Non-colonising Gut Bacteria

★ There are 134 'non-colonising' bacteria.

Bacteria Phylum O2 Tol Opt Temp Opt pH Pathogenicity Studies Number Studies Notes
Actinobacillus ureae Proteobacteria FANA 37 Opportunistic Infection Lagier2016, Zeller2014 2 Breaks down urea.
Actinomyces canis Actinobacteria FANA Opportunistic Pathogen McLaughlin2010, RajilicStojanovic2014 2
Actinomyces dentalis Actinobacteria SANA Opportunistic Infection Lagier2016, Byrd2020 2 Produces acetic and lactic acids from glucose fermentation.
Actinomyces georgiae Actinobacteria FANA 37 Opportunistic Infection Lagier2012b, RajilicStojanovic2014 2
Actinomyces israelii Actinobacteria ANA Opportunistic Pathogen Lagier2016, Byrd2020 2
Actinosynnema mirum Actinobacteria AER Non/unknown Pathogen Zeller2014 1 Aerobic and inability to grow at 37C suggests this not a gut coloniser.
Aerococcus vaginalis Firmicutes FANA Non/unknown Pathogen De2020 1
Aeromonas eucrenophila Proteobacteria FANA 30 Opportunistic Pathogen Lagier2016 1
Aeromonas schubertii Proteobacteria FANA Opportunistic Infection Lagier2016 1 Mannitol-negative fermentation. Unlikely gut coloniser.
Aeromonas taiwanensis Proteobacteria FANA 30 8.5-9.5 Opportunistic Infection Lagier2016 1
Alkaliphilus oremlandii Firmicutes SANA 37 8.4 Non/unknown Pathogen 0 Able to reduce As(V) and thiosulfate (electron acceptors). No growth at or below pH 7.5 suggests it is not a gut coloniser
Alkaliphilus transvaalensis Firmicutes SANA 40 10 Non/unknown Pathogen PerezBrocal2015 1 Requires high pH (minimum 8.5) suggest it is not a gut coloniser
Alkanindiges illinoisensis Proteobacteria AER Rare Opportunist Lagier2016 1 Only hydrocarbons and Tween surfactants support good growth. Able to degrade squalene.
Ammonifex degensii Firmicutes SANA 70 7.5 Non/unknown Pathogen New2022 1 Cannot grow when temperatures drop below 57C, so likely not a gut coloniser.
Anoxybacillus flavithermus Firmicutes FANA 60 6-9 Non/unknown Pathogen Lagier2016, Zeller2014 2 Weak growth at 37 degrees so unlikely to be a gut coloniser.
Aquincola tertiaricarbonis Proteobacteria SAER 30 6.0-7.0 Non/unknown Pathogen Yang2020 1 Degrades t-butanol, a breakdown product of MTBE. Obligate aerobe, so likely a gut non-coloniser.
Arthrobacter agilis Actinobacteria AER Non/unknown Pathogen Lagier2016 1 Skin commensal but can't grow at 37C. Gut transient.
Arthrobacter parietis Actinobacteria AER 22-30 7-8 Non/unknown Pathogen Lagier2016 1 Doesn't grow well at 37C, so probably a gut transient organism.
Arthrobacter pigmenti Actinobacteria AER 22-30 8-9 Non/unknown Pathogen Lagier2016 1 Doesn't grow well at 37C, so probably a gut non-coloniser.
Azotobacter vinelandii Proteobacteria SAER 20-30 Non/unknown Pathogen Zeller2014 1 Obligate aerobe and low optimum temperature suggest it is not a gut coloniser.
Bacillus anthracis Firmicutes FANA Dangerous Pathogen Zou2019 1 Causative agent of the disease anthrax.
Bacillus baekryungensis Firmicutes AER 8.5-9.5 Non/unknown Pathogen Lagier2016 1 Requires sodium and can withstand 20% salt concentration.
Bacillus methanolicus Firmicutes SAER 55 Non/unknown Pathogen King2019 1 Obligate aerobe and high salt required for optimum growth, so likely a gut non-coloniser.
Bartonella vinsonii Proteobacteria AER Possible Pathogen Lagier2016 1
Bhargavaea cecembensis Firmicutes AER 37 7-7.5 Non/unknown Pathogen Lagier2016 1
Bordetella bronchiseptica Proteobacteria SAER 35-37 Known Pathogen Lagier2016, Zeller2014 2 Few isolates from humans; likely a gut non-coloniser
Bordetella trematum Proteobacteria AER 37 Known Pathogen Pandey2012, Lagier2016 2
Brevibacillus thermoruber Firmicutes SAER 45-48 7.0 Opportunistic Infection 0 Obligate aerobe and high salt required for optimum growth, so likely a gut non-coloniser.
Brevibacterium otitidis Actinobacteria FANA Rare Opportunist Lagier2016 1
Brucella melitensis Proteobacteria AER Dangerous Pathogen Lagier2016 1
Buchnera aphidicola Proteobacteria Non/unknown Pathogen De2020, New2022 2
Caldicellulosiruptor diazotrophicus Firmicutes 70 6.5 Non/unknown Pathogen New2022 1 Optimum growth temperature is 70C, so likely not a gut coloniser.
Caloranaerobacter azorensis Firmicutes ANA 65 7 Non/unknown Pathogen New2022 1 No growth at 37C, so unlikely to be a gut coloniser.
Campylobacter avium Proteobacteria Micr Possible Pathogen De2020 1
Campylobacter sputorum Proteobacteria Micr Opportunistic Pathogen Lagier2016 1
Capnocytophaga gingivalis Bacteroidetes FANA 37 Possible Pathogen Lagier2016 1 Grows better in air by completely respiring glucose
Carnobacterium divergens Firmicutes FANA Non/unknown Pathogen Lagier2016, Byrd2020 2
Carnobacterium mobile Firmicutes FANA Non/unknown Pathogen Lagier2016 1
Cerasibacillus quisquiliarum Firmicutes SAER 50 8-9 Non/unknown Pathogen Lagier2016 1 Doesn't oxidise glucose or most common carbohydrates. Has a very high optimum growth temp (50C), so likely to be a gut non-coloniser.
Chlamydia trachomatis Chlamydiae SANA Known Pathogen Lagier2016 1 C. trachomatis is an obligate intracellular parasite that synthesises and accumulates glycogen. Survives outside the cell by producing infectious and resistant elementary bodies ('EB').
Chloracidobacterium thermophilum Acidobacteria Micr 51 7 Non/unknown Pathogen 0 Cells have chlorosomes used for photosynthesis. High minimum growth temperature suggests it is not a gut coloniser
Chryseobacterium viscerum Bacteroidetes AER 25 Non/unknown Pathogen Byrd2020 1 An aerobe that can't grow at 37C suggests this is a non-coloniser of the gut.
Comamonas aquatica Proteobacteria AER 30-35 Opportunistic Pathogen De2020 1
Coraliomargarita akajimensis Verrucomicrobia SAER Non/unknown Pathogen Qin2012 1 Obligate aerobe and low optimum temperature suggest it is not a gut coloniser.
Corynebacterium diphtheriae Actinobacteria ANA 30-37 Known Pathogen Lagier2016 1
Dehalobacter restrictus Firmicutes SANA 25-30 6.8-7.6 Non/unknown Pathogen Byrd2020, New2022 2 Dechlorinates tetra- and trichlorethane. Non-fermentative. Unlikely gut coloniser.
Deinococcus geothermalis Deinococcus-Thermus AER 47 6.5 Non/unknown Pathogen De2020, New2022 2 High optimum growth temperature so likely not a gut coloniser.
Dermacoccus barathri Actinobacteria AER 28 Non/unknown Pathogen Lagier2016 1 Borderline cold mesophile, with optimum growth temp of 28C. Unlikely gut coloniser.
Desulfovibrio trichonymphae Proteobacteria ANA Non/unknown Pathogen New2022 1 Intracellular mutualist of Trichonympha agilis protist. Suited to H2/SO4 respiration, which prevents the buildup of H2 and subsequent inhibition of the fermentation process in the hindgut.
Desulfurobacterium thermolithotrophum Aquificae ANA 70 6.25 Non/unknown Pathogen Byrd2020, New2022 2 Optimum growth temperature is 70C, so likely not a gut coloniser.
Elizabethkingia miricola Bacteroidetes AER 28-37 Non/unknown Pathogen Lagier2016 1
Flavobacterium caeni Bacteroidetes SAER 20-25 6.5-7.5 Non/unknown Pathogen Byrd2020, De2020 2 Strict aerobe and only grows at 30C, so likely to be a non-coloniser of the gut. Significant descrepancy between some data reported by Fujii2014 and that originally reported by Liu2010a.
Francisella tularensis Proteobacteria Micr 37 Dangerous Pathogen Lagier2016 1 Facultative intracellular parasite. Causes tularemia in humans. Can reach epidemic levels and is transmitted by zoonotic means.
Fredinandcohnia humi Firmicutes FANA 30 7 Non/unknown Pathogen Lagier2016 1
Gemmatimonas groenlandica Gemmatimonadetes AER 20-25 7.3 Non/unknown Pathogen New2022 1 Yeast extract used as a N source. Likely not a gut coloniser because maximum temperature for growth is 32C.
Geodermatophilus obscurus Actinobacteria AER 24-28 Non/unknown Pathogen Zeller2014 1 Aerobic and poor growth at 37C suggests this not a gut coloniser.
Gracilibacillus thailandensis Firmicutes SAER 37 7 Non/unknown Pathogen Lagier2016 1 Obligate aerobe and high salt required for optimum growth, so likely a gut non-coloniser.
Halobacillus karajensis Firmicutes SAER 34-38 7.5-8.5 Non/unknown Pathogen Lagier2016 1 Sodium required for growth. Likely a gut non-coloniser because its optimum growth is with high salt and is an obligate aerobe.
Halomonas muralis Proteobacteria SAER 25-35 Non/unknown Pathogen Cassir2015 1 Strictly aerobic and inability to grow at 37C suggests this not a gut coloniser.
Halomonas salina Proteobacteria Non/unknown Pathogen Lagier2016 1 Requires both Na+ and Mg2+ along with chloride or sulfate counterions.
Helicobacter felis Proteobacteria Micr Known Pathogen Lagier2016 1
Helicobacter heilmannii Proteobacteria Micr 37 Possible Pathogen Lagier2016, Byrd2020 2
Helicobacter pylori Proteobacteria Micr 37 Known Pathogen Bik2006, Tyakht2013, RajilicStojanovic2014, Lagier2016, Forster2019, De2020, Zeller2014, Vachida2019 8
Holophaga foetida Acidobacteria SANA 28-32 6.8-7.5 Non/unknown Pathogen De2020 1 Transforms methoxyaryl groups to methylsulfide.
Janibacter hoylei Actinobacteria AER 30 9 Non/unknown Pathogen Lagier2016 1 Resistant to UV light
Labilithrix luteola Proteobacteria SAER 20-30 6-8 Non/unknown Pathogen New2022 1 Low maximum growth temperature (30C) and strictly aerobic requirements makes this likely a gut non-coloniser.
Lacticigenium naphtae Firmicutes FANA 30 7.0 Non/unknown Pathogen De2020 1 Likely not a gut coloniser since it doesn't grow at body temperature
Lapidilactobacillus dextrinicus Firmicutes FANA 37 Non/unknown Pathogen Lagier2016 1
Legionella bozemanae Proteobacteria AER Known Pathogen Lagier2016 1
Legionella pneumophila Proteobacteria AER Known Pathogen Lagier2016 1
Lentilactobacillus kefiri Firmicutes Micr 30 Non/unknown Pathogen Lagier2016, Byrd2020 2 Probiotic.
Leptospira interrogans Spirochaetes Micr 28-30 7.2-7.6 Known Pathogen Lagier2016 1 Consumes no carbohydrates or amino acids, just lipids.
Leuconostoc gelidum subsp. gasicomitatum Firmicutes ANA 4-15 Non/unknown Pathogen Zeller2014, Vachida2019 2 Inability to grow at 37C suggests this not a gut coloniser.
Limosilactobacillus frumenti Firmicutes FANA Non/unknown Pathogen Lagier2016 1
Limosilactobacillus ingluviei Firmicutes FANA 42 Non/unknown Pathogen Lagier2016, Hu2019 2
Liquorilactobacillus satsumensis Firmicutes FANA Non/unknown Pathogen Lagier2016, De2020 2
Massilia brevitalea Proteobacteria SAER 15 7.0-7.5 Non/unknown Pathogen McLaughlin2010 1 Grows best at 15C, so likely a gut non-coloniser.
Massilia timonae Proteobacteria SAER Opportunistic Pathogen Lagier2016 1 Significant variation reported for assimilation of some substrates between references. Kampfer2011 used to override discrepancies. Likely a gut non-coloniser.
Methylobacterium jeotgali Proteobacteria SAER 30 7.0 Non/unknown Pathogen McLaughlin2010, RajilicStojanovic2014 2 Obligate aerobe, no spore formation and doesn't grow at 37C, so probably a gut non-coloniser.
Methylobacterium mesophilicum Proteobacteria SAER Opportunistic Infection Walker2011, RajilicStojanovic2014 2 Obligate aerobe, no spore formation and doesn't grow at 37C, so probably a gut non-coloniser.
Methylobacterium radiotolerans Proteobacteria SAER Non/unknown Pathogen RajilicStojanovic2014, Lagier2016, Zeller2014 3 Obligate aerobe, no spore formation and doesn't grow at 37C, so probably a gut non-coloniser.
Methylorubrum extorquens Proteobacteria SAER 25-30 7 Non/unknown Pathogen McLaughlin2010, Walker2011, Zeller2014 3 Obligate aerobe, no spore formation and doesn't grow at 37C, so probably a gut non-coloniser.
Microbacterium ginsengisoli Actinobacteria SAER Non/unknown Pathogen Yang2020 1 Obligate aerobe, no spore formation and doesn't grow at 37C, so probably a gut non-coloniser.
Microbacterium luteolum Actinobacteria SAER 28 Possible Pathogen RajilicStojanovic2014 1 Obligate aerobe, no spore formation and doesn't grow at 37C, so probably a gut non-coloniser.
Microbacterium testaceum Actinobacteria SAER 20-30 7.0-8.0 Non/unknown Pathogen Yang2020, Zeller2014 2 Obligate aerobe, no spore formation and doesn't grow at 37C, so probably a gut non-coloniser.
Mycobacterium tuberculosis Actinobacteria AER 37 6.4-7.0 Dangerous Pathogen Lagier2016 1
Mycobacterium tuberculosis variant africanum Actinobacteria AER 37 Dangerous Pathogen Lagier2016 1
Mycolicibacterium aubagnense Actinobacteria AER 30 Rare Opportunist Yang2020 1
Natronorubrum bangense Euryarchaeota SAER 45 9.0-9.5 Non/unknown Pathogen New2022 1 Requires minimum 12% salt concentration and high pH to grow. Therefore likely to be a gut non-coloniser.
Neisseria gonorrhoeae Proteobacteria AER 35-37 Known Pathogen Lagier2016, Zeller2014 2 Found only in humans.
Oceanobacillus oncorhynchi Firmicutes FANA 30-37 Non/unknown Pathogen Lagier2016 1 Likely gut non-coloniser because this organism doesn't grow below pH 9.
Paenarthrobacter ilicis Actinobacteria AER 25-30 Non/unknown Pathogen Lagier2016 1 Unlikely gut coloniser because this organism doesn't grow at 37C.
Paracoccus marcusii Proteobacteria AER 25-30 Non/unknown Pathogen PerezBrocal2015 1 Aerobic and poor growth at 35C suggests this not a gut coloniser.
Paraliobacillus quinghaiensis Firmicutes SAER 37 8.0 Non/unknown Pathogen Lagier2016 1 Obligate aerobe and high salt required for optimum growth, so likely a gut non-coloniser.
Paucilactobacillus oligofermentans Firmicutes FANA Non/unknown Pathogen Lagier2016 1 Unlikely gut coloniser because this organism doesn't grow at 37C.
Pedobacter cryoconitis Proteobacteria AER 20 7 Non/unknown Pathogen New2022 1 Low optimum temperatures (25C) makes this likely not a gut coloniser.
Pedobacter terricola Bacteroidetes AER 25 6.5-7.5 Non/unknown Pathogen De2020 1 Not likely to be a gut coloniser because this organism doesn't grow at 37C.
Pseudomonas alcaligenes Proteobacteria AER Opportunistic Pathogen Lagier2016 1
Pseudomonas boreopolis Proteobacteria AER Non/unknown Pathogen Lagier2016 1
Pseudomonas caricapapayae Proteobacteria AER 30 Non/unknown Pathogen Lagier2016 1
Pseudomonas chlororaphis Proteobacteria AER 30 Non/unknown Pathogen Lagier2016 1
Pseudomonas gessardii Proteobacteria AER 30 Non/unknown Pathogen Lagier2016, Yang2020 2
Pseudomonas japonica Proteobacteria AER Non/unknown Pathogen McLaughlin2010, Lagier2016 2
Pseudomonas libanensis Proteobacteria AER 30 Non/unknown Pathogen Lagier2016 1
Pseudomonas lundensis Proteobacteria AER 25 Rare Opportunist Lagier2016, Byrd2020 2 Borderline cold mesophile, so likely not a gut coloniser.
Pseudomonas massiliensis Proteobacteria AER 37 7.5 Non/unknown Pathogen Lagier2016 1
Pseudomonas migulae Proteobacteria AER 37 Non/unknown Pathogen Lagier2016 1
Pseudomonas mosselii Proteobacteria AER 30 Opportunistic Pathogen Lagier2016 1
Pseudomonas rhodesiae Proteobacteria AER 30 Non/unknown Pathogen Lagier2016, Byrd2020 2
Pseudomonas taetrolens Proteobacteria AER Non/unknown Pathogen Lagier2016 1
Pseudomonas xanthomarina Proteobacteria AER Non/unknown Pathogen Cassir2015, Lagier2016 2
Rhodococcus jostii Actinobacteria AER 15-30 Non/unknown Pathogen Zeller2014 1 Aerobic and no growth at 37C suggests this not a gut coloniser.
Rhodothermus marinus Bacteroidetes SAER 65 7 Non/unknown Pathogen New2022, Zeller2014 2 High minimum growth temperature (55C) and strict aerobic nature suggests this organism is likely a gut non-coloniser.
Roseobacter denitrificans Proteobacteria AER 20-30 7.0-8.0 Non/unknown Pathogen Zeller2014 1 Aerobic and low growth temperatures of 20-30C suggests this is not a gut coloniser.
Rubinisphaera brasiliensis Planctomycetes FANA 27-35 Non/unknown Pathogen King2019 1
Rubrobacter xylanophilus Actinobacteria AER 60 Non/unknown Pathogen Cassir2015 1 Hydrolyses xylan. High optimum growth temperature suggests it is not a regular gut commensal
Saccharofermentans acetigenes Firmicutes SANA 37 6.5 Non/unknown Pathogen De2020 1 Fumarate is a product of fermentation of glucose.
Salimicrobium jeotgali Firmicutes SAER 30 7.0-8.0 Non/unknown Pathogen Lagier2016 1 Likely to be a non-coloniser of the gut because it is strictly aerobic and has an optimal growth rate at high salt concentrations.
Salinisphaera halophila Proteobacteria SAER 25-30 7.0 Non/unknown Pathogen Lagier2016 1 Likely a gut non-coloniser because it requires high salt and is strictly aerobic.
Salmonella enterica subsp. arizonae Proteobacteria FANA Possible Pathogen Lagier2016 1
Silanimonas lenta Proteobacteria SAER 47 9.0 Non/unknown Pathogen RajilicStojanovic2014 1 Obligate aerobe and high salt required for optimum growth, so likely a gut non-coloniser.
Sphingomonas aerolata Proteobacteria AER Non/unknown Pathogen Lagier2016 1 Unlikely gut coloniser because this organism doesn't grow at 37C.
Spiribacter roseus Proteobacteria SAER 37 7.5-8.0 Non/unknown Pathogen New2022 1 Strict aerobe and high optimum salt concentration suggests this organism is likely to be a gut non-coloniser.
Spirochaeta thermophila Spirochaetes SANA 66-68 7.5 Non/unknown Pathogen New2022 1 Very high optimum temperature (66-68) suggests this organism is not a gut coloniser.
Sporosarcina aquimarina Firmicutes FANA 25 6.5-7.0 Non/unknown Pathogen Lagier2016 1 Not likely to be a gut coloniser because this organism doesn't grow well at 37C.
Thalassobacillus devorans Firmicutes SAER 37 7.0 Non/unknown Pathogen Lagier2016, Forster2019 2 Obligate aerobe and high salt required for optimum growth, so likely a gut non-coloniser.
Thermaerobacter marianensis Firmicutes SAER 74-76 7.0-7.5 Non/unknown Pathogen New2022, Zeller2014 2 Very high minimum growth temperature (50C) and strictly aerobic nature suggests this is a gut non-coloniser.
Thermolithobacter ferrireducens Firmicutes SANA 73 Non/unknown Pathogen 0 Reduces Fe(III). Non-coloniser due to very high minimum growth temperature.
Ureibacillus thermosphaericus Firmicutes SAER 60 Opportunistic Pathogen Hoyles2012, RajilicStojanovic2014, Lagier2016, Byrd2020 4 Obligate aerobe and high salt required for optimum growth, so likely a gut non-coloniser.
Virgibacillus senegalensis Firmicutes SAER 37 7.5 Non/unknown Pathogen Lagier2016 1 Likely gut non-coloniser because its optimum growth is with high salt and is an obligate aerobe.
Yangia pacifica Proteobacteria SAER 37 7.5 Non/unknown Pathogen New2022 1 Obligate aerobe and high salt required for optimum growth, so likely a gut non-coloniser.
Yersinia pestis Proteobacteria FANA 28-29 7.2-7.4 Known Pathogen Byrd2020, New2022 2 Highly dangerous pathogen. Not a long term coloniser of the human gut.
Yonghaparkia alkaliphila Actinobacteria SAER 30 9.0 Non/unknown Pathogen McLaughlin2010, RajilicStojanovic2014 2 Obligate aerobe, no spore formation and doesn't grow at 38C, so probably a gut non-coloniser.
Zunongwangia profunda Bacteroidetes SAER 25-30 Non/unknown Pathogen Qin2012 1 Strictly aerobic and low optimum growth conditions suggests this not a gut coloniser.