Opportunistic Pathogen Tyakht2013, Lagier2016, Forster2019, Vachida2019, Qin2012 5
Eggerthella guodeyinii Actinobacteria ANA Non/unknown Pathogen New2022 1 Acid is not formed from sugars.
Eggerthella sinensis Actinobacteria SANA Rare Opportunist Zou2019, Yang2020 2
Eggerthella timonensis Actinobacteria SANA 37 Non/unknown Pathogen Lagier2016, Byrd2020 2
Eikenella corrodens Proteobacteria FANA 32-43 7.0-8.0 Opportunistic Pathogen RajilicStojanovic2014, Lagier2016, Yang2020, Zeller2014, Vachida2019 5
Ellagibacter isourolithinifaciens Actinobacteria SANA Non/unknown Pathogen 0
Empedobacter brevis Bacteroidetes AER Opportunistic Pathogen Lagier2016 1
Empedobacter falsenii Bacteroidetes AER Opportunistic Pathogen RajilicStojanovic2014, Yang2020 2
Enhydrobacter aerosaccus Proteobacteria FANA 37-39 Non/unknown Pathogen Yang2020, Hu2019 2
Enorma phocaeensis Actinobacteria SANA Non/unknown Pathogen Byrd2020 1
Enorma timonensis Actinobacteria SANA 37 Non/unknown Pathogen Lagier2016 1
Enterobacter cloacae subsp. dissolvens Proteobacteria FANA Opportunistic Pathogen Zou2019 1
Enterobacter hormaechei subsp. steigerwaltii Proteobacteria FANA Opportunistic Pathogen 0
Enterobacter hormaechei subsp. xiangfangensis Proteobacteria FANA Non/unknown Pathogen Yang2020 1
Enterobacter kobei Proteobacteria FANA Opportunistic Pathogen Lagier2016, Byrd2020, New2022 3
Enterobacter ludwigii Proteobacteria FANA 36 Possible Pathogen RajilicStojanovic2014, Lagier2016, Zou2019, Byrd2020, PerezBrocal2015 5
Enterobacter massiliensis Proteobacteria AER 30-37 Non/unknown Pathogen RajilicStojanovic2014, Lagier2016, Forster2019 3
Enterobacter mori Proteobacteria FANA 28 7 Non/unknown Pathogen Byrd2020, Vachida2019 2 Optimum growth temperature is 28C. In 4% of healthy Europeans (unseenbio.com).
Enterobacter roggenkampii Proteobacteria FANA Non/unknown Pathogen New2022, Wang2020a 2
Enterobacter soli Proteobacteria FANA Non/unknown Pathogen Byrd2020 1
Enterobacter timonensis Proteobacteria FANA Non/unknown Pathogen Lagier2016, Byrd2020 2
Enterococcus asini Firmicutes FANA Non/unknown Pathogen RajilicStojanovic2014, Lagier2016, Zou2019, Vachida2019 4
Enterococcus burkinafasonensis Firmicutes AER 37 Non/unknown Pathogen 0
Enterococcus caccae Firmicutes FANA Non/unknown Pathogen RajilicStojanovic2014, Lagier2016 2
Enterococcus canintestini Firmicutes FANA 37 Non/unknown Pathogen Lagier2016 1
Enterococcus canis Firmicutes FANA 37 Opportunistic Infection Lagier2016 1
Enterococcus cecorum Firmicutes FANA Rare Opportunist McLaughlin2010, RajilicStojanovic2014, Lagier2016, Byrd2020, New2022, Li2019b 6
Enterococcus columbae Firmicutes FANA 35-37 Non/unknown Pathogen Byrd2020 1
Enterococcus diestrammenae Firmicutes FANA 30-37 8.0-9.0 Non/unknown Pathogen Lagier2016 1
Enterococcus dispar Firmicutes FANA Rare Opportunist RajilicStojanovic2014, Lagier2016, Byrd2020, Vachida2019 4
Enterococcus eurekensis Firmicutes FANA 37 Non/unknown Pathogen Lagier2016 1
Enterococcus gallinarum Firmicutes FANA Opportunistic Pathogen Tyakht2013, RajilicStojanovic2014, Cassir2015, Lagier2016, Zou2019, Almeida2019, Forster2019, Byrd2020, Hu2019, Zeller2014, Vachida2019, Wang2020a 12 In 1% of Europeans (unseenbio.com).
Enterococcus gilvus Firmicutes FANA Opportunistic Infection Lagier2016, Byrd2020, New2022, Vachida2019 4
Enterococcus haemoperoxidus Firmicutes FANA 37 Non/unknown Pathogen 0
Enterococcus hermanniensis Firmicutes FANA Non/unknown Pathogen Lagier2016, De2020 2
Enterococcus italicus Firmicutes FANA 37 Non/unknown Pathogen Lagier2016, Byrd2020, De2020, Zeller2014 4
Enterococcus lactis Firmicutes FANA 37 7.5 Non/unknown Pathogen De2020 1
Enterococcus malodoratus Firmicutes FANA Opportunistic Pathogen Lagier2016, Byrd2020 2
Enterococcus massiliensis Firmicutes FANA 37 Non/unknown Pathogen Lagier2016 1
Enterococcus mediterraneensis Firmicutes ANA Non/unknown Pathogen 0
Enterococcus moraviensis Firmicutes FANA 35-37 Non/unknown Pathogen 0
Enterococcus mundtii Firmicutes FANA Rare Opportunist Lagier2016, Byrd2020 2 Found in human breast milk (Jeurink2013).
Enterococcus pallens Firmicutes FANA Opportunistic Pathogen Lagier2016 1
Enterococcus phoeniculicola Firmicutes FANA 30-37 8 Non/unknown Pathogen RajilicStojanovic2014, Lagier2016 2
Enterococcus pseudoavium Firmicutes FANA Rare Opportunist Woodmansey2004, RajilicStojanovic2014, Lagier2016, Byrd2020 4
Enterococcus raffinosus Firmicutes FANA Opportunistic Pathogen Favier2002, Lagier2016, Byrd2020, Vachida2019 4
Enterococcus saccharolyticus Firmicutes FANA 37 Opportunistic Infection RajilicStojanovic2014, Lagier2016, Dubinkina2017 3
Enterococcus sulfureus Firmicutes FANA Non/unknown Pathogen Yang2020 1
Enterococcus thailandicus Firmicutes FANA Possible Pathogen Lagier2016, Byrd2020 2
Enterococcus timonensis Firmicutes FANA 37 Non/unknown Pathogen 0
Enterococcus villorum Firmicutes FANA Opportunistic Pathogen Lagier2016, Byrd2020 2
Enteroscipio rubneri Actinobacteria SANA Non/unknown Pathogen Byrd2020 1
Erwinia teleogrylli Proteobacteria FANA 7 Non/unknown Pathogen Byrd2020, De2020 2
Erysipelothrix larvae Firmicutes FANA 37 8 Non/unknown Pathogen De2020 1
Escherichia dysenteriae Proteobacteria None Byrd2020 1 Isolation and characterisation not yet published.
Escherichia ruysiae Proteobacteria FANA 37 Possible Pathogen 0 The organism was lost from the patient's gut after less than one month
Ethanoligenens harbinense Firmicutes SANA 35 4.5-5.0 Non/unknown Pathogen Byrd2020, New2022, Zeller2014, Qin2012 4
Eubacterium barkeri Firmicutes SANA 37 Non/unknown Pathogen Finegold1974, Finegold1977, RajilicStojanovic2014, Lagier2016 4
Eubacterium brachy Firmicutes SANA 37 Opportunistic Infection Woodmansey2004, RajilicStojanovic2014, Lagier2016, Byrd2020, De2020, Vachida2019 6
Eubacterium infirmum Firmicutes SANA Opportunistic Pathogen Lagier2016, Byrd2020, Yang2020, Hu2019, Vachida2019, Qin2012 6
Eubacterium maltosivorans Firmicutes SANA 35-37 7.0-7.5 Non/unknown Pathogen New2022 1
Eubacterium multiforme Firmicutes SANA 37 Opportunistic Infection RajilicStojanovic2014 1
Eubacterium nodatum Firmicutes SANA 37 Opportunistic Pathogen Byrd2020, Yang2020 2
Eubacterium oxidoreducens Firmicutes SANA 39-41 7.4 Non/unknown Pathogen Byrd2020, Yang2020 2
Eubacterium plexicaudatum Firmicutes SANA 37 Non/unknown Pathogen Byrd2020 1
Eubacterium pyruvativorans Firmicutes ANA Non/unknown Pathogen Byrd2020, De2020 2 High G+C for Clostridium/Eubacteria species. Net producer of mainly caproate, plus valerate. Net consumer of acetate, propionate and butyrate.
Eubacterium ruminantium Firmicutes SANA 37 Non/unknown Pathogen Moore1974, RajilicStojanovic2014, Lagier2016, Byrd2020 4
Eubacterium saphenum Firmicutes SANA Opportunistic Pathogen Bik2006, RajilicStojanovic2014, Byrd2020, De2020, Zeller2014, Vachida2019 6
Eubacterium sulci Firmicutes SANA 37 Opportunistic Pathogen McLaughlin2010, RajilicStojanovic2014, Byrd2020, Yang2020 4
Eubacterium uniforme Firmicutes SANA 38 Non/unknown Pathogen Byrd2020 1
Eubacterium xylanophilum Firmicutes SANA Non/unknown Pathogen Byrd2020, Yang2020 2
Eubacterium yurii Firmicutes SANA 34-37 Opportunistic Pathogen Lagier2016, Zeller2014 2
Ewingella americana Proteobacteria FANA Causes Illness Byrd2020 1
Exiguobacterium aurantiacum Firmicutes FANA 37 8.5-9.5 Non/unknown Pathogen RajilicStojanovic2014, Lagier2016, Yang2020 3
Exiguobacterium marinum Firmicutes FANA 30-37 6.5-8.5 Non/unknown Pathogen Forster2019 1
Exiguobacterium mexicanum Firmicutes FANA Non/unknown Pathogen Zou2019 1
Exiguobacterium undae Firmicutes FANA 37 Non/unknown Pathogen Forster2019 1
Ezakiella massiliensis Bacteroidetes SANA Rare Opportunist New2022 1 In 1% of Europeans (unseenbio.com). Rare coloniser.
Ezakiella peruensis Firmicutes SANA 37 7.7 Non/unknown Pathogen Yang2020 1
Facklamia hominis Firmicutes FANA Opportunistic Infection Lagier2016, Byrd2020 2
Facklamia languida Firmicutes FANA 37 Opportunistic Pathogen Lagier2016 1
Faecalibacillus faecis Firmicutes SANA 37 6.0 Non/unknown Pathogen 0
Faecalibacillus intestinalis Firmicutes SANA 37 6.0 Non/unknown Pathogen New2022 1
Faecalibaculum rodentium Firmicutes SANA 37 7 Non/unknown Pathogen Byrd2020, New2022 2
Faecalimonas umbilicata Firmicutes SANA 37 7 Non/unknown Pathogen Jeong2021, Minerbi2019 2
Fastidiosipila sanguinis Firmicutes Micr Opportunistic Pathogen Lagier2016, Byrd2020, New2022 3
Fenollaria timonensis Firmicutes ANA Non/unknown Pathogen Lagier2016, Byrd2020, De2020 3
Fermentimonas caenicola Bacteroidetes FANA 37-40 7.1 Non/unknown Pathogen King2019 1
Ferrimonas balearica Proteobacteria FANA Non/unknown Pathogen Forster2019 1 Uses Fe(III) and Mn(IV) as electron acceptors. Requires sodium for growth.
Flaviflexus massiliensis Actinobacteria AER Non/unknown Pathogen Lagier2016 1
Flavobacterium cheniae Bacteroidetes AER 7.5 Non/unknown Pathogen RajilicStojanovic2014 1
Flavobacterium lindanitolerans Bacteroidetes AER 37 7.5 Opportunistic Pathogen RajilicStojanovic2014, Lagier2016 2
Flavobacterium sakaeratica Bacteroidetes None Non/unknown Pathogen RajilicStojanovic2014 1
Flexispira rappini Proteobacteria Micr Non/unknown Pathogen RajilicStojanovic2014 1
Flintibacter butyricus Firmicutes SANA Non/unknown Pathogen Diamanti2020 1
Franconibacter pulveris Proteobacteria FANA Non/unknown Pathogen Byrd2020, De2020 2
Fretibacterium fastidiosum Synergistetes SANA 37 6-7 Non/unknown Pathogen Vachida2019 1 Asaccharolytic. Growth stimulated by the presence of Fusobacterium nucleatum subsp. nucleatum.
Fructilactobacillus sanfranciscensis Firmicutes Micr 30 Non/unknown Pathogen Byrd2020, Yang2020, Hu2019, Zeller2014, Vachida2019 5
Fucophilus fucoidanolyticus Verrucomicrobia AER Non/unknown Pathogen 0 Digests algal-derived fucoidan compounds (sulfated fucosyl polysaccharides).
Fundidesulfovibrio putealis Proteobacteria SANA 30 7.0 Non/unknown Pathogen De2020 1 Uses sulfate, sulfite and thiosulfate as electron acceptors
Fusobacterium canifelinum Fusobacteria SANA Opportunistic Pathogen Lagier2016 1
Fusobacterium massiliense Fusobacteria SANA 37 Non/unknown Pathogen Lagier2016 1
Fusobacterium naviforme Fusobacteria SANA Opportunistic Pathogen Benno1986, Mangin2004, Dubourg2013, RajilicStojanovic2014, Lagier2016 5
Fusobacterium necrogenes Fusobacteria SANA Opportunistic Pathogen Finegold1974, Benno1986, Benno1989, RajilicStojanovic2014, Lagier2016, Yang2020 6
Fusobacterium necrophorum subsp. funduliforme Fusobacteria SANA Opportunistic Pathogen Lagier2016 1
Fusobacterium nucleatum subsp. animalis Fusobacteria SANA 35-37 7 Possible Pathogen Tyakht2013, Byrd2020, Yang2020, Jie2017 4
Fusobacterium nucleatum subsp. polymorphum Fusobacteria SANA 35-37 7 Opportunistic Pathogen Yang2020 1
Fusobacterium nucleatum subsp. vincentii Fusobacteria SANA 35-37 7 Opportunistic Pathogen Yang2020 1
Fusobacterium perfoetens Fusobacteria SANA 37 Non/unknown Pathogen 0
Fusobacterium ulcerans Fusobacteria SANA 37 Opportunistic Pathogen Tyakht2013, Lagier2016, Zou2019, Forster2019, Byrd2020, New2022, Dubinkina2017, Hu2019, Jeong2021, Jie2017, Zeller2014, Vachida2019, Wang2020a 13 Few Europeans have it (unseenbio.com).
Gabonia massiliensis Bacteroidetes ANA 37 Non/unknown Pathogen Lagier2016 1
Gabonibacter timonensis Bacteroidetes None Non/unknown Pathogen 0
Gallibacterium anatis Proteobacteria FANA Opportunistic Pathogen Forster2019, Zeller2014 2 Description for G. anatis bv anatis, not the haemolytic biovar.
Gemella asaccharolytica Firmicutes FANA Opportunistic Pathogen Byrd2020, Yang2020 2
Georgenia muralis Actinobacteria FANA 28-37 Non/unknown Pathogen RajilicStojanovic2014, Lagier2016 2
Gleimia europaea Actinobacteria FANA Opportunistic Pathogen Lagier2016, Byrd2020, Vachida2019 3
Globicatella sulfidifaciens Firmicutes FANA 37-42 Possible Pathogen Lagier2016, Byrd2020 2
Glutamicibacter protophormiae Actinobacteria FANA 6.0-8.5 Non/unknown Pathogen Yang2020 1
Gorbachella massiliensis Firmicutes SANA Non/unknown Pathogen Lagier2016 1
Gordonia alkanivorans Actinobacteria FANA Non/unknown Pathogen Zeller2014 1
Gordonia terrae Actinobacteria AER Opportunistic Pathogen McLaughlin2010, RajilicStojanovic2014 2
Gordonibacter massiliensis Actinobacteria SANA Non/unknown Pathogen Lagier2016, Byrd2020 2
Gorillibacterium timonense Firmicutes FANA Non/unknown Pathogen Lagier2016 1
Gracilibacillus dipsosauri Firmicutes FANA 45 7.5 Non/unknown Pathogen Lagier2016 1
Gracilibacillus massiliensis Firmicutes AER 37 7.0-8.0 Non/unknown Pathogen Lagier2016 1
Gracilibacillus phocaeensis Firmicutes None Non/unknown Pathogen 0
Gracilibacillus timonensis Firmicutes None 37 Non/unknown Pathogen Lagier2016 1
Granulicatella para-adiacens Firmicutes FANA Opportunistic Pathogen McLaughlin2010, Lagier2016, Wang2005, Bik2006, Walker2011, RajilicStojanovic2014 6
Grimontia hollisae Proteobacteria FANA Opportunistic Pathogen RajilicStojanovic2014, Lagier2016 2 Requires Na+ for growth.
Haemophilus ducreyi Proteobacteria AER Known Pathogen 0 Produces many peptidases.
Haemophilus paraphrohaemolyticus Proteobacteria FANA Opportunistic Pathogen Byrd2020, Yang2020, Hu2019, Vachida2019 4
Haemophilus quentini Proteobacteria FANA Rare Opportunist RajilicStojanovic2014, Byrd2020 2
Hafnia paralvei Proteobacteria FANA 28-37 Opportunistic Pathogen Byrd2020, Yang2020 2
Hahella ganghwensis Proteobacteria AER 35 7-8 Non/unknown Pathogen De2020 1 Sodium required for growth.
Halobacillus ihumii Firmicutes SAER Non/unknown Pathogen 0 Strictly halophilic.
Halobacillus salinus Firmicutes FANA 30-37 7.0 Non/unknown Pathogen Lagier2016 1 Requires at least 2% salt concentration for optimal growth.
Haloferax massiliensis Euryarchaeota AER Non/unknown Pathogen Lagier2016 1 A halophilic archea
Haloimpatiens massiliensis Firmicutes SANA Non/unknown Pathogen 0
Halomonas massiliensis Proteobacteria FANA 37 7 Non/unknown Pathogen Lagier2016 1
Harryflintia acetispora Firmicutes SANA 37-41 7.0-8.5 Non/unknown Pathogen Zou2019 1
Hathewaya histolytica Firmicutes SANA 35 Opportunistic Pathogen Lagier2016, New2022 2
Hathewaya limosa Firmicutes SANA 37 7 Opportunistic Pathogen Finegold1977, RajilicStojanovic2014 2
Hathewaya massiliensis Firmicutes SANA Non/unknown Pathogen 0
Helcobacillus massiliensis Actinobacteria AER 37 Opportunistic Pathogen Lagier2016 1
Helcococcus sueciensis Firmicutes FANA Opportunistic Infection De2020 1
Helicobacter cinaedi Proteobacteria Micr Known Pathogen Tyakht2013, RajilicStojanovic2014, Lagier2016, Forster2019, Byrd2020, Vachida2019 6
Helicobacter fennelliae Proteobacteria Micr 37 Rare Opportunist Lagier2016 1
Helicobacter pametensis Proteobacteria Micr 37-42 Possible Pathogen Forster2019 1
Helicobacter rodentium Proteobacteria Micr 37 Opportunistic Pathogen Forster2019 1
Helicobacter winghamensis Proteobacteria Micr Non/unknown Pathogen Tyakht2013, RajilicStojanovic2014, Lagier2016, Forster2019 4
Herbaspirillum huttiense Proteobacteria AER 25-37 7 Non/unknown Pathogen Yang2020 1
Hespellia porcina Firmicutes SANA Non/unknown Pathogen PerisBondia2011, RajilicStojanovic2014 2
Hespellia stercorisuis Firmicutes SANA Non/unknown Pathogen PerisBondia2011, RajilicStojanovic2014, Byrd2020 3
Histophilus somni Proteobacteria FANA Possible Pathogen Byrd2020, New2022, Zeller2014 3
Howardella ureilytica Firmicutes SANA Non/unknown Pathogen RajilicStojanovic2014, De2020, Yang2020 3
Hugonella massiliensis Actinobacteria SANA 37 7 Non/unknown Pathogen 0
Hungatella saccharolyticum Firmicutes None Byrd2020 1 Isolation and characterisation not yet published.
Hungatella xylanolytica Firmicutes SANA 30 7.0 Rare Opportunist Lagier2016 1
Hydrogenoanaerobacterium saccharovorans Firmicutes SANA 37 6.5-7.0 Non/unknown Pathogen PerisBondia2011, RajilicStojanovic2014, Byrd2020 3
Hymenobacter rigui Bacteroidetes AER 25-30 6 Non/unknown Pathogen RajilicStojanovic2014 1
Hyphomicrobium facile Proteobacteria AER 6.5-7 Non/unknown Pathogen Yang2020 1
Ihubacter massiliensis Firmicutes SANA Non/unknown Pathogen Lagier2016, Jeong2021 2
Ihuprevotella massiliensis Bacteroidetes ANA Non/unknown Pathogen 0
Ileibacterium valens Firmicutes SANA 37 Non/unknown Pathogen Byrd2020 1
Inediibacterium massiliense Firmicutes SANA 37 Non/unknown Pathogen Lagier2016 1
Intestinibacillus massiliensis Firmicutes SANA Non/unknown Pathogen Byrd2020 1
Intestinimonas gabonensis Firmicutes SANA 37 Non/unknown Pathogen Lagier2016 1
Intestinimonas timonensis Firmicutes SANA Non/unknown Pathogen Lagier2016, Jeong2021 2
Isoptericola variabilis Actinobacteria FANA Non/unknown Pathogen Lagier2016, Zeller2014 2 Cellulolytic and xylanolytic
Janibacter anophelis Actinobacteria AER 35 Non/unknown Pathogen Yang2020 1
Janibacter terrae Actinobacteria AER 28-30 7.0-8.0 Non/unknown Pathogen McLaughlin2010, RajilicStojanovic2014 2
Jeotgalicoccus halotolerans Firmicutes FANA 30-35 7.0-8.0 Non/unknown Pathogen Yang2020 1
Johnsonella ignava Firmicutes SANA Opportunistic Infection Byrd2020, De2020 2
Jonquetella anthropi Synergistetes SANA 37-42 Opportunistic Pathogen Byrd2020, New2022, Zeller2014, Vachida2019 4 Carbohydrates are not fermented.
Kallipyga gabonensis Firmicutes SANA 37 5 Non/unknown Pathogen Lagier2016 1
Kallipyga massiliensis Firmicutes SANA 37 Non/unknown Pathogen RajilicStojanovic2014, Lagier2016, Byrd2020 3
Kandleria vitulina Firmicutes FANA Non/unknown Pathogen RajilicStojanovic2014, Byrd2020 2
Kerstersia gyiorum Proteobacteria None 33-37 Opportunistic Pathogen RajilicStojanovic2014, Lagier2016 2
Khelaifiella massiliensis Firmicutes SANA Non/unknown Pathogen Byrd2020 1
Kineothrix alysoides Firmicutes SANA 35-40 7 Non/unknown Pathogen Byrd2020 1
Kingella kingae Proteobacteria AER 33-37 Opportunistic Infection Lagier2016 1
Klebsiella pneumoniae subsp. ozaenae Proteobacteria FANA Possible Pathogen Finegold1974, Finegold1977, Zou2019 3
Klebsiella pneumoniae subsp. rhinoscleromatis Proteobacteria FANA Known Pathogen Zou2019 1
Kluyvera cryocrescens Proteobacteria FANA Possible Pathogen McLaughlin2010, Lagier2016, Byrd2020 3
Kluyvera georgiana Proteobacteria FANA Non/unknown Pathogen Lagier2016, Byrd2020, Yang2020 3
Kluyvera intermedia Proteobacteria FANA 30-37 Opportunistic Pathogen Byrd2020 1
Kocuria marina Actinobacteria AER Non/unknown Pathogen RajilicStojanovic2014, Lagier2016 2
Kocuria varians Actinobacteria AER 22-37 Non/unknown Pathogen Lagier2016 1
Krasilnikoviella flava Actinobacteria AER Non/unknown Pathogen RajilicStojanovic2014, Lagier2016 2
Kurthia gibsonii Firmicutes AER Opportunistic Infection RajilicStojanovic2014, Lagier2016 2
Kurthia massiliensis Firmicutes SAER 25-50 7.0-9.0 Non/unknown Pathogen RajilicStojanovic2014, Lagier2016, Forster2019, Byrd2020 4
Kurthia senegalensis Firmicutes SAER Non/unknown Pathogen RajilicStojanovic2014, Lagier2016 2
Kurthia sp. Dielmo Firmicutes AER Non/unknown Pathogen RajilicStojanovic2014, Lagier2016 2
Kurthia zopfii Firmicutes AER Opportunistic Infection 0
Kytococcus schroeteri Actinobacteria AER 37 Opportunistic Pathogen Pfleiderer2013, RajilicStojanovic2014, Lagier2016 3
Kytococcus sedentarius Actinobacteria AER 28-36 Opportunistic Infection Pfleiderer2013, RajilicStojanovic2014, Lagier2016, Zeller2014 4
Lachnoanaerobaculum orale Firmicutes SANA 37 6.5-7.0 Non/unknown Pathogen Lagier2016 1
Lachnoanaerobaculum saburreum Firmicutes SANA 37 6.5-7.5 Opportunistic Infection RajilicStojanovic2014, Byrd2020, Zeller2014, Vachida2019, Qin2012 5
Lachnoanaerobaculum umeaense Firmicutes SANA 6.5-7.0 Non/unknown Pathogen RajilicStojanovic2014, Lagier2016, Byrd2020, New2022 4
Lachnobacterium bovis Firmicutes SANA 39-42 Non/unknown Pathogen Zupancic2012, RajilicStojanovic2014, Salonen2014, Byrd2020 4
Lachnoclostridium bouchesdurhonense Firmicutes None Non/unknown Pathogen Lagier2016 1
Lachnoclostridium massiliosenegalense Firmicutes ANA Non/unknown Pathogen 0
Lachnoclostridium pacaense Firmicutes ANA Non/unknown Pathogen Minerbi2019 1
Lachnoclostridium phocaeense Firmicutes SANA 37 Opportunistic Infection Diamanti2020, New2022, Wang2020a 3
Lachnoclostridium touaregense Firmicutes ANA Non/unknown Pathogen 0
Lachnospira multipara Firmicutes ANA Non/unknown Pathogen Byrd2020 1
Lacrimispora aerotolerans Firmicutes SANA 38 Non/unknown Pathogen Lagier2016 1
Lacrimispora amygdalina Firmicutes ANA 45 7.0-7.5 Non/unknown Pathogen Lagier2016 1
Lacrimispora celerecrescens Firmicutes SANA 30-37 7 Possible Pathogen Zupancic2012, Lagier2016 2 Cellulolytic.
Lacticaseibacillus casei Firmicutes FANA Rare Opportunist Finegold1977, Benno1989, Heilig2002, DalBello2006, Tyakht2013, RajilicStojanovic2014, Lagier2016, Forster2019, Byrd2020, Dubinkina2017, Jie2017, Zeller2014, Vachida2019 13 An unlikely permanent inhabitant of the colon. Found in human breast milk (Jeurink2013).
Lactiplantibacillus paraplantarum Firmicutes FANA Non/unknown Pathogen Lagier2016, Byrd2020 2
Lactiplantibacillus pentosus Firmicutes FANA Non/unknown Pathogen DalBello2006, RajilicStojanovic2014, Lagier2016, Zou2019, Vachida2019 5
Lactiplantibacillus xiangfangensis Firmicutes FANA 30 Non/unknown Pathogen Yang2020 1
Lactobacillus delbrueckii subsp. bulgaricus Firmicutes Micr 40-44 Non/unknown Pathogen Tyakht2013, Lagier2016, Dubinkina2017, Jie2017 4
Lactobacillus equicursoris Firmicutes SANA Non/unknown Pathogen Vachida2019 1
Lactobacillus hamsteri Firmicutes SANA Non/unknown Pathogen Zupancic2012 1
Lactobacillus helveticus Firmicutes FANA Non/unknown Pathogen Finegold1977, Woodmansey2004, Tyakht2013, RajilicStojanovic2014, Lagier2016, Forster2019, Byrd2020, New2022, Dubinkina2017, Hu2019, Zeller2014 11 A probiotic, but only present in the faeces of 3% of Europeans (unseenbio.com). Found in human breast milk (Jeurink2013).
Lactobacillus iners Firmicutes FANA Rare Opportunist McLaughlin2010, RajilicStojanovic2014, Lagier2016, Forster2019, Byrd2020, Yang2020, New2022, Jeong2021, Zeller2014, Vachida2019, PerezBrocal2015 11 Rare coloniser.
Lactobacillus kefiranofaciens Firmicutes FANA Non/unknown Pathogen Zeller2014 1
Lactobacillus leichmannii Firmicutes FANA Non/unknown Pathogen Moore1974, Holdeman1976, Finegold1977, RajilicStojanovic2014, Lagier2016 5
Lactobacillus rogosae Firmicutes SANA 37 Non/unknown Pathogen Moore1974, RajilicStojanovic2014, Lagier2016, Yang2020, Minerbi2019 5
Lactococcus cremoris Firmicutes FANA Opportunistic Infection Finegold1974, Finegold1977, Lagier2016, New2022, Dubinkina2017, Jie2017 6
Lactococcus petauri Firmicutes FANA 20-40 Non/unknown Pathogen Byrd2020 1
Lactococcus plantarum Firmicutes FANA Non/unknown Pathogen Woodmansey2004, RajilicStojanovic2014, Lagier2016 3 In 5% of Europeans (unseenbio.com). Rare coloniser. Probiotic.
Lagierella massiliensis Firmicutes SANA 37 Non/unknown Pathogen Lagier2016 1
Laribacter hongkongensis Proteobacteria FANA Opportunistic Pathogen RajilicStojanovic2014, Lagier2016, Zeller2014 3
Lascolabacillus massiliensis Bacteroidetes FANA Non/unknown Pathogen Lagier2016 1
Latilactobacillus sakei subsp. carnosus Firmicutes FANA Non/unknown Pathogen 0
Lawsonella clevelandensis Actinobacteria SANA 35 Possible Pathogen Byrd2020, De2020, New2022 3
Leclercia adecarboxylata Proteobacteria FANA Possible Pathogen Lagier2016, Byrd2020, New2022 3
Lederbergia galactosidilyticus Firmicutes FANA 25-37 Non/unknown Pathogen Lagier2016 1
Lelliottia amnigena Proteobacteria FANA 30 Opportunistic Pathogen Lagier2016, Byrd2020 2
Lelliottia nimipressuralis Proteobacteria FANA Non/unknown Pathogen Byrd2020 1
Leminorella grimontii Proteobacteria FANA Possible Pathogen RajilicStojanovic2014, Lagier2016 2
Leminorella richardii Proteobacteria FANA Opportunistic Infection RajilicStojanovic2014, Lagier2016 2
Lentibacillus massiliensis Firmicutes None Non/unknown Pathogen Lagier2016 1
Lentibacillus timonensis Firmicutes SAER 37 Non/unknown Pathogen 0
Lentilactobacillus hilgardii Firmicutes FANA 4.5-5.5 Non/unknown Pathogen Tyakht2013, Forster2019 2 In 1% of Europeans (unseenbio.com). Rare coloniser.
Lentilactobacillus parabuchneri Firmicutes FANA Non/unknown Pathogen DalBello2006, RajilicStojanovic2014, Lagier2016, Byrd2020 4 In 1% of Europeans (unseenbio.com). Rare coloniser.
Leptotrichia amnionii Fusobacteria ANA 35-37 7.0-7.4 Non/unknown Pathogen Bik2006, Walker2011, RajilicStojanovic2014 3
Leptotrichia buccalis Fusobacteria SANA 35-37 7.0-7.4 Known Pathogen Walker2011, RajilicStojanovic2014, Lagier2016, De2020, Zeller2014 5
Leptotrichia hofstadii Fusobacteria ANA 37 Non/unknown Pathogen Zeller2014, Vachida2019 2
Leptotrichia hongkongensis Fusobacteria FANA Opportunistic Pathogen 0
Leptotrichia massiliensis Fusobacteria FANA 30 Non/unknown Pathogen Lagier2016 1
Leptotrichia shahii Fusobacteria FANA 37 Opportunistic Infection Vachida2019 1
Leptotrichia wadei Fusobacteria ANA Non/unknown Pathogen Byrd2020, New2022, Vachida2019 3 In 3% of Europeans (unseenbio.com). Rare coloniser.
Leuconostoc gelidum Firmicutes FANA Non/unknown Pathogen RajilicStojanovic2014, Byrd2020, New2022, Zeller2014, Vachida2019 5
Leuconostoc holzapfelii Firmicutes FANA Non/unknown Pathogen 0 Slime is produced from sucrose
Leuconostoc kimchii Firmicutes FANA Non/unknown Pathogen Zeller2014 1
Leuconostoc mesenteroides subsp. cremoris Firmicutes FANA 25-30 6.5 Non/unknown Pathogen Tyakht2013, Lagier2016 2
Levyella massiliensis Firmicutes None Non/unknown Pathogen Byrd2020 1
Ligilactobacillus agilis Firmicutes FANA Non/unknown Pathogen Lagier2016, Byrd2020, Yang2020, New2022, PerezBrocal2015 5
Ligilactobacillus murinus Firmicutes FANA Opportunistic Pathogen Lagier2016, Forster2019, Byrd2020 3 In 1% of Europeans (unseenbio.com). Rare coloniser.
Limosilactobacillus antri Firmicutes FANA Non/unknown Pathogen Tyakht2013, RajilicStojanovic2014, Lagier2016, Forster2019, Dubinkina2017, Zeller2014 6
Limosilactobacillus caccae Firmicutes SANA 37 Non/unknown Pathogen 0
Limosilactobacillus mucosae Firmicutes FANA Non/unknown Pathogen RajilicStojanovic2014, Lagier2016, Zou2019, Byrd2020, Yang2020, New2022, Hu2019, Jie2017, Vachida2019, Wang2020a, Qin2012, Li2019b, PerezBrocal2015 13 In 4% of Europeans (unseenbio.com), i.e., a rare coloniser.
Limosilactobacillus vaginalis Firmicutes FANA Opportunistic Pathogen Heilig2002, DalBello2006, RajilicStojanovic2014, Lagier2016, Forster2019, Byrd2020, Yang2020, New2022, Dubinkina2017, Zeller2014, Vachida2019, Wang2020a, PerezBrocal2015 13 In 3% of Europeans, so a rare coloniser. Found in human breast milk (Jeurink2013).
Limosilactobacillus walteri Firmicutes FANA Non/unknown Pathogen 0
Listeria floridensis Firmicutes FANA 37-41 Non/unknown Pathogen De2020 1
Listeria grayi Firmicutes FANA Non/unknown Pathogen Tyakht2013, Lagier2016, Forster2019, Zeller2014 4
Listeria innocua Firmicutes FANA Non/unknown Pathogen Tyakht2013, Lagier2016, Forster2019, Qin2012 4
Listeria ivanovii Firmicutes FANA Possible Pathogen Lagier2016 1
Listeria marthii Firmicutes FANA 30-37 Non/unknown Pathogen Yang2020 1
Listeria monocytogenes Firmicutes FANA Known Pathogen Lagier2016, New2022 2
Listeria seeligeri Firmicutes FANA Opportunistic Infection Lagier2016 1
Listeria welshimeri Firmicutes FANA Non/unknown Pathogen Lagier2016, Byrd2020, Qin2012 3
Litchfieldia alkalitelluris Firmicutes FANA 9.0-9.5 Non/unknown Pathogen Cassir2015 1
Longicatena caecimuris Firmicutes None Non/unknown Pathogen Zou2019 1
Luxibacter massiliensis Firmicutes FANA 37 7.5 Non/unknown Pathogen 0
Lysinibacillus boronitolerans Firmicutes AER 37 7.0 Non/unknown Pathogen Lagier2016 1 Tolerates 100 mM boron, with some strains able to grow with 150 mM boron.
Lysinibacillus fusiformis Firmicutes SAER Non/unknown Pathogen Hoyles2012, Pfleiderer2013, RajilicStojanovic2014, Cassir2015, Lagier2016, Zeller2014 6
Lysinibacillus sphaericus Firmicutes AER Opportunistic Pathogen Taylor1985, Walker2011, RajilicStojanovic2014, Lagier2016, Zeller2014 5
Lysinibacillus varians Firmicutes AER Non/unknown Pathogen Lagier2016 1 Can grow in the presence of 150 mM borate
Lysinibacillus xylanilyticus Firmicutes AER 30 Non/unknown Pathogen Lagier2016 1
Lysobacter soli Proteobacteria AER 30 7.0-7.5 Non/unknown Pathogen RajilicStojanovic2014, Lagier2016 2
Macellibacteroides fermentans Bacteroidetes SANA 35-40 6.5-7.5 Non/unknown Pathogen Cassir2015, Lagier2016 2
Mageeibacillus indolicus Firmicutes SANA 35-42 Possible Pathogen King2019, Byrd2020, New2022, Qin2012, LeChatelier2013 5
Mailhella massiliensis Proteobacteria SANA Non/unknown Pathogen Byrd2020, De2020 2
Mammaliicoccus fleurettii Firmicutes FANA Non/unknown Pathogen Byrd2020 1
Mammaliicoccus lentus Firmicutes FANA Non/unknown Pathogen Lagier2016, Forster2019, Byrd2020, Yang2020 4
Mammaliicoccus sciuri Firmicutes FANA 35-40 Non/unknown Pathogen RajilicStojanovic2014, Lagier2016, Yang2020, Li2019b 4
Mannheimia granulomatis Proteobacteria FANA Opportunistic Pathogen Forster2019 1
Mannheimia haemolytica Proteobacteria FANA Known Pathogen De2020 1
Mannheimia succiniciproducens Proteobacteria FANA 37-39 6-7 Non/unknown Pathogen Tyakht2013 1
Marasmitruncus massiliensis Firmicutes ANA Non/unknown Pathogen 0
Marseilla massiliensis Bacteroidetes ANA Non/unknown Pathogen Lagier2016 1
Marseillibacter massiliensis Firmicutes SANA Non/unknown Pathogen Lagier2016, De2020, Minerbi2019 3
Massilia haematophila Proteobacteria FANA 25-30 Rare Opportunist Yang2020 1
Massilibacillus massiliensis Firmicutes ANA Non/unknown Pathogen Lagier2016 1
Massilibacterium senegalense Firmicutes FANA 37 Non/unknown Pathogen Lagier2016 1
Massilicoli timonensis Firmicutes SANA 37 7 Non/unknown Pathogen 0
Massiliimalia massiliensis Firmicutes SANA 37 Non/unknown Pathogen Lagier2016 1
Massiliprevotella massiliensis Bacteroidetes ANA Non/unknown Pathogen Lagier2016, De2020, Minerbi2019 3
Massilistercora timonensis Firmicutes SANA 37 7 Non/unknown Pathogen New2022, Wang2020a 2
Mediterranea massiliensis Bacteroidetes SANA 37 7 Non/unknown Pathogen Lagier2016 1
Mediterraneibacter massiliensis Firmicutes ANA 37 7.2 Non/unknown Pathogen 0
Megamonas rupellensis Firmicutes SANA 37 7 Non/unknown Pathogen Rothschild2018, Hu2019, Vachida2019 3
Megasphaera cerevisiae Firmicutes SANA 28 Non/unknown Pathogen Byrd2020 1
Megasphaera indica Firmicutes SANA 37 Non/unknown Pathogen Lagier2016, Zou2019, Minerbi2019 3
Megasphaera massiliensis Firmicutes SANA 37 Non/unknown Pathogen Lagier2016, Byrd2020, Urban2020, Minerbi2019 4
Megasphaera stantonii Firmicutes SANA 42 Non/unknown Pathogen New2022 1
Merdibacter massiliensis Firmicutes ANA Non/unknown Pathogen Byrd2020 1
Merdimonas faecis Firmicutes SANA 37 6.8 Non/unknown Pathogen 0
Mesobacillus jeotgali Firmicutes FANA 30-35 7.0-8.0 Non/unknown Pathogen Lagier2016 1
Mesobacillus subterraneus Firmicutes FANA 30-40 7.0-9.0 Non/unknown Pathogen Lagier2016 1 Is able to reduce Fe(III) and Mn(IV) in addition to Nitrate
Mesorhizobium loti Proteobacteria AER Non/unknown Pathogen RajilicStojanovic2014, Zeller2014 2
Mesosutterella multiformis Proteobacteria SANA 37 Non/unknown Pathogen 0
Metabacillus idriensis Firmicutes AER Opportunistic Pathogen McLaughlin2010 1
Metabacillus litoralis Firmicutes AER 37 Non/unknown Pathogen Lagier2016 1
Metabacillus niabensis Firmicutes FANA 30 7.0 Non/unknown Pathogen Lagier2016 1
Metakosakonia massiliensis Proteobacteria AER 30-37 Non/unknown Pathogen Byrd2020 1
Metaprevotella massiliensis Bacteroidetes SANA 37 Non/unknown Pathogen Lagier2016 1
Methanobrevibacter arboriphilus Euryarchaeota SANA 30-37 7.5-8.0 Non/unknown Pathogen Lagier2016 1 Autotrophic, converting H2/CO2 to methane.
Methanobrevibacter millerae Euryarchaeota SANA 36-42 7.0-8.0 Non/unknown Pathogen Lagier2016 1 Uses H2/CO2 or formate to produce methane. Requires acetate and yeast extract components for growth.
Methanobrevibacter oralis Euryarchaeota SANA 36-38 6.9-7.4 Non/unknown Pathogen Lagier2016, De2020 2 Requires H2/CO2 and produces methane. Fecal extract (with VFA) was required for growth.
Methanobrevibacter ruminantium Euryarchaeota SANA 39 6.5-7.7 Non/unknown Pathogen Lagier2016, Zeller2014 2 Uses H2 and formate to produce methane. Widely distributed in the rumen of various animals.
Methanococcus voltae Euryarchaeota SANA 32-40 6.7-7.4 Non/unknown Pathogen Qin2012 1 Uses only H2 and/or formate with CO2 as an electron acceptor, producing methane in the process.
Methanomassiliicoccus intestinalis Euryarchaeota SANA Non/unknown Pathogen King2019 1
Methanomassiliicoccus luminyensis Candidatus Thermoplasmatota SANA 37 7.6 Non/unknown Pathogen Lagier2016 1
Methanomethylophilus alvus Candidatus Thermoplasmatota None Non/unknown Pathogen 0 A methanogen consuming methanol.
Methylorubrum aminovorans Proteobacteria AER 30 Non/unknown Pathogen Yang2020 1
Methyloversatilis discipulorum Proteobacteria AER 25-37 6.6-8.0 Non/unknown Pathogen Yang2020 1 Can fix nitrogen.
Methyloversatilis universalis Proteobacteria AER 30-37 7.5-8 Non/unknown Pathogen McLaughlin2010, RajilicStojanovic2014, Byrd2020 3
Microbacterium aurum Actinobacteria AER 30 Rare Opportunist Pfleiderer2013, RajilicStojanovic2014, Lagier2016 3
Microbacterium paraoxydans Actinobacteria FANA Rare Opportunist RajilicStojanovic2014, Lagier2016, Yang2020 3
Microbispora rosea Actinobacteria AER 6.0-7.0 Non/unknown Pathogen PerezBrocal2015 1
Micrococcus lylae Actinobacteria AER Non/unknown Pathogen Hoyles2012, Pfleiderer2013, RajilicStojanovic2014, Lagier2016 4
Micrococcus terreus Actinobacteria AER 33 7.0 Non/unknown Pathogen De2020 1
Micromonospora aurantiaca Actinobacteria AER Non/unknown Pathogen RajilicStojanovic2014, Lagier2016 2
Micropruina glycogenica Actinobacteria AER 30 7.0 Non/unknown Pathogen Cassir2015 1 Able to accumulate large amounts of glycogen; grows slowly
Microvirga massiliensis Proteobacteria AER Non/unknown Pathogen RajilicStojanovic2014, Lagier2016 2
Millionella massiliensis Bacteroidetes ANA Non/unknown Pathogen 0
Miniphocaeibacter massiliensis Firmicutes ANA Non/unknown Pathogen Byrd2020 1
Mixta calida Proteobacteria FANA Possible Pathogen Lagier2016 1
Mixta intestinalis Proteobacteria FANA 7 Non/unknown Pathogen 0
Mobilibacterium massiliense Firmicutes ANA Non/unknown Pathogen 0
Mobilibacterium timonense Firmicutes ANA Non/unknown Pathogen 0
Mobilicoccus massiliensis Actinobacteria FANA 37 Non/unknown Pathogen Lagier2016 1
Mobiluncus curtisii Actinobacteria ANA Non/unknown Pathogen McLaughlin2010, RajilicStojanovic2014, Byrd2020, New2022, Zeller2014, Vachida2019 6
Moellerella wisconsensis Proteobacteria FANA Opportunistic Pathogen RajilicStojanovic2014, Lagier2016 2
Mogibacterium diversum Firmicutes SANA Causes Illness RajilicStojanovic2014, Byrd2020, New2022 3
Mogibacterium neglectum Firmicutes SANA Causes Illness Wang2005, Bik2006, RajilicStojanovic2014 3
Mogibacterium pumilum Firmicutes SANA Opportunistic Pathogen Byrd2020, Yang2020, New2022 3 Produces phenylacetate as the sole end product of PY or PYG broth; otherwise mostly inert to biochemical tests.
Mogibacterium timidum Firmicutes SANA Causes Illness Woodmansey2004, RajilicStojanovic2014, Lagier2016, Byrd2020 4
Mordavella massiliensis Firmicutes SANA Non/unknown Pathogen 0
Moryella indoligenes Firmicutes SANA Opportunistic Infection RajilicStojanovic2014, Yang2020, PerezBrocal2015 3
Mucispirillum schaedleri Deferribacteres SANA 37 Non/unknown Pathogen 0
Murdochiella asaccharolytica Firmicutes SANA Opportunistic Pathogen Lagier2016 1
Murdochiella massiliensis Firmicutes SANA Non/unknown Pathogen Lagier2016, Byrd2020 2
Murdochiella vaginalis Firmicutes SANA 37 Opportunistic Pathogen Byrd2020, New2022 2 In 4% of Europeans (unseenbio.com). Rare coloniser.
Murimonas intestini Firmicutes SANA Non/unknown Pathogen Forster2019, Yang2020 2
Mycobacterium colombiense Actinobacteria AER Opportunistic Pathogen Lagier2016, Zeller2014 2
Mycobacterium florentinum Actinobacteria AER Opportunistic Pathogen RajilicStojanovic2014, Lagier2016 2
Mycobacterium fortuitum Actinobacteria AER Opportunistic Pathogen RajilicStojanovic2014, Lagier2016 2
Mycobacterium gastri Actinobacteria AER Opportunistic Pathogen Byrd2020 1
Mycobacterium gordonae Actinobacteria AER 37 Opportunistic Pathogen Lagier2016 1
Mycobacterium interjectum Actinobacteria AER Opportunistic Pathogen Lagier2016 1
Mycobacterium lentiflavum Actinobacteria AER Opportunistic Pathogen Lagier2016 1
Mycobacterium simiae Actinobacteria AER 37 Opportunistic Pathogen Lagier2016 1
Mycobacterium terrae Actinobacteria AER Opportunistic Pathogen Lagier2016 1
Mycolicibacterium houstonense Actinobacteria Micr Opportunistic Pathogen Byrd2020 1
Mycolicibacterium neoaurum Actinobacteria Micr Known Pathogen Byrd2020 1
Mycoplasma hominis Tenericutes FANA 37 Opportunistic Pathogen Tyakht2013, RajilicStojanovic2014, Lagier2016, Yang2020, Hu2019, Zeller2014 6
Mycoplasma muris Tenericutes ANA 37 Non/unknown Pathogen De2020 1
Mycoplasma pneumoniae Tenericutes FANA 37 Known Pathogen RajilicStojanovic2014 1
Necropsobacter rosorum Proteobacteria None Possible Pathogen 0
Negativicoccus massiliensis Firmicutes Micr Non/unknown Pathogen Lagier2016, Byrd2020 2
Negativicoccus succinicivorans Firmicutes SANA Possible Pathogen Pfleiderer2013, RajilicStojanovic2014, Lagier2016 3
Neglecta timonensis Firmicutes SANA Non/unknown Pathogen Lagier2016, Minerbi2019 2
Neisseria bacilliformis Proteobacteria AER Opportunistic Infection Zeller2014 1
Neisseria canis Proteobacteria AER Opportunistic Infection Lagier2016 1
Neisseria flava Proteobacteria AER 35-37 Opportunistic Infection Bik2006, RajilicStojanovic2014 2
Neisseria lactamica Proteobacteria AER 35-36 Rare Opportunist De2020, Zeller2014 2 Rarely pathogenic. The only Neisseria sp. to produce acid from lactose.
Neisseria macacae Proteobacteria AER 35-37 Non/unknown Pathogen Tyakht2013, RajilicStojanovic2014, Lagier2016, Forster2019, Zeller2014 5
Neisseria mucosa Proteobacteria AER 35-37 Opportunistic Pathogen RajilicStojanovic2014, Lagier2016, Byrd2020, New2022, Zeller2014 5
Neisseria oralis Proteobacteria FANA Rare Opportunist Yang2020, PerezBrocal2015 2
Neisseria perflava Proteobacteria AER 35-37 Opportunistic Pathogen Pfleiderer2013, RajilicStojanovic2014, Lagier2016, Byrd2020 4
Neisseria polysaccharea Proteobacteria AER 37 Non/unknown Pathogen Zeller2014 1 Not known to cause human disease.
Neisseria shayeganii Proteobacteria FANA Opportunistic Infection De2020 1
Neisseria sicca Proteobacteria Micr Opportunistic Pathogen Yang2020, Vachida2019 2
Neisseria subflava Proteobacteria AER 35-37 Opportunistic Pathogen Wang2005, Bik2006, Walker2011, RajilicStojanovic2014, Lagier2016, Byrd2020, Yang2020, New2022, Zeller2014, Vachida2019, Li2019b, PerezBrocal2015 12 In 6% of Europeans (unseenbio.com). Rare coloniser.
Neoactinobaculum massilliense Actinobacteria ANA 37 Non/unknown Pathogen 0
Neobacillus bataviensis Firmicutes FANA 30 7.0-8.0 Non/unknown Pathogen Lagier2016, Byrd2020 2
Neobacillus jeddahensis Firmicutes FANA 37 Non/unknown Pathogen Lagier2016 1
Neobacillus massiliamazoniensis Firmicutes FANA 37 7 Non/unknown Pathogen 0
Neobacillus niacini Firmicutes AER 7 Non/unknown Pathogen RajilicStojanovic2014, Lagier2016 2
Neobacillus soli Firmicutes FANA 30 7.0-8.0 Non/unknown Pathogen Lagier2016 1
Neofamilia massiliensis Firmicutes None Non/unknown Pathogen Lagier2016, De2020 2
Nesterenkonia massiliensis Actinobacteria AER 37 Non/unknown Pathogen Lagier2016 1
Niallia nealsonii Firmicutes FANA 30-35 Non/unknown Pathogen RajilicStojanovic2014, Lagier2016 2
Niameybacter massiliensis Firmicutes SANA Non/unknown Pathogen Lagier2016, Byrd2020 2
Nigerium massiliense Actinobacteria FANA Non/unknown Pathogen Lagier2016 1
Nitrosomonas eutropha Proteobacteria AER 30 7.5-8.0 Non/unknown Pathogen 0 Can tolerate 0.6M ammonia concentrations. Contains carboxysomes.
Nocardia asteroides Actinobacteria AER Known Pathogen Lagier2016 1 Contains aerial hyphae.
Nocardia brevicatena Actinobacteria AER 36 6.3 Non/unknown Pathogen Byrd2020 1
Nocardia cyriacigeorgica Actinobacteria AER Non/unknown Pathogen Zeller2014 1
Nocardia otitidiscaviarum Actinobacteria AER Non/unknown Pathogen Byrd2020 1
Nosocomiicoccus massiliensis Firmicutes AER 37 Rare Opportunist Lagier2016 1
Noviherbaspirillum massiliense Proteobacteria AER 28-37 7.5-8.0 Non/unknown Pathogen RajilicStojanovic2014, Lagier2016, Forster2019 3
Numidum massiliense Firmicutes FANA 37 Non/unknown Pathogen Lagier2016 1
Obesumbacterium proteus Proteobacteria FANA 32 Non/unknown Pathogen Byrd2020, Yang2020 2
Oceanobacillus caeni Firmicutes AER 30-40 7.0 Non/unknown Pathogen Hoyles2012, RajilicStojanovic2014, Lagier2016 3
Oceanobacillus jeddahense Firmicutes AER 37 7.5 Non/unknown Pathogen Lagier2016 1
Oceanobacillus manasiensis Firmicutes AER 30-37 8-10 Non/unknown Pathogen Lagier2016 1 Apparently aerobic but lacks catalase and oxidase activities.
Oceanobacillus massiliensis Firmicutes SAER 30-37 7-8 Non/unknown Pathogen RajilicStojanovic2014, Lagier2016, Forster2019 3
Oceanobacillus sojae Firmicutes AER 30-35 8.5 Non/unknown Pathogen Lagier2016 1
Oerskovia turbata Actinobacteria FANA Opportunistic Infection Lagier2016 1 Shows extensive branching, but lacks aerial hyphae.
Okadaella gastrococcus Firmicutes None Known Pathogen 0 Intracellular parasite.
Olegusella massiliensis Actinobacteria SANA 37 Non/unknown Pathogen Byrd2020 1
Oleidesulfovibrio alaskensis Proteobacteria SANA 37 7 Non/unknown Pathogen Tyakht2013, New2022, Zeller2014 3 Can use sulfate, thiosulfate and sulfite to oxidise organic acids and alcohols.
Oleidesulfovibrio vietnamensis Proteobacteria SANA 37 7.5 Non/unknown Pathogen 0
Oligella urethralis Proteobacteria AER 30-37 Opportunistic Pathogen Lagier2016, Byrd2020 2
Olsenella congonensis Actinobacteria SANA Non/unknown Pathogen 0
Olsenella massiliensis Actinobacteria SANA Non/unknown Pathogen Lagier2016 1
Olsenella phocaeensis Actinobacteria SANA 37 Non/unknown Pathogen Lagier2016, Byrd2020 2
Olsenella profusa Actinobacteria Micr Opportunistic Pathogen RajilicStojanovic2014, Byrd2020, Vachida2019 3 Differences in enzyme activities between published reports are labelled 'vr' and might represent strain variability.
Olsenella timonensis Actinobacteria SANA Non/unknown Pathogen Lagier2016, New2022 2
Olsenella uli Actinobacteria Micr Opportunistic Pathogen RajilicStojanovic2014, Lagier2016, Byrd2020, New2022, Zeller2014, Vachida2019 6
Olsenella urininfantis Actinobacteria SANA Non/unknown Pathogen Byrd2020 1
Oribacterium asaccharolyticum Firmicutes SANA 37 Non/unknown Pathogen Byrd2020 1 Requires yeast extract for growth.
Oribacterium parvum Firmicutes SANA 37 Opportunistic Pathogen 0
Ornithinibacillus massiliensis Firmicutes AER Non/unknown Pathogen 0
Ornithobacterium rhinotracheale Bacteroidetes Micr Opportunistic Pathogen Forster2019, King2019, New2022 3
Oscillibacter massiliensis Firmicutes SANA Non/unknown Pathogen Lagier2016, Minerbi2019 2
Oscillibacter ruminantium Firmicutes SANA 40 6.0 Non/unknown Pathogen Byrd2020 1
Oscillospira guillermondii Firmicutes ANA Non/unknown Pathogen Zupancic2012, Salonen2014 2
Ottowia massiliensis Pseudomonadota AER Non/unknown Pathogen 0
Pacaella massiliensis Synergistetes SANA Non/unknown Pathogen Lagier2016 1
Paenarthrobacter aurescens Actinobacteria AER Non/unknown Pathogen Lagier2016 1
Paenibacillus amylolyticus Firmicutes FANA 28-30 Non/unknown Pathogen Lagier2016, Byrd2020, PerezBrocal2015 3
Paenibacillus anaericanus Firmicutes FANA 30-35 7.7 Non/unknown Pathogen Lagier2016 1
Paenibacillus antibioticophila Firmicutes FANA Non/unknown Pathogen Dubourg2013, RajilicStojanovic2014, Lagier2016 3
Paenibacillus azoreducens Firmicutes FANA 37 Non/unknown Pathogen Lagier2016 1 Can reduce the azo dye remazol and decolourise it.
Paenibacillus bouchesdurhonensis Firmicutes FANA 37 Non/unknown Pathogen Lagier2016 1
Paenibacillus chitinolyticus Firmicutes AER 25-37 Rare Opportunist Forster2019 1
Paenibacillus cineris Firmicutes FANA 7.0 Non/unknown Pathogen Lagier2016 1
Paenibacillus daejeonensis Firmicutes FANA 30 8.0 Non/unknown Pathogen RajilicStojanovic2014, Lagier2016 2
Paenibacillus dendritiformis Firmicutes FANA 37 Non/unknown Pathogen Lagier2016 1
Paenibacillus durus Firmicutes FANA 30–37 Non/unknown Pathogen Benno1986, RajilicStojanovic2014 2
Paenibacillus faecis Firmicutes FANA Non/unknown Pathogen 0
Paenibacillus favisporus Firmicutes FANA 37 7 Non/unknown Pathogen Lagier2016 1 Xylanolytic.
Paenibacillus glucanolyticus Firmicutes FANA 30 Non/unknown Pathogen RajilicStojanovic2014, Lagier2016 2
Paenibacillus ihuae Firmicutes FANA Non/unknown Pathogen Lagier2016 1
Paenibacillus ihumii Firmicutes FANA 37 Non/unknown Pathogen Lagier2016 1
Paenibacillus illinoisensis Firmicutes FANA 37 7.0 Non/unknown Pathogen RajilicStojanovic2014, Lagier2016 2
Paenibacillus jamilae Firmicutes FANA 30 7 Non/unknown Pathogen Lagier2016 1
Paenibacillus kribbensis Firmicutes FANA 30-37 6.5-8.0 Non/unknown Pathogen Zou2019, Byrd2020 2
Paenibacillus lactis Firmicutes FANA 30–40 7.0 Non/unknown Pathogen RajilicStojanovic2014, Lagier2016, Qin2012 3
Paenibacillus larvae Firmicutes FANA 30-37 Non/unknown Pathogen Lagier2016 1
Paenibacillus lautus Firmicutes FANA 28–30 Rare Opportunist RajilicStojanovic2014, Lagier2016, Forster2019 3
Paenibacillus macerans Firmicutes FANA 30 Opportunistic Infection Lagier2016 1 Can fix N2 under anaerobic conditions.
Paenibacillus motobuensis Firmicutes FANA 37 8.0 Possible Pathogen Lagier2016, Forster2019 2
Paenibacillus pabuli Firmicutes FANA 28-30 Non/unknown Pathogen Lagier2016 1
Paenibacillus pasadenensis Firmicutes None Non/unknown Pathogen Lagier2016 1
Paenibacillus phocaensis Firmicutes FANA 37 7 Non/unknown Pathogen Lagier2016 1
Paenibacillus polymyxa Firmicutes FANA 30 Rare Opportunist Lagier2016 1
Paenibacillus provencensis Firmicutes AER 30-37 Opportunistic Infection RajilicStojanovic2014, Lagier2016 2
Paenibacillus pueri Firmicutes AER 37 Non/unknown Pathogen RajilicStojanovic2014, Lagier2016 2
Paenibacillus rubinfantis Firmicutes FANA 37 Non/unknown Pathogen Lagier2016 1
Paenibacillus sabinae Firmicutes FANA 30 7.2 Non/unknown Pathogen King2019 1
Paenibacillus senegalensis Firmicutes FANA 37 Non/unknown Pathogen Pfleiderer2013, RajilicStojanovic2014, Lagier2016, Forster2019 4
Paenibacillus senegalimassiliensis Firmicutes FANA Non/unknown Pathogen Lagier2016 1
Paenibacillus timonensis Firmicutes FANA 30–37 Rare Opportunist RajilicStojanovic2014, Lagier2016 2
Paenibacillus tuaregi Firmicutes FANA 37 Non/unknown Pathogen 0
Paenibacillus typhae Firmicutes FANA 28-30 7.0-7.5 Non/unknown Pathogen Lagier2016 1
Paenibacillus urinalis Firmicutes FANA 30-37 Opportunistic Infection Lagier2016 1
Paenibacillus xylanilyticus Firmicutes FANA 37 7 Non/unknown Pathogen Lagier2016 1 Xylanolytic.
Paeniclostridium ghonii Firmicutes SANA 30-37 6-7 Opportunistic Pathogen Finegold1974, RajilicStojanovic2014, Lagier2016 3
Paludibacter jiangxiensis Bacteroidetes SANA 37 7.0 Non/unknown Pathogen De2020 1
Paludicola psychrotolerans Firmicutes ANA 25-30 Non/unknown Pathogen 0 Chitinolytic, growing on chitin as the only carbon source
Pantoea conspicua Proteobacteria FANA 28-30 Opportunistic Infection De2020 1
Pantoea eucalypti Proteobacteria FANA Possible Pathogen 0
Pantoea septica Proteobacteria FANA 28-30 Known Pathogen Lagier2016 1
Pantoea vagans Proteobacteria FANA Non/unknown Pathogen Zeller2014 1
Papillibacter cinnamivorans Firmicutes SANA 37 7.5 Non/unknown Pathogen RajilicStojanovic2014, Salonen2014, Byrd2020 3
Parabacteroides faecis Bacteroidetes SANA Non/unknown Pathogen Lagier2016, Yang2020 2
Parabacteroides massiliensis Bacteroidetes SANA Non/unknown Pathogen Lagier2016, Chen2020 2
Parabacteroides pacaensis Bacteroidetes SANA 37 7 Non/unknown Pathogen 0
Parabacteroides pekinense Bacteroidetes SANA 35 Non/unknown Pathogen 0
Parabacteroides provencensis Bacteroidetes SANA 37 7 Non/unknown Pathogen 0
Paraburkholderia fungorum Proteobacteria None Opportunistic Pathogen Yang2020 1
Paraclostridium benzoelyticum Firmicutes SANA 30-35 7.0-8.0 Non/unknown Pathogen 0 Produces antimicrobials.
Paracoccus aminovorans Proteobacteria AER 6.5-8.0 Non/unknown Pathogen PerezBrocal2015 1
Paracoccus denitrificans Proteobacteria AER 36 7.6 Non/unknown Pathogen Hu2019 1
Paracoccus yeei Proteobacteria AER Opportunistic Pathogen McLaughlin2010, RajilicStojanovic2014, Lagier2016 3
Paraeggerthella hongkongensis Actinobacteria SANA Possible Pathogen RajilicStojanovic2014 1
Paramuribaculum intestinale Bacteroidetes SANA Non/unknown Pathogen Byrd2020 1
Pararheinheimera texasensis Proteobacteria AER 30-37 Non/unknown Pathogen Forster2019 1
Parascardovia denticolens Actinobacteria ANA 37-39 6.7-7.3 Rare Opportunist Byrd2020, New2022, Hu2019, Zeller2014, Vachida2019 5 In 6% of Europeans (unseenbio.com). Rare coloniser. Found in human breast milk (Jeurink2013).
Parasporobacterium paucivorans Firmicutes SANA 34-37 6.5-7.0 Non/unknown Pathogen Nam2008a, RajilicStojanovic2014, Byrd2020, De2020 4
Parasutterella secunda Proteobacteria SANA Non/unknown Pathogen RajilicStojanovic2014, Lagier2016, Yang2020, Jeong2021 4
Paratractidigestivibacter faecalis Actinobacteria SANA 37 7 Non/unknown Pathogen 0
Parolsenella catena Actinobacteria SANA 37 7.0 Non/unknown Pathogen New2022 1
Parolsenella massiliensis Actinobacteria ANA 37 Non/unknown Pathogen Byrd2020, De2020, New2022 3
Parvibacter caecicola Actinobacteria SANA 25-37 Non/unknown Pathogen 0
Pasteurella aerogenes Proteobacteria FANA Non/unknown Pathogen 0
Pasteurella dagmatis Proteobacteria ANA Opportunistic Pathogen Lagier2016 1
Pasteurella multocida Proteobacteria AER 36-42 Known Pathogen Lagier2016, De2020, New2022, Zeller2014 4
Pauljensenia cellulosilytica Actinobacteria AER Byrd2020 1 Isolation and characterisation not yet published.
Pauljensenia hongkongensis Actinobacteria SANA Opportunistic Pathogen Byrd2020, New2022 2
Pauljensenia odontolyticus Actinobacteria AER Byrd2020, Chen2020 2 Isolation and characterisation not yet published.
Pauljensenia turicensis Actinobacteria None Byrd2020 1 Isolation and characterisation not yet published.
Pediococcus acidilactici Firmicutes FANA Opportunistic Pathogen Dubourg2013, Tyakht2013, RajilicStojanovic2014, Lagier2016, Almeida2019, Forster2019, Byrd2020, Dubinkina2017, Zeller2014, Vachida2019 10 In 1% of Europeans (unseenbio.com). Rare coloniser. A probiotic.
Pediococcus claussenii Firmicutes None Non/unknown Pathogen 0
Pedomicrobium ferrugineum Proteobacteria AER 29-30 9.0 Non/unknown Pathogen Bik2006, RajilicStojanovic2014 2
Pelistega indica Proteobacteria AER 30-35 8 Non/unknown Pathogen Lagier2016 1
Pelobacter propionicus Proteobacteria SANA 33 7.0-8.0 Non/unknown Pathogen Zeller2014 1 Produces butyrate, but only from butanol.
Pelomonas aquatica Proteobacteria None Non/unknown Pathogen Yang2020 1
Pelomonas puraquae Proteobacteria None Non/unknown Pathogen Yang2020 1
Pelomonas saccharophila Proteobacteria AER 25-32 Non/unknown Pathogen RajilicStojanovic2014 1
Peptococcus niger Firmicutes SANA 37 Opportunistic Pathogen Woodmansey2004, Walker2011, RajilicStojanovic2014, Salonen2014, Lagier2016, Byrd2020 6
Peptoniphilus catoniae Firmicutes SANA 37 6.5 Non/unknown Pathogen 0
Peptoniphilus colimassiliensis Firmicutes SANA 37 Non/unknown Pathogen 0
Peptoniphilus duerdenii Firmicutes SANA Rare Opportunist Byrd2020, Yang2020, Zeller2014, Vachida2019 4
Peptoniphilus gorbachii Firmicutes SANA Opportunistic Infection deGoffau2013, Lagier2016 2
Peptoniphilus grossensis Firmicutes SANA 37 Non/unknown Pathogen Pfleiderer2013, RajilicStojanovic2014, Lagier2016, Byrd2020 4
Peptoniphilus indolicus Firmicutes SANA Opportunistic Pathogen Benno1984, RajilicStojanovic2014, Byrd2020 3
Peptoniphilus ivorii Firmicutes SANA Opportunistic Pathogen New2022 1 Carbohydrates are not fermented.
Peptoniphilus koenoeneniae Firmicutes SANA Rare Opportunist Lagier2016 1
Peptoniphilus obesi Firmicutes SANA 37 Non/unknown Pathogen Lagier2016, Forster2019 2
Peptoniphilus pacaensis Firmicutes SANA 37 Non/unknown Pathogen Lagier2016 1
Peptoniphilus phoceensis Firmicutes ANA 37 Non/unknown Pathogen Lagier2016, Byrd2020 2
Peptoniphilus senegalensis Firmicutes SANA 37 Non/unknown Pathogen RajilicStojanovic2014, Lagier2016, Forster2019, Byrd2020 4
Peptoniphilus timonensis Firmicutes SANA 37 Non/unknown Pathogen Pfleiderer2013, RajilicStojanovic2014, Lagier2016, Forster2019 4
Peptostreptococcus russellii Firmicutes SANA 37 Non/unknown Pathogen Lagier2016, Byrd2020 2
Peribacillus simplex Firmicutes AER Rare Opportunist Hoyles2012, Pfleiderer2013, RajilicStojanovic2014, Lagier2016, Forster2019, Yang2020 6
Petrimonas sulfuriphila Bacteroidetes SANA 37-40 Non/unknown Pathogen Lagier2016 1 Reduces elemental sulfur.
Petrobacter succinatimandens Proteobacteria SAER 55 6.9 Non/unknown Pathogen PerezBrocal2015 1
Phenylobacterium haematophilum Proteobacteria None 37 Rare Opportunist RajilicStojanovic2014 1
Phocaeicola paurosaccharolyticus Bacteroidetes SANA 35 7.7 Non/unknown Pathogen Byrd2020, De2020, Urban2020 3
Phoenicibacter congonensis Actinobacteria SANA 37 Non/unknown Pathogen New2022 1
Phyllobacterium myrsinacearum Proteobacteria AER 28-34 Non/unknown Pathogen RajilicStojanovic2014, Yang2020 2
Pigmentiphaga kullae Proteobacteria AER Non/unknown Pathogen 0
Plesiomonas shigelloides Proteobacteria FANA Opportunistic Pathogen RajilicStojanovic2014, Lagier2016, Byrd2020, Yang2020, Hu2019, PerezBrocal2015 6
Pluralibacter gergoviae Proteobacteria FANA 30 Opportunistic Pathogen Byrd2020 1 In 6% of Europeans (unseenbio.com). Rare coloniser.
Pontibacillus litoralis Firmicutes FANA 35 7.5 Non/unknown Pathogen Byrd2020 1
Porphyromonas bennonis Bacteroidetes SANA 37 Opportunistic Pathogen Lagier2016, Byrd2020, Yang2020, Chen2020, Hu2019, Vachida2019 6
Porphyromonas canoris Bacteroidetes SANA Non/unknown Pathogen Byrd2020 1
Porphyromonas levii Bacteroidetes SANA 35-37 Non/unknown Pathogen Byrd2020 1
Porphyromonas macacae Bacteroidetes ANA Opportunistic Pathogen Byrd2020 1
Pragia fontium Proteobacteria FANA 22–37 Non/unknown Pathogen 0
Prevotella albensis Bacteroidetes ANA Opportunistic Pathogen RajilicStojanovic2014, Lagier2016, Byrd2020 3
Prevotella amnii Bacteroidetes ANA Opportunistic Infection RajilicStojanovic2014, Byrd2020, Jeong2021, Zeller2014, Vachida2019 5
Prevotella aurantiaca Bacteroidetes SANA Opportunistic Infection Urban2020 1
Prevotella baroniae Bacteroidetes SANA Opportunistic Pathogen Forster2019, Byrd2020, Yang2020, Vachida2019 4
Prevotella bryantii Bacteroidetes ANA Opportunistic Pathogen RajilicStojanovic2014, Byrd2020, Dubinkina2017, Zeller2014, Urban2020 5
Prevotella conceptionensis Bacteroidetes ANA Rare Opportunist RajilicStojanovic2014, Lagier2016, Byrd2020, Urban2020 4
Prevotella dentasini Bacteroidetes SANA Non/unknown Pathogen Byrd2020 1
Prevotella enoeca Bacteroidetes ANA Opportunistic Infection Woodmansey2004, RajilicStojanovic2014, Lagier2016, Byrd2020, De2020, New2022 6
Prevotella falsenii Bacteroidetes None Byrd2020 1 Isolation and characterisation not yet published.
Prevotella histicola Bacteroidetes SANA Non/unknown Pathogen Byrd2020, Vachida2019 2
Prevotella ihumii Bacteroidetes SANA 37 Non/unknown Pathogen Byrd2020, Urban2020 2
Prevotella jejuni Bacteroidetes SANA 37 6-7 Non/unknown Pathogen Lagier2016, Byrd2020, New2022, Urban2020 4
Prevotella loescheii Bacteroidetes SANA Opportunistic Pathogen Woodmansey2004, RajilicStojanovic2014, Lagier2016, Byrd2020 4
Prevotella maculosa Bacteroidetes SANA Possible Pathogen Byrd2020, Urban2020 2
Prevotella marseillensis Bacteroidetes ANA 37 7.5 Non/unknown Pathogen 0
Prevotella marshii Bacteroidetes SANA Opportunistic Pathogen Byrd2020, De2020, Zeller2014 3
Prevotella merdae Bacteroidetes ANA Non/unknown Pathogen 0
Prevotella micans Bacteroidetes SANA Opportunistic Infection Forster2019, De2020 2
Prevotella multiformis Bacteroidetes SANA Non/unknown Pathogen Byrd2020, Zeller2014, Vachida2019 3
Prevotella nanceiensis Bacteroidetes SANA Possible Pathogen RajilicStojanovic2014, Lagier2016, Byrd2020, Vachida2019 4
Prevotella oulorum Bacteroidetes SANA Non/unknown Pathogen Bik2006, Zupancic2012, RajilicStojanovic2014, Byrd2020, Vachida2019 5
Prevotella pallens Bacteroidetes SANA Opportunistic Pathogen Bik2006, RajilicStojanovic2014, Lagier2016, Byrd2020, Zeller2014, Vachida2019 6
Prevotella paludivivens Bacteroidetes SANA 30 5.7-6.7 Non/unknown Pathogen Byrd2020 1 Haemin significantly stimulates growth. Growth at 37C is delayed compared with that at 30C.
Prevotella phocaeensis Bacteroidetes SANA Non/unknown Pathogen Urban2020 1
Prevotella pleuritidis Bacteroidetes SANA Opportunistic Infection Vachida2019 1
Prevotella rara Bacteroidetes SANA 37 7-8 Non/unknown Pathogen 0
Prevotella rectalis Bacteroidetes SANA 37 Non/unknown Pathogen 0
Prevotella saccharolytica Bacteroidetes SANA 35 7 Non/unknown Pathogen Byrd2020, Urban2020 2
Prevotella salivae Bacteroidetes SANA 37 7-7.3 Opportunistic Infection Tyakht2013, Lagier2016, Forster2019, Byrd2020, Zeller2014, Vachida2019 6 Homoacetogen.
Prevotella seregens Bacteroidetes None Byrd2020 1 Is 'Prevotella seregens' actually Hallella seregens (Moore and Moore)? No record of Prevotella seregens published.
Prevotella shahii Bacteroidetes ANA Non/unknown Pathogen RajilicStojanovic2014, Byrd2020 2
Priestia flexa Firmicutes SAER Non/unknown Pathogen Pfleiderer2013, RajilicStojanovic2014, Lagier2016, Yang2020 4
Priestia megaterium Firmicutes FANA 30 Opportunistic Pathogen Taylor1985, Pfleiderer2013, RajilicStojanovic2014, Lagier2016, New2022 5 May be able to persist in the gut, albeit in low numbers, by residing in niches close to epithelial cells (Ilinskaya2017).
Prochlorococcus marinus Cyanobacteria AER Non/unknown Pathogen Yang2020 1
Propionibacterium acidifaciens Actinobacteria ANA Opportunistic Infection Lagier2016, Byrd2020, New2022 3
Propionibacterium freudenreichii Actinobacteria ANA Non/unknown Pathogen RajilicStojanovic2014, Lagier2016, Forster2019, Byrd2020, Zeller2014 5
Propionimicrobium lymphophilum Actinobacteria ANA Known Pathogen Lagier2016, Forster2019 2
Prosthecobacter fluviatilis Verrucomicrobia AER 30 6.5-7.0 Non/unknown Pathogen McLaughlin2010, RajilicStojanovic2014 2
Proteus penneri Proteobacteria FANA 37 Known Pathogen Tyakht2013, RajilicStojanovic2014, Lagier2016, Vachida2019 4
Proteus vulgaris Proteobacteria FANA 40 Opportunistic Pathogen Woodmansey2004, RajilicStojanovic2014, Lagier2016, Byrd2020 4
Providencia heimbachae Proteobacteria FANA 37 Possible Pathogen Lagier2016 1
Providencia rustigianii Proteobacteria FANA 37 Rare Opportunist Tyakht2013, RajilicStojanovic2014, Lagier2016, Forster2019 4
Providencia stuartii Proteobacteria FANA Opportunistic Pathogen Woodmansey2004, Tyakht2013, RajilicStojanovic2014, Lagier2016 4
Pseudarthrobacter oxydans Actinobacteria AER Possible Pathogen RajilicStojanovic2014, Lagier2016 2
Pseudescherichia vulneris Proteobacteria FANA Opportunistic Pathogen Byrd2020 1
Pseudobutyrivibrio ruminis Firmicutes SANA 39 Non/unknown Pathogen 0
Pseudochrobactrum asaccharolyticum Proteobacteria FANA Opportunistic Infection Lagier2016 1
Pseudochrobactrum saccharolyticum Proteobacteria AER Non/unknown Pathogen Yang2020 1
Pseudocitrobacter anthropi Proteobacteria FANA Non/unknown Pathogen Lagier2016, Yang2020 2
Pseudocitrobacter faecalis Proteobacteria FANA Non/unknown Pathogen Lagier2016 1
Pseudoclavibacter alba Actinobacteria AER 30 Opportunistic Pathogen Lagier2016 1
Pseudoclavibacter sp. Timone Actinobacteria AER Possible Pathogen RajilicStojanovic2014, Lagier2016 2
Pseudoglutamicibacter albus Actinobacteria AER Rare Opportunist RajilicStojanovic2014, Lagier2016 2
Pseudomonas aeruginosa Proteobacteria AER Opportunistic Pathogen Finegold1977, Benno1984, Taylor1985, Benno1986, Benno1989, MacFarlane2004, Woodmansey2004, RajilicStojanovic2014, Lagier2016, Almeida2019, Forster2019, Byrd2020, New2022, Zeller2014, Vachida2019 15 In 7% of Europeans (unseenbio.com). Rare coloniser.
Pseudomonas alcaliphila Proteobacteria AER Non/unknown Pathogen RajilicStojanovic2014 1
Pseudomonas asiatica Proteobacteria AER 30 Non/unknown Pathogen 0
Pseudomonas citronellolis Proteobacteria AER 31 Possible Pathogen 0 In 1% of Europeans (unseenbio.com). Rare coloniser.
Pseudomonas fragi Proteobacteria AER 30 Non/unknown Pathogen Lagier2016, Byrd2020, Yang2020, Vachida2019 4 In 9% of Europeans (unseenbio.com). Rare coloniser.
Pseudomonas fulva Proteobacteria AER Possible Pathogen Lagier2016, Zeller2014 2
Pseudomonas mendocina Proteobacteria AER 35 Opportunistic Pathogen McLaughlin2010, Zeller2014 2
Pseudomonas putida Biovar A Proteobacteria AER 25-30 Opportunistic Pathogen Wang2005, Frank2007, RajilicStojanovic2014, Lagier2016, Zeller2014 5 In 4% of Europeans (unseenbio.com). Rare coloniser.
Pseudomonas putida Biovar B Proteobacteria AER 25-30 Opportunistic Pathogen Wang2005, Frank2007, RajilicStojanovic2014, Lagier2016 4 In 4% of Europeans (unseenbio.com). Rare coloniser.
Pseudomonas saudiphocaensis Proteobacteria AER Non/unknown Pathogen Lagier2016 1
Pseudomonas veronii Proteobacteria AER Non/unknown Pathogen PerezBrocal2015 1
Pseudoprevotella muciniphila Bacteroidetes SANA 39 7.5 Non/unknown Pathogen New2022 1 Mucin-degrading bacterium
Pseudopropionibacterium massiliense Actinobacteria ANA 37 Non/unknown Pathogen 0
Pseudoramibacter alactolyticus Firmicutes SANA 35-37 6.0-8.0 Opportunistic Pathogen Benno1986, RajilicStojanovic2014, Lagier2016, Byrd2020, Zeller2014, Vachida2019 6
Pseudoruegeria marinistellae Proteobacteria FANA 25-30 7.0-8.0 Non/unknown Pathogen De2020 1
Pseudoruminococcus massiliensis Firmicutes SANA 37 6.5-7 Non/unknown Pathogen 0
Pseudoxanthomonas mexicana Proteobacteria AER 30-37 Non/unknown Pathogen McLaughlin2010, Walker2011, RajilicStojanovic2014 3
Pseudoxanthomonas spadix Proteobacteria AER Non/unknown Pathogen Zeller2014 1
Pseudoxanthomonas suwonensis Proteobacteria AER 30 Non/unknown Pathogen Zeller2014 1
Pseudoxanthomonas taiwanensis Proteobacteria AER 50 8.0 Non/unknown Pathogen PerezBrocal2015 1
Psychrobacter fulvigenes Proteobacteria AER 25-28 Non/unknown Pathogen 0
Psychrobacter phenylpyruvicus Proteobacteria AER Opportunistic Infection Lagier2016 1
Pusillimonas faecalis Firmicutes SANA Non/unknown Pathogen 0
Ralstonia mannitolilytica Proteobacteria AER Opportunistic Pathogen RajilicStojanovic2014 1
Ralstonia pickettii Biovar Va-1&2 Proteobacteria AER Opportunistic Pathogen McLaughlin2010, Forster2019, Yang2020, Zeller2014, Vachida2019 5 Biovars Va-1 and Va-2 combined.
Raoultella planticola Proteobacteria FANA Opportunistic Pathogen RajilicStojanovic2014, Lagier2016, Byrd2020, Wang2020a 4
Raoultella terrigena Proteobacteria FANA Opportunistic Pathogen RajilicStojanovic2014, Lagier2016, Byrd2020 3
Raoultibacter massiliensis Actinobacteria Micr 37 Non/unknown Pathogen Lagier2016, Byrd2020 2
Raoultibacter timonensis Actinobacteria Micr 37 Non/unknown Pathogen Byrd2020, De2020 2
Rhodococcus erythropolis Actinobacteria AER 30 Opportunistic Pathogen Walker2011, RajilicStojanovic2014, Lagier2016, Zeller2014 4
Rhodococcus hoagii Actinobacteria AER Opportunistic Pathogen Taylor1985, RajilicStojanovic2014, Lagier2016, Zeller2014 4
Rhodococcus rhodochrous Actinobacteria AER Opportunistic Infection RajilicStojanovic2014, Lagier2016 2
Riemerella columbina Bacteroidetes AER Possible Pathogen Forster2019 1
Rikenella microfusus Bacteroidetes SANA 37 Non/unknown Pathogen Byrd2020, Minerbi2019 2
Risungbinella massiliensis Firmicutes AER 37 7.0 Non/unknown Pathogen Lagier2016 1
Robertmurraya kyonggiensis Firmicutes FANA 30-37 8-9 Non/unknown Pathogen Lagier2016 1
Robertmurraya massiliosenegalensis Firmicutes AER 30 Non/unknown Pathogen RajilicStojanovic2014, Lagier2016, Forster2019 3
Robinsoniella peoriensis Firmicutes SANA Opportunistic Pathogen RajilicStojanovic2014, Lagier2016, Byrd2020, PerezBrocal2015 4
Romboutsia hominis Firmicutes SANA Non/unknown Pathogen New2022 1
Romboutsia ilealis Firmicutes SANA 37 7.0-7.5 Non/unknown Pathogen Yang2020, New2022, Wang2020a 3
Romboutsia maritimum Firmicutes SANA Non/unknown Pathogen Byrd2020 1 Full characterisation of this organism hasn't been published.
Romboutsia weinsteinii Firmicutes SANA Non/unknown Pathogen Byrd2020 1 Characterisation not yet published.
Roseomonas gilardii Proteobacteria FANA Known Pathogen Lagier2016 1
Roseomonas mucosa Proteobacteria AER Possible Pathogen RajilicStojanovic2014, Lagier2016, PerezBrocal2015 3
Rossellomorea marisflavi Firmicutes AER 30-37 6.0-8.0 Non/unknown Pathogen Pfleiderer2013, RajilicStojanovic2014, Lagier2016 3
Rossellomorea vietnamensis Firmicutes AER 30-40 Non/unknown Pathogen Lagier2016 1
Rothia koreensis Actinobacteria AER 30-37 5-6 Non/unknown Pathogen Lagier2016 1
Rothia kristinae Actinobacteria FANA Opportunistic Pathogen RajilicStojanovic2014, Lagier2016, Byrd2020 3
Rothia terrae Actinobacteria FANA 35 7.0-8.0 Non/unknown Pathogen Lagier2016 1
Rubeoparvulum massiliense Firmicutes FANA 37 Non/unknown Pathogen Lagier2016 1
Ruminiclostridium cellobioparum Firmicutes SANA 30-37 7.0-7.5 Non/unknown Pathogen Benno1989, RajilicStojanovic2014, Lagier2016 3
Ruminiclostridium josui Firmicutes SANA 45 7.0 Non/unknown Pathogen McLaughlin2010, Byrd2020 2 Strongly degrades and consumes cellulose.
Ruminococcus phoceensis Firmicutes ANA Non/unknown Pathogen 0
Rummeliibacillus stabekisii Firmicutes AER 28-32 Non/unknown Pathogen Lagier2016, New2022 2
Rummeliibacillus suwonensis Firmicutes FANA 37-45 6.5-8.0 Non/unknown Pathogen Lagier2016 1
Ruoffia tabacinasalis Firmicutes FANA Non/unknown Pathogen Pfleiderer2013, RajilicStojanovic2014, Lagier2016, Yang2020 4
Salinivibrio costicola Proteobacteria FANA 37 7.5 Non/unknown Pathogen Lagier2016 1
Salmonella bongori Proteobacteria FANA Opportunistic Pathogen Lagier2016, Byrd2020, Zeller2014 3
Salmonella enterica subsp. enterica serovar Enteritidis Proteobacteria FANA Known Pathogen Lagier2016 1
Salmonella enterica subsp. enterica serovar Paratyphi A Proteobacteria FANA Known Pathogen Tyakht2013, Lagier2016 2
Salmonella enterica subsp. enterica serovar Typhi Proteobacteria FANA Dangerous Pathogen Tyakht2013, Lagier2016 2
Salmonella enterica subsp. enterica serovar Typhimurium Proteobacteria FANA Known Pathogen Tyakht2013, Lagier2016, Dubinkina2017 3
Sanguibacter massiliensis Actinobacteria SANA Non/unknown Pathogen 0
Sarcina maxima Firmicutes ANA 30-35 Non/unknown Pathogen RajilicStojanovic2014 1
Scardovia inopinata Actinobacteria ANA 39-42 6.9-7.4 Opportunistic Infection RajilicStojanovic2014, De2020, New2022, Hu2019, Zeller2014, Vachida2019 6
Schaalia cardiffensis Actinobacteria FANA Opportunistic Pathogen RajilicStojanovic2014, New2022, Vachida2019 3
Schaalia hyovaginalis Actinobacteria FANA Non/unknown Pathogen Cassir2015 1
Schaalia meyeri Actinobacteria ANA 30-37 Opportunistic Pathogen New2022 1
Schaalia radingae Actinobacteria FANA Opportunistic Pathogen RajilicStojanovic2014, Lagier2016, Forster2019 3
Schaalia turicensis Actinobacteria FANA Opportunistic Pathogen RajilicStojanovic2014, Lagier2016, Hu2019, Vachida2019 4
Sediminibacillus massiliensis Firmicutes None Non/unknown Pathogen 0
Selenomonas artemidis Firmicutes SANA 37 Opportunistic Infection Zeller2014 1
Selenomonas bovis Firmicutes SANA 39 7.0-7.2 Non/unknown Pathogen Byrd2020, Vachida2019 2
Selenomonas flueggei Firmicutes SANA 37-45 Opportunistic Infection Zeller2014, Vachida2019 2
Selenomonas infelix Firmicutes SANA 37-45 Opportunistic Infection Vachida2019 1
Selenomonas noxia Firmicutes SANA 30-37 Opportunistic Pathogen De2020, Yang2020, Zeller2014, Vachida2019 4
Selenomonas sputigena Firmicutes SANA 35-40 Possible Pathogen Lagier2016, De2020, New2022, Zeller2014, Vachida2019 5
Senegalia massiliensis Firmicutes Micr 37 Non/unknown Pathogen Lagier2016 1
Senegalimassilia faecalis Actinobacteria SANA 37 7.0 Non/unknown Pathogen 0
Serratia ficaria Proteobacteria FANA Non/unknown Pathogen RajilicStojanovic2014 1
Serratia fonticola Proteobacteria FANA Opportunistic Pathogen Woodmansey2004, RajilicStojanovic2014, Lagier2016 3
Serratia liquefaciens Proteobacteria FANA Opportunistic Pathogen RajilicStojanovic2014, Lagier2016, Byrd2020, Vachida2019 4
Serratia odorifera Proteobacteria FANA Opportunistic Pathogen Zeller2014 1 Differences in enzyme activities between published reports are labelled 'vr' and might represent strain variability.
Serratia quinivorans Proteobacteria FANA Opportunistic Infection Yang2020 1
Serratia ureilytica Proteobacteria FANA Non/unknown Pathogen Lagier2016, Byrd2020 2
Sharpea azabuensis Firmicutes SANA 37 Non/unknown Pathogen Byrd2020 1
Shewanella carassii Proteobacteria FANA 35 Non/unknown Pathogen 0
Shewanella decolorationis Proteobacteria FANA 20-30 8.0 Non/unknown Pathogen Byrd2020 1 A dye-decolourising bacterium. Reduces Fe(III) to Fe(II) using lactate as an electron donor.
Shewanella xiamenensis Proteobacteria FANA 7.0 Non/unknown Pathogen Lagier2016 1 Reduces Fe(III) to Fe(II) using lactate as an electron donor.
Shigella boydii Proteobacteria FANA Known Pathogen Lagier2016, New2022 2
Shuttleworthia satelles Firmicutes SANA Non/unknown Pathogen Byrd2020, Zeller2014, Vachida2019 3
Slackia equolifaciens Actinobacteria SANA Non/unknown Pathogen RajilicStojanovic2014, Lagier2016 2
Slackia exigua Actinobacteria SANA Opportunistic Pathogen RajilicStojanovic2014, Lagier2016, Byrd2020, Zeller2014, Vachida2019 5
Slackia faecicanis Actinobacteria SANA Non/unknown Pathogen 0
Slackia heliotrinireducens Actinobacteria SANA 40 6.5-7.0 Non/unknown Pathogen Byrd2020, De2020, New2022, Zeller2014, Qin2012 5
Slackia isoflavoniconvertens Actinobacteria SANA Non/unknown Pathogen RajilicStojanovic2014, Lagier2016 2 Produces equol (an isoflavandiol aestrogen) from daidzein.
Sneathia sanguinegens Fusobacteria ANA 35-37 Opportunistic Pathogen Aujoulat2014, Byrd2020, Yang2020 3
Sneathia vaginalis Fusobacteria ANA Possible Pathogen Byrd2020 1 Sneathia vaginalis same as 'Sneathia amnii'. Simple metabolism, utilising glycogen, maltose and glucose.
Sodaliphilus pleomorphus Bacteroidetes SANA Non/unknown Pathogen New2022 1 Probably uses fructan and amylose.
Soleaferrea massiliensis Firmicutes FANA 37 Non/unknown Pathogen Pfleiderer2013, RajilicStojanovic2014, Lagier2016, Byrd2020 4
Solibaculum mannosilyticum Firmicutes ANA 37 7.0 Non/unknown Pathogen 0
Sorangium cellulosum Proteobacteria None Non/unknown Pathogen New2022, Zeller2014 2 Produces sporangioles and myxospores. Metabolites include epothilone, soraphen, sorangicin, and tartrolon.
Sphingobacterium faecium Bacteroidetes AER Non/unknown Pathogen 0
Sphingobacterium multivorum Bacteroidetes AER Opportunistic Pathogen RajilicStojanovic2014, Lagier2016 2
Sphingobacterium siyangense Bacteroidetes SAER 30-37 6.0-8.0 Non/unknown Pathogen 0
Sphingobacterium spiritivorum Bacteroidetes FANA Opportunistic Pathogen Qin2012 1
Sphingomonas azotifigens Proteobacteria AER 25-37 Non/unknown Pathogen PerezBrocal2015 1
Sphingomonas hankookensis Proteobacteria FANA 7.0 Non/unknown Pathogen Yang2020 1
Sphingomonas melonis Proteobacteria AER Non/unknown Pathogen Yang2020 1
Sphingomonas panni Proteobacteria Micr Non/unknown Pathogen McLaughlin2010, RajilicStojanovic2014 2
Sphingomonas paucimobilis Proteobacteria AER Opportunistic Pathogen McLaughlin2010, RajilicStojanovic2014, Lagier2016, Byrd2020 4
Sphingomonas pseudosanguinis Proteobacteria AER Non/unknown Pathogen RajilicStojanovic2014, Lagier2016, Yang2020 3
Sphingomonas yabuuchiae Proteobacteria AER Non/unknown Pathogen PerezBrocal2015 1
Spirochaeta coccoides Spirochaetes ANA 30 7.4 Non/unknown Pathogen Qin2012 1
Sporobacter termitidis Firmicutes SANA 32-35 6.7-7.2 Non/unknown Pathogen Salonen2014, Byrd2020 2 Produces methanethiol.
Sporolactobacillus nakayamae subsp. racemicus Firmicutes FANA Non/unknown Pathogen 0
Sporosarcina luteola Firmicutes FANA 25-30 7.0 Non/unknown Pathogen Lagier2016 1
Staphylococcus arlettae Firmicutes FANA Non/unknown Pathogen RajilicStojanovic2014, Lagier2016 2
Staphylococcus auricularis Firmicutes FANA 30-40 Non/unknown Pathogen RajilicStojanovic2014, Lagier2016 2
Staphylococcus capitis subsp. capitis Firmicutes FANA 30-40 Rare Opportunist Dubourg2013, Pfleiderer2013, RajilicStojanovic2014, Lagier2016, Yang2020, Zeller2014 6 Found in human breast milk (Jeurink2013).
Staphylococcus caprae Firmicutes FANA Opportunistic Pathogen Pfleiderer2013, RajilicStojanovic2014, Lagier2016 3
Staphylococcus carnosus Firmicutes FANA Non/unknown Pathogen Lagier2016, Byrd2020, Zeller2014 3
Staphylococcus cohnii subsp. cohnii Firmicutes FANA Opportunistic Infection Dubourg2013, Pfleiderer2013, Aujoulat2014, RajilicStojanovic2014, Lagier2016, Yang2020 6
Staphylococcus condimenti Firmicutes FANA Non/unknown Pathogen RajilicStojanovic2014, Lagier2016 2
Staphylococcus devriesei Firmicutes FANA 35 Non/unknown Pathogen Lagier2016 1
Staphylococcus equorum subsp. equorum Firmicutes AER 30 Non/unknown Pathogen RajilicStojanovic2014, Lagier2016, Byrd2020, PerezBrocal2015 4
Staphylococcus gallinarum Firmicutes FANA Non/unknown Pathogen Lagier2016, Yang2020 2
Staphylococcus hyicus Firmicutes FANA Possible Pathogen Lagier2016 1
Staphylococcus intermedius Firmicutes FANA 30-40 Possible Pathogen Taylor1985, Dubourg2013, RajilicStojanovic2014, Lagier2016 4
Staphylococcus kloosii Firmicutes AER Non/unknown Pathogen MacFarlane2004, Woodmansey2004, RajilicStojanovic2014, Lagier2016 4
Staphylococcus lugdunensis Firmicutes FANA Opportunistic Pathogen RajilicStojanovic2014, Lagier2016, Almeida2019 3
Staphylococcus nepalensis Firmicutes FANA 30 Opportunistic Pathogen Lagier2016, Forster2019 2
Staphylococcus petrasii Firmicutes FANA Opportunistic Pathogen Lagier2016, Byrd2020 2
Staphylococcus pettenkoferi Firmicutes FANA Possible Pathogen RajilicStojanovic2014, Lagier2016, Yang2020 3
Staphylococcus pseudintermedius Firmicutes FANA Opportunistic Pathogen Forster2019, Byrd2020 2
Staphylococcus saccharolyticus Firmicutes ANA 30-37 Opportunistic Pathogen Benno1984, RajilicStojanovic2014, Lagier2016 3
Staphylococcus saprophyticus subsp. saprophyticus Firmicutes FANA 28-35 Known Pathogen Pfleiderer2013, Cassir2015, Byrd2020, Yang2020, Dubinkina2017, Zeller2014 6
Staphylococcus schleiferi subsp. schleiferi Firmicutes FANA Opportunistic Pathogen RajilicStojanovic2014, Lagier2016, Byrd2020 3
Staphylococcus simiae Firmicutes FANA Non/unknown Pathogen Cassir2015 1
Staphylococcus simulans Firmicutes FANA 25-40 Opportunistic Pathogen MacFarlane2004, Woodmansey2004, RajilicStojanovic2014, Lagier2016, De2020 5
Staphylococcus xylosus Firmicutes FANA 25-35 Known Pathogen RajilicStojanovic2014, Cassir2015, Lagier2016, Forster2019, Byrd2020 5
Stenotrophomonas rhizophila Proteobacteria AER Non/unknown Pathogen RajilicStojanovic2014, Lagier2016, Yang2020 3 Show antifungal activity against C. albicans, Rhizoctonia solani, Sclerotinia sclerotiiorum and Verticillium dahliae. Produces trehalose and glucosylglycerol as osmolytes.
Streptobacillus hongkongensis Fusobacteria FANA 35-37 Opportunistic Pathogen De2020 1
Streptococcus alactolyticus Firmicutes FANA Non/unknown Pathogen RajilicStojanovic2014, Lagier2016, PerezBrocal2015 3
Streptococcus anginosus subsp. whileyi Firmicutes FANA Opportunistic Pathogen Zou2019 1
Streptococcus caballi Firmicutes FANA 35 7.3-7.4 Non/unknown Pathogen Forster2019 1 Homoacetogen.
Streptococcus castoreus Firmicutes FANA 37 Opportunistic Infection Lagier2016, Forster2019 2
Streptococcus danieliae Firmicutes FANA 37 Non/unknown Pathogen De2020 1
Streptococcus didelphis Firmicutes FANA Opportunistic Pathogen Forster2019, De2020 2 Initial catalase activity is lost in subsequent cultures.
Streptococcus downei Firmicutes FANA Non/unknown Pathogen Yang2020, Zeller2014, Vachida2019 3
Streptococcus dysgalactiae Firmicutes FANA 37 Opportunistic Pathogen RajilicStojanovic2014, Lagier2016, Byrd2020, New2022, Zeller2014, Vachida2019 6
Streptococcus equi subsp. equi Firmicutes FANA 37 Known Pathogen RajilicStojanovic2014, Byrd2020, De2020, New2022 4
Streptococcus ferus Firmicutes FANA 37-42 Non/unknown Pathogen De2020 1
Streptococcus henryi Firmicutes FANA Non/unknown Pathogen Forster2019 1
Streptococcus hyovaginalis Firmicutes FANA 37 Non/unknown Pathogen Forster2019, Byrd2020 2
Streptococcus lactarius Firmicutes FANA Non/unknown Pathogen 0 Found in human breast milk (Jeurink2013). Probably a rare or transient gut inhabitant but has not been reported to have been isolated from faeces.
Streptococcus macedonicus Firmicutes FANA 37-42 Non/unknown Pathogen Byrd2020, New2022, Hu2019, Vachida2019 4
Streptococcus merionis Firmicutes FANA 37 Non/unknown Pathogen Forster2019 1
Streptococcus oralis subsp. tigurinus Firmicutes FANA 37 Opportunistic Pathogen Lagier2016, Hu2019, Vachida2019 3
Streptococcus orisratti Firmicutes FANA Non/unknown Pathogen Byrd2020 1
Streptococcus ovis Firmicutes FANA Opportunistic Pathogen Forster2019, Byrd2020 2
Streptococcus pantholopis Firmicutes FANA Non/unknown Pathogen De2020 1
Streptococcus parasuis Firmicutes FANA Non/unknown Pathogen De2020 1
Streptococcus parauberis Firmicutes FANA 35-37 Known Pathogen Dubourg2013, RajilicStojanovic2014, Byrd2020, Zeller2014 4
Streptococcus peroris Firmicutes FANA Opportunistic Infection RajilicStojanovic2014, Lagier2016, Yang2020, Dubinkina2017, Zeller2014, Vachida2019 6
Streptococcus plurextorum Firmicutes FANA 37 Possible Pathogen Forster2019 1
Streptococcus porci Firmicutes FANA 37 Possible Pathogen Forster2019 1
Streptococcus pseudoporcinus Firmicutes FANA 37 Opportunistic Pathogen Lagier2016, New2022, Zeller2014 3
Streptococcus rubneri Firmicutes FANA 37 Possible Pathogen Zou2019 1
Streptococcus sinensis Firmicutes FANA 37 Opportunistic Pathogen Byrd2020, De2020 2
Streptococcus suis Firmicutes FANA Opportunistic Pathogen Lagier2016, King2019, Byrd2020, Yang2020, New2022, Zeller2014 6
Streptococcus thoraltensis Firmicutes FANA Non/unknown Pathogen RajilicStojanovic2014, Lagier2016, Forster2019 3
Streptococcus uberis Firmicutes FANA Known Pathogen Finegold1974, RajilicStojanovic2014, Cassir2015, Lagier2016, Byrd2020 5
Streptococcus viridans Firmicutes FANA Non/unknown Pathogen RajilicStojanovic2014, Lagier2016 2
Streptomyces koyangensis Actinobacteria AER Non/unknown Pathogen Lagier2016 1 Produces 4-phenyl-3-butenoic acid, which inhibits several plant-pathogenic fungi.
Streptomyces misionensis Actinobacteria AER Non/unknown Pathogen RajilicStojanovic2014, Lagier2016 2
Streptomyces thermoviolaceus Actinobacteria AER Non/unknown Pathogen Hoyles2012, RajilicStojanovic2014, Lagier2016 3
Subdoligranulum formicile Firmicutes SANA Non/unknown Pathogen 0
Succinivibrio dextrinosolvens Proteobacteria SANA Possible Pathogen RajilicStojanovic2014, Byrd2020, De2020, New2022 4
Sulfurospirillum deleyianum Proteobacteria Micr 7.0-7.1 Non/unknown Pathogen De2020 1 Can reduce elemental sulfur but not sulfate.
Sutterella faecalis Proteobacteria SANA 37 8 Non/unknown Pathogen New2022 1 Asaccharolytic.
Sutterella massiliensis Proteobacteria SANA Non/unknown Pathogen Lagier2016, Minerbi2019 2
Sutterella megalosphaeroides Proteobacteria SANA 37 Non/unknown Pathogen New2022 1
Sutterella seckii Proteobacteria None Non/unknown Pathogen 0
Sutterella stercoricanis Proteobacteria Micr Non/unknown Pathogen McLaughlin2010, Walker2011, RajilicStojanovic2014 3
Sutterella timonensis Proteobacteria SANA Non/unknown Pathogen 0
Syntrophococcus sucromutans Firmicutes SANA 35-42 6.4 Non/unknown Pathogen 0 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)
Syntrophomonas zehnderi Firmicutes FANA 7.0 Non/unknown Pathogen Byrd2020 1 Grows in co-culture with hydrogenophilic archaea. Consumes mainly saturated fatty acids C4:0-C18:0.
Tatumella ptyseos Proteobacteria FANA Possible Pathogen RajilicStojanovic2014, Lagier2016 2
Tepidanaerobacter acetatoxydans Firmicutes ANA Non/unknown Pathogen Byrd2020, New2022 2
Terrahaemophilus aromaticivorans Proteobacteria None Non/unknown Pathogen Walker2011, Chung2019 2
Terribacillus aidingensis Firmicutes None 30-37 6-7 Non/unknown Pathogen Lagier2016 1
Terrisporobacter mayombei Firmicutes SANA 33 7.3 Non/unknown Pathogen Lagier2016, Forster2019, Minerbi2019 3
Terrisporobacter othiniensis Firmicutes ANA Opportunistic Pathogen Byrd2020 1 Full characterisation not yet published.
Terrisporobacter petrolearius Firmicutes SANA 40 7.0-7.5 Non/unknown Pathogen Minerbi2019 1 Uses sulfite as an electron acceptor.
Tessaracoccus massiliensis Actinobacteria FANA 37 Non/unknown Pathogen Lagier2016, Byrd2020 2
Tetragenococcus koreensis Firmicutes FANA 30 9.0 Non/unknown Pathogen Lagier2016 1
Tetragenococcus solitarius Firmicutes FANA 25-30 7.0-8.0 Opportunistic Infection Woodmansey2004, RajilicStojanovic2014, Lagier2016 3
Thauera terpenica Proteobacteria FANA 32 Non/unknown Pathogen Yang2020 1
Thermoanaerobacterium thermosaccharolyticum Firmicutes SANA 55-62 7.8 Non/unknown Pathogen Qin2012 1
Thermophilibacter mediterraneus Actinobacteria SANA Non/unknown Pathogen Byrd2020 1 Full characterisation not yet published.
Thomasclavelia saccharogumia Firmicutes SANA Non/unknown Pathogen RajilicStojanovic2014, Lagier2016, Yang2020, PerezBrocal2015 4
Tidjanibacter massiliensis Bacteroidetes ANA Non/unknown Pathogen Lagier2016 1
Timonella senegalensis Actinobacteria FANA 37 Non/unknown Pathogen RajilicStojanovic2014, Lagier2016, Forster2019 3
Tissierella praeacuta Firmicutes SANA 37 Opportunistic Pathogen Benno1984, Walker2011, RajilicStojanovic2014, Lagier2016, Byrd2020 5
Trabulsiella guamensis Proteobacteria FANA Non/unknown Pathogen RajilicStojanovic2014, Lagier2016, Byrd2020 3
Tractidigestivibacter scatoligenes Actinobacteria SANA Non/unknown Pathogen Zou2019, Byrd2020, Yang2020 3 Produces skatole.
Traorella massiliensis Firmicutes SANA 37 7-8 Non/unknown Pathogen Byrd2020 1
Treponema berlinense Spirochaetes SANA Non/unknown Pathogen RajilicStojanovic2014, De2020 2
Treponema denticola Spirochaetes ANA Possible Pathogen Zeller2014, Vachida2019, Qin2012 3
Treponema pectinovorum Spirochaetes SANA 37 Possible Pathogen De2020 1
Treponema peruense Spirochaetes SANA 37 Non/unknown Pathogen New2022 1
Treponema succinifaciens Spirochaetes SANA 35-39 Non/unknown Pathogen King2019, Yang2020, New2022, Zeller2014, Vachida2019 5
Treponema vincentii Spirochaetes ANA Possible Pathogen Vachida2019 1
Trueperella bernardiae Actinobacteria FANA Opportunistic Pathogen RajilicStojanovic2014, Lagier2016, Byrd2020 3
Trueperella pyogenes Actinobacteria FANA 37 Possible Pathogen RajilicStojanovic2014, Cassir2015, Lagier2016, Byrd2020, New2022 5
Turicimonas muris Proteobacteria FANA Non/unknown Pathogen Byrd2020, New2022, Minerbi2019 3 In 1% of Europeans (unseenbio.com). Rare coloniser.
Ureaplasma parvum Tenericutes FANA 35-37 6.0-7.0 Possible Pathogen RajilicStojanovic2014 1
Ureaplasma urealyticum Tenericutes FANA 35-37 6.0-7.0 Known Pathogen RajilicStojanovic2014, Lagier2016, Zeller2014 3
Ureibacillus massiliensis Firmicutes AER 30-37 Opportunistic Pathogen RajilicStojanovic2014, Lagier2016 2
Urinicoccus timonensis Firmicutes SANA Non/unknown Pathogen 0
Urmitella timonensis Firmicutes ANA Non/unknown Pathogen Lagier2016 1
Uruburuella suis Proteobacteria FANA Opportunistic Pathogen Yang2020 1
Vagococcus carniphilus Firmicutes FANA Non/unknown Pathogen Lagier2016 1
Vagococcus fluvialis Firmicutes FANA Opportunistic Pathogen Lagier2016 1
Vagococcus lutrae Firmicutes FANA Non/unknown Pathogen Lagier2016 1
Vagococcus penaei Firmicutes FANA Non/unknown Pathogen Lagier2016, Zou2019 2
Vagococcus teuberi Firmicutes FANA Non/unknown Pathogen Lagier2016 1
Varibaculum cambriense Actinobacteria SANA Opportunistic Pathogen RajilicStojanovic2014, Lagier2016, Forster2019, Byrd2020, Vachida2019 5
Varibaculum timonense Actinobacteria SANA 37 7.5 Non/unknown Pathogen 0
Variovorax boronicumulans Proteobacteria None 30 7 Non/unknown Pathogen RajilicStojanovic2014 1
Veillonella denticariosi Firmicutes SANA Opportunistic Infection Lagier2016, Byrd2020 2
Veillonella infantium Firmicutes ANA Non/unknown Pathogen Byrd2020 1
Veillonella magna Firmicutes Micr 37-40 Non/unknown Pathogen De2020 1 Putrescine is required for growth.
Veillonella montpellierensis Firmicutes SANA Opportunistic Pathogen Byrd2020 1
Veillonella nakazawae Firmicutes SANA Rare Opportunist New2022 1
Veillonella ratti Firmicutes SANA Non/unknown Pathogen McLaughlin2010, RajilicStojanovic2014, Vachida2019 3
Vescimonas coprocola Firmicutes SANA Non/unknown Pathogen 0
Vescimonas fastidiosa Firmicutes SANA Non/unknown Pathogen 0
Vibrio alginolyticus Proteobacteria FANA Possible Pathogen Lagier2016 1
Vibrio cincinnatiensis Proteobacteria FANA Opportunistic Pathogen Lagier2016, Forster2019 2
Vibrio fluvialis Proteobacteria FANA Opportunistic Pathogen RajilicStojanovic2014, Lagier2016 2 Data combined for biovars I and II, plus other strains.
Vibrio furnissii Proteobacteria FANA Opportunistic Pathogen RajilicStojanovic2014, Lagier2016, Yang2020 3
Vibrio metoecus Proteobacteria FANA Opportunistic Pathogen Lagier2016, De2020 2 Close relative of V. cholerae.
Vibrio metschnikovii Proteobacteria FANA Rare Opportunist Lagier2016 1
Vibrio mimicus Proteobacteria FANA Opportunistic Pathogen RajilicStojanovic2014, Lagier2016, Zeller2014 3
Vibrio natriegens Proteobacteria FANA 7.5 Non/unknown Pathogen Yang2020 1
Vibrio parahaemolyticus Proteobacteria FANA Opportunistic Pathogen RajilicStojanovic2014, Lagier2016, De2020 3
Vibrio proteolyticus Proteobacteria FANA Non/unknown Pathogen De2020 1
Vibrio vulnificus Proteobacteria FANA Known Pathogen Lagier2016 1 Includes all biogroups (1-3). Can cause food poisoning. Colonises the mucus layer at the expense of Phocaeicola vulgatus, killing the latter.
Virgibacillus dakarensis Firmicutes AER Non/unknown Pathogen 0
Virgibacillus dokdonensis Firmicutes FANA 37 7.0-8.0 Non/unknown Pathogen Lagier2016 1
Virgibacillus doumboii Firmicutes SAER 37 Non/unknown Pathogen 0
Virgibacillus halodenitrificans Firmicutes FANA 35-40 7.4-7.5 Non/unknown Pathogen Lagier2016 1
Virgibacillus ihumii Firmicutes SAER 7.5 Non/unknown Pathogen 0 Halophilic
Virgibacillus massiliensis Firmicutes SAER 37 7.5 Non/unknown Pathogen Lagier2016 1
Virgibacillus ndiopensis Firmicutes AER Non/unknown Pathogen 0
Virgibacillus pantothenticus Firmicutes FANA Non/unknown Pathogen Lagier2016 1
Virgibacillus proomii Firmicutes FANA 37 Non/unknown Pathogen Hoyles2012, RajilicStojanovic2014, Lagier2016 3
Vitreoscilla massiliensis Proteobacteria Micr Non/unknown Pathogen Lagier2016, Byrd2020 2
Vitreoscilla stercoraria Proteobacteria AER Non/unknown Pathogen De2020 1
Weeksella virosa Firmicutes AER Opportunistic Pathogen Lagier2016 1
Weizmannia coagulans Firmicutes FANA 40-57 7.0 Opportunistic Infection Zou2019, PerezBrocal2015 2
Winkia neuii Actinobacteria FANA Opportunistic Pathogen Lagier2016, Almeida2019, Forster2019 3
Wolinella succinogenes Proteobacteria ANA Non/unknown Pathogen Tyakht2013 1 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.
Xylanimonas cellulosilytica Actinobacteria FANA 30 7 Non/unknown Pathogen Zeller2014 1
Yersinia aldovae Proteobacteria FANA 28-29 Non/unknown Pathogen 0
Yersinia aleksiciae Proteobacteria FANA Opportunistic Pathogen RajilicStojanovic2014, Lagier2016 2
Yersinia alsatica Proteobacteria FANA Non/unknown Pathogen 0
Yersinia artesiana Proteobacteria FANA Non/unknown Pathogen 0
Yersinia bercovieri Proteobacteria FANA Non/unknown Pathogen RajilicStojanovic2014, Lagier2016, Byrd2020 3
Yersinia frederiksenii Proteobacteria FANA Opportunistic Pathogen RajilicStojanovic2014, Lagier2016, Byrd2020 3
Yersinia intermedia Proteobacteria FANA 22-28 Opportunistic Pathogen Cassir2015, Lagier2016, Byrd2020 3 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)
Yersinia kristensenii subsp. kristensenii Proteobacteria FANA Opportunistic Pathogen RajilicStojanovic2014, Lagier2016 2 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.
Yersinia kristensenii subsp. rochesterensis Proteobacteria FANA 28-29 Non/unknown Pathogen 0
Yersinia massiliensis Proteobacteria FANA Non/unknown Pathogen Byrd2020 1
Yersinia mollaretii Proteobacteria FANA Non/unknown Pathogen Lagier2016 1
Yersinia occitanica Proteobacteria FANA Non/unknown Pathogen 0
Yersinia proxima Proteobacteria FANA Non/unknown Pathogen 0
Yersinia rohdei Proteobacteria FANA 28-29 Opportunistic Infection RajilicStojanovic2014, Lagier2016 2
Yersinia vastinensis Proteobacteria FANA Non/unknown Pathogen 0
Yokenella regensburgei Proteobacteria FANA Possible Pathogen RajilicStojanovic2014, Lagier2016, Dubinkina2017 3