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All species have been isolated from - or detected in - human faeces, intestinal mucosa or other parts of the GI tract. With a few exceptions, only organisms that have been cultured and characterised to some degree have been included. This is a living document; it will be updated when new information is forthcoming.
These organisms are found frequently enough in gut microbiome surveys to qualify, and many were discovered and characterised decades ago. They can be arbitrarily divided into 3 main groups: 87 'widespread' microbes - or those that appear in most surveys from different locations; 141 'moderate' microbes - probably locally dominant geographically, but not as widespread; 275 'minor' colonisers - likely locally important but not as frequent or abundant.
The majority of bacteria that have been detected in faecal samples or gut biopsies can be considered as 'rare' colonisers (1446) because they occur infrequently, or as either 'unlikely' colonisers (568) or 'non-colonisers' (134) because they are transient from the upper GI (mouth, stomach, ingested with food), are (strictly) aerobic non-spore formers, are known pathogens, or are not mesophilic.
Viruses and eukaryotes including fungi, yeasts, protozoa, algae or multicelled parasites are not included in this database. Also, unassigned species (e.g., Clostridium_M sp000431375) and multiple strains of known species are not included (with a few exceptions).
Baseline microbiota were established by pioneers in the field, namely Sydney Finegold, Holdeman & Moore, and Yoshimi Benno, almost fifty years ago. In their respective studies, healthy volunteers from Japan, Hawaii and North America provided stool samples from which many bacteria were cultured and characterised at the species level. Since then, over sixty species-level surveys have been published, and the methods for detecting microbes has improved. For the purposes of creating this database, the frequency of gut microbes in the real world is estimated by how often they're detected in microbiome surveys (see Table 2 at the bottom for a list of surveys). Although a number of these studies show biases it is reasonable to assume the large dataset taken as a whole will reduce the impact of any such bias.
An important weighting factor is provided by 'lived experience' resources, such as the company, unseenbio.com, which has data from actual patient screening (see Table 3 for weighted 'exceptions'). This company has public-facing data which shows the preponderance of any given microbe in healthy Europeans. This information has helped adjust the microbiome heirarchy.
The microbes have been placed into six groups, ranging from widespread to transient (non-colonising)(Table 1). A list of each group is available by clicking on the link.
Some provisos to keep in mind: frequency of detection doesn't necessarily correlate with abundance. In addition, keystone species - those that are highly influential on the microbiome composition - may only be relatively sparse. The same applies to temporary microbes; transient organisms can apparently still impact the ecology within the gut and affect the host.
Table 1: The table below summarises the division of the gut microflora. Prevalence thresholds are survey counts.
| Colonisation Prevalence | Prevalence Thresholds | Unique Microbes | Notes |
|---|---|---|---|
| Widespread | ≥ 23 | 87 | Surveys must be from at least two geographical regions. See also exceptions table. |
| Moderate | 15 - 22 | 141 | Usually very frequent in at least one geographical area. See also exceptions table. |
| Minor | 7-14 | 275 | Can be dominant in a localised population. See also exceptions table. |
| Rare | 0-6 | 1446 | Rarely dominant, usually present in much less than 1% (Plesiomonas shigelloides is an exception). See also exceptions table. |
| Unlikely | Various | 568 | Temporary colonisers, transient organisms, strict aerobes. |
| Non-coloniser | Various | 134 | Pathogens, misassigned, transient organisms. |
Many people may be familiar with commonly encountered gut bacteria. These could include: common commensals, such as Bacteroides thetaiotaomicron, Phocaeicola vulgatus and Ruminococcus bromii; pathogens, such as Vibrio cholerae, Salmonella enterica and Campylobacter jejuni; and bugs that can be both commensal and pathogenic, such as Escherichia coli ("E coli"), Bacteroides fragilis and Clostridioides difficile ("C-diff"). However, an individual might not have any of these bacteria in their microbiome.
It appears as though there is no single bacterium that is part of everyone's (healthy) microbiome makeup. Although a healthy person will harbour between 70->1000 individual species of gut microbes at any given time in their life, only a small handful of microorganisms are common to most people. These organisms are detected in the majority of faecal surveys - whether through culturomics or gene sequencing approaches - and are among the group that has been categorised here as being 'widespread'. There is no "one set" of bacteria that suits everyone because of functional redundancy (Schluter2012, Costello2009). In other words, there are bacteria occupying the same ecological niche that can do the same job within the microbiome.
Caveats: A lot of the most recognisable bacteria from the human gut were discovered 50-odd years ago (or more). But are they widespread because they're truly common, or are they just easier to isolate and culture? There has also traditionally been an emphasis on characterising pathogenic organisms, many of which are facultative anaerobes and are mostly straightforward to isolate and identify. Likewise, some common colonic bacteria are opportunistic pathogens. Organisms of clinical significance have been subject to a lot of attention and tend to be well characterised. This could be a source of detection bias because S16 rRNA probes were likely established for these first.
Another anomaly is one of underrepresentation of some bacteria due to technical issues. For example, a very common bacterial strain might be a species-in-waiting, i.e., the strain might meet the criteria required to define it as a species, but is yet to be isolated, characterised and named (these parts are time consuming). Or the recurring detection of a genetic sequence may be insufficient to identify it to the species level. Neither of these types of microbes are included in the current database but will be a source of data bias.
As mentioned above, some organisms might be hard to detect because the generic S16 rRNA probes used to amplify bacterial genes may not be suitable. This can lead to underrepresentation in surveys.
Moderately common gut microbes ('moderate') might be considered to be dominant but spatially restricted. That is, they could be important within one human population as a result of similarities in diet (e.g., Chinese vs Mediterranean diets), family (genetics and/or proximity) or because of the local environment, but be scarce or absent in another survey from a different location.
Caveats: Not all populations are represented, and those that are do not have the same level of coverage. Studies from Africa are scarce, for example. Researchers, such as Drancourt, Lagier, Raoult, and Fournier, and coworkers, have endeavoured to explore this rich source of novel bacteria, but much still needs to be done to understand the diversity of localised microbiota there. The caveats described previously apply here also.
The term 'minor' has been used here to describe microbes that show up occasionally, around 10-15% of the time. This could include microbes that are endemic to a particular population or might be associated with a localised (and transient) outbreak of a pathogenic nature.
Some semi-transient species considered to be good for gut health also might be included here. Lactobacillus bacteria are a diverse group in terms of their spatial and temporal colonising behaviours. Latilactobacillus sakei, for example, is detected in faeces in about 10 studies but appears to be sparce and temporary in its ability to colonise (Rossi2016). Levilactobacillus brevis and Lactiplantibacillus pentosus appear to act the same way (Rossi2016).
Caveats: Gut microbiome persistence - and even abundance - might not necessarily correlate with a microbe's level of influence. An organism can be highly influential in a number of ways, including being an essential part of a metabolic bacterial consortium (e.g., initiating the cleavage of mucin), by suppressing (or aggravating) immune responses, or by helping to exclude pathogenic species. Further to this point, mucus-associated bacteria are often present in higher amounts closer to the epithelium than in the lumen. Surveys concentrating exclusively on faeces might underestimate these localised microflora.
Simply put, uncommon - or 'rare' - species are those that show up in only a few (or no) studies. The cut-off here is ≤ 5 studies. This tends to be a default for newly characterised organisms, at least until additional information allows them to be placed in a more suitable category.
Caveats: Aside from the previous provisos, another factor to consider is that the detection of a microbe in any given study may occur only once, i.e., it is part of a single subject's microbiome. Perhaps that person ate food contaminated with an organism that subsequently made its way through the travails of the digestive system and was picked up in the screen. In an ideal world it would be useful to aggregate all the subject data and base species abundance on the whole dataset, but not all sources report at the individual level.
Conversely, an important microbe might fly under the radar because a species has been split among subspecies or strains. To illustrate this point, a recent faecal analysis of a subject returned several designations for the keystone species, Faecalibacterium prausnitzii, including F. prausnitzii_A, _B and _C. The abundance of individual strains with respect to the total was less than 2.5% but the combined abundance amounted to about 6% - quite a difference. A second sample from the same person a year later showed the presence of types _A, _C, _D, _G, _I and _J, where no individual strain represented more than 2%, but the aggregate was 5.2%. Clearly, as time passes and our collective knowledge increases, existing species will undergo further splitting based on genotyping. Currently, the database only accounts for the sum of the phenotypic strains at the species and subspecies level, not the strain level. This is recognised as a potential issue since species strains can differ critically and selective processes may favour one strain over another, depending a person's individual physiology and established microbiome.
A final point here: recently isolated, characterised and named species will suffer from underrepresentation in preceding surveys, even though they might have been present in the form of an alias (e.g., Bacteroides xylanisolvens vs its synonym, 'Bacteroides sp 2 1 16'). All efforts have been made to capture synonyms and use current taxonomic naming conventions, however assigning lab-designated strains (e.g., 'Blautia_A sp000285855') to actual published species is currently beyond the scope of this project.
The category designated as 'unlikely coloniser' will be rather controversial. Here, species may be detected in several studies but are unlikely to play a significant role in a healthy gut microbe (apart from the temporary affects of pathogens, of course). To fit into this category, an organism might have an optimal growth temperature, salt requirement or pH outside the range of body, which would likely hamper its persistence in a competitive environment. Similarly, strict aerobes cannot grow under anaerobic conditions and although some aerobic bacteria inhabit the caecum and upper GI tract, they generally cannot persist for long in the gut.
Finally, pathogens known to cause illness (e.g., Salmonella enterica strains, Yersinia pestis) are considered unlikely colonisers simply because they generally don't belong in a healthy microbiome.
Caveats: There are exceptions to the rule, especially when it comes to aerobic bacteria. Bacillus massiliogabonensis is a strictly aerobic commensal that has been cultured from fresh stool samples. Other Bacillus and Lactobacillus species might influence host immune responses and metabolism as part of a secretome microbial consortium (Ilinskaya2017), where transient microbes play a functional role by releasing metabolites, enzymes or bacteriocides as they journey through the GIT.
When an RNA sequence has been attributed to an organism that is very unlikely to be associated with humans, the bug is deposited in the category 'non-coloniser'. Interesting cases include Alkaliphilus transvaalensis, a highly alkaliphilic species growing deep underground, or Desulforudis audaxviator, an organism so strange it reproduces (at most) once a year!
Since this database ostensibly covers only the intestinal tract a stomach resident, such as Helicobacter pylori, would not be considered an intestinal coloniser despite being picked up in 8 studies. It would also be labelled as a non-coloniser.
Caveats: Being an extremophile doesn't necessary preclude a species from having strains that can survive in the GIT. Archaea, including some recently discovered haloarchaea (Kim2020b) in Korean subjects, have been found to be prevalent in humans. As a consequence, it would be presumptuous to exclude all seemly wierd microbes in the absence of additional information. It has therefore been decided to keep them until it becomes clear they don't belong.
Most database entries are derived from published surveys and studies (see the sortable table below). In addition, Bergey's Manual of Systematic Bacteriology, the Culture Collection University of Gothenburg and individual papers available online account for a significant number as well.
Groups of pathogenic bacteria might have been detected in clinical sources associated with the gastrointestinal tract; this presumes the organism at least temporarily resides in the gut and is therefore included, but doesn't assume it is a member of the usual gut microbiome.
Table 2: Citation table for the surveys used in this project. The table is sortable by clicking on the headings.
| Citation | Year | Authors | Title | DOI/PMID |
|---|---|---|---|---|
| Benno1989 | 1989 |
Benno, Y.; Endo, K.; Mizutani, T.; Namba, Y.; Komori, T.; Mitsuoka, T. |
Comparison of fecal microflora of elderly persons in rural and urban areas of Japan. | 10.1128/aem.55.5.1100-1105.1989 |
| Browne2016 | 2016 |
Browne, Hilary P.; Forster, Samuel C.; Anonye, Blessing O.; Kumar, Nitin; Neville, B. Anne; Stares, Mark D.; Goulding, David; Lawley, Trevor D. |
Culturing of 'unculturable' human microbiota reveals novel taxa and extensive sporulation. | 10.1038/nature17645 |
| Diamanti2020 | 2020 |
Diamanti, Andrea Picchianti; Panebianco, Concetta; Salerno, Gerardo; Rosa, Roberta Di; Salemi, Simonetta; Sorgi, Maria Laura; Meneguzzi, Giorgia; Mariani, Maria Benedetta; Rai, Alessandra; Iacono, Dalila; Sesti, Giorgio; Pazienza, Valerio; Lagana, Bruno |
Impact of Mediterranean Diet on Disease Activity and Gut Microbiota Composition of Rheumatoid Arthritis Patients. | 10.3390/microorganisms8121989 |
| Lagier2012b | 2012 |
Lagier, J.-C.; Armougom, F.; Million, M.; Hugon, P.; Pagnier, I.; Robert, C.; Bittar, F.; Fournous, G.; Gimenez, G.; Maraninchi, M.; Trape, J.-F.; Koonin, E. V.; Scola, B. La; Raoult, D. |
Microbial culturomics: paradigm shift in the human gut microbiome study. | 10.1111/1469-0691.12023 |
| Pfleiderer2013 | 2013 |
Pfleiderer, A.; Lagier, J.-C.; Armougom, F.; Robert, C.; Vialettes, B.; Raoult, D. |
Culturomics identified 11 new bacterial species from a single anorexia nervosa stool sample. | 10.1007/s10096-013-1900-2 |
| RajilicStojanovic2014 | 2014 |
Rajili-Stojanovi M, de Vos WM. |
The first 1000 cultured species of the human gastrointestinal microbiota. | 10.1111/1574-6976.12075 |
| Walker2011 | 2011 |
Walker AW, Sanderson JD, Churcher C, Parkes GC, Hudspith BN, Rayment N, Brostoff J, Parkhill J, Dougan G, Petrovska L. |
High-throughput clone library analysis of the mucosa-associated microbiota reveals dysbiosis and differences between inflamed and non-inflamed regions of the intestine in inflammatory bowel disease. | 10.1186/1471-2180-11-7 |
| Hoyles2012 | 2012 |
Hoyles L, Honda H, Logan NA, Halket G, La Ragione RM, McCartney AL. |
Recognition of greater diversity of Bacillus species and related bacteria in human faeces. | 10.1016/j.resmic.2011.10.004 |
| Chung2019 | 2019 |
Wing Sun Faith Chung, Alan W Walker, Joan Vermeiren, Paul O Sheridan, Douwina Bosscher, Vicenta Garcia-Campayo, Julian Parkhill, Harry J Flint, Sylvia H Duncan |
Impact of carbohydrate substrate complexity on the diversity of the human colonic microbiota. | 10.1093/femsec/fiy201 |
| King2019 | 2019 |
King CH, Desai H, Sylvetsky AC, LoTempio J, Ayanyan S, Carrie J, Crandall KA, Fochtman BC, Gasparyan L, Gulzar N, Howell P, Issa N, Krampis K, Mishra L, Morizono H, Pisegna JR, Rao S, Ren Y, Simonyan V, Smith K, VedBrat S, Yao MD, Mazumder R. |
Baseline human gut microbiota profile in healthy people and standard reporting template. | 10.1371/journal.pone.0206484 |
| Moore1974 | 1974 |
Moore WE, Holdeman LV. |
Human fecal flora: the normal flora of 20 Japanese-Hawaiians. | 10.1128/am.27.5.961-979.1974 |
| Chung2016 | 2016 |
Chung WS, Walker AW, Louis P, Parkhill J, Vermeiren J, Bosscher D, Duncan SH, Flint HJ. |
Modulation of the human gut microbiota by dietary fibres occurs at the species level. | 10.1186/s12915-015-0224-3 |
| Salonen2014 | 2014 |
Salonen A, Lahti L, Salojärvi J, Holtrop G, Korpela K, Duncan SH, Date P, Farquharson F, Johnstone AM, Lobley GE, Louis P, Flint HJ, de Vos WM. |
Impact of diet and individual variation on intestinal microbiota composition and fermentation products in obese men. | 10.1038/ismej.2014.63 |
| Finegold1974 | 1974 |
Sydney M. Finegold, Howard R. Attebery and Vera L. Sutter |
Effect of diet on human fecal flora: comparison of Japanese and American diets | 10.1093/ajcn/27.12.1456 |
| Aujoulat2014 | 2014 |
Aujoulat F, Roudière L, Picaud JC, Jacquot A, Filleron A, Neveu D, Baum TP, Marchandin H, Jumas-Bilak E. |
Temporal dynamics of the very premature infant gut dominant microbiota. | 10.1186/s12866-014-0325-0 |
| De2020 | 2020 |
De R, Mukhopadhyay AK, Dutta S. |
Metagenomic analysis of gut microbiome and resistome of diarrheal fecal samples from Kolkata, India, reveals the core and variable microbiota including signatures of microbial dark matter. | 10.1186/s13099-020-00371-8 |
| Yang2020 | 2020 |
Yang J, Pu J, Lu S, Bai X, Wu Y, Jin D, Cheng Y, Zhang G, Zhu W, Luo X, Rosselló-Móra R, Xu J. |
Species-Level Analysis of Human Gut Microbiota With Metataxonomics. | 10.3389/fmicb.2020.02029 |
| Lagier2016 | 2016 |
Lagier JC, Khelaifia S, Alou MT, Ndongo S, Dione N, Hugon P, Caputo A, Cadoret F, Traore SI, Seck EH, Dubourg G, Durand G, Mourembou G, Guilhot E, Togo A, Bellali S, Bachar D, Cassir N, Bittar F, Delerce J, Mailhe M, Ricaboni D, Bilen M, Dangui Nieko NP, Dia Badiane NM, Valles C, Mouelhi D, Diop K, Million M, Musso D, Abrahão J, Azhar EI, Bibi F, Yasir M, Diallo A, Sokhna C, Djossou F, Vitton V, Robert C, Rolain JM, La Scola B, Fournier PE, Levasseur A, Raoult D. |
Culture of previously uncultured members of the human gut microbiota by culturomics. | 10.1038/nmicrobiol.2016.203 |
| McLaughlin2010 | 2010 |
McLaughlin SD, Walker AW, Churcher C, Clark SK, Tekkis PP, Johnson MW, Parkhill J, Ciclitira PJ, Dougan G, Nicholls RJ, Petrovska L. |
The bacteriology of pouchitis: a molecular phylogenetic analysis using 16S rRNA gene cloning and sequencing. | 10.1097/SLA.0b013e3181e3dc8b |
| Forster2019 | 2019 |
Forster SC, Kumar N, Anonye BO, Almeida A, Viciani E, Stares MD, Dunn M, Mkandawire TT, Zhu A, Shao Y, Pike LJ, Louie T, Browne HP, Mitchell AL, Neville BA, Finn RD, Lawley TD. |
A human gut bacterial genome and culture collection for improved metagenomic analyses. | 10.1038/s41587-018-0009-7. |
| Almeida2019 | 2019 |
Almeida A, Mitchell AL, Boland M, Forster SC, Gloor GB, Tarkowska A, Lawley TD, Finn RD. |
A new genomic blueprint of the human gut microbiota. | 10.1038/s41586-019-0965-1 |
| Zou2019 | 2019 |
Zou Y, Xue W, Luo G, Deng Z, Qin P, Guo R, Sun H, Xia Y, Liang S, Dai Y, Wan D, Jiang R, Su L, Feng Q, Jie Z, Guo T, Xia Z, Liu C, Yu J, Lin Y, Tang S, Huo G, Xu X, Hou Y, Liu X, Wang J, Yang H, Kristiansen K, Li J, Jia H, Xiao L. |
1,520 reference genomes from cultivated human gut bacteria enable functional microbiome analyses. | 10.1038/s41587-018-0008-8 |
| Nielsen2014 | 2014 |
Nielsen HB, Almeida M, Juncker AS, Rasmussen S, Li J, Sunagawa S, Plichta DR, Gautier L, Pedersen AG, Le Chatelier E, Pelletier E, Bonde I, Nielsen T, Manichanh C, Arumugam M, Batto JM, Quintanilha Dos Santos MB, Blom N, Borruel N, Burgdorf KS, Boumezbeur F, Casellas F, Doré J, Dworzynski P, Guarner F, Hansen T, Hildebrand F, Kaas RS, Kennedy S, Kristiansen K, Kultima JR, Léonard P, Levenez F, Lund O, Moumen B, Le Paslier D, Pons N, Pedersen O, Prifti E, Qin J, Raes J, Sørensen S, Tap J, Tims S, Ussery DW, Yamada T; MetaHIT Consortium, Renault P, Sicheritz-Ponten T, Bork P, Wang J, Brunak S, Ehrlich SD; |
MetaHIT Consortium. Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes. | 10.1038/nbt.2939 |
| Tyakht2013 | 2013 |
Tyakht AV, Kostryukova ES, Popenko AS, Belenikin MS, Pavlenko AV, Larin AK, Karpova IY, Selezneva OV, Semashko TA, Ospanova EA, Babenko VV, Maev IV, Cheremushkin SV, Kucheryavyy YA, Shcherbakov PL, Grinevich VB, Efimov OI, Sas EI, Abdulkhakov RA, Abdulkhakov SR, Lyalyukova EA, Livzan MA, Vlassov VV, Sagdeev RZ, Tsukanov VV, Osipenko MF, Kozlova IV, Tkachev AV, Sergienko VI, Alexeev DG, Govorun VM. |
Human gut microbiota community structures in urban and rural populations in Russia. | 10.1038/ncomms3469 |
| Rothschild2018 | 2018 |
Rothschild D, Weissbrod O, Barkan E, Kurilshikov A, Korem T, Zeevi D, Costea PI, Godneva A, Kalka IN, Bar N, Shilo S, Lador D, Vila AV, Zmora N, Pevsner-Fischer M, Israeli D, Kosower N, Malka G, Wolf BC, Avnit-Sagi T, Lotan-Pompan M, Weinberger A, Halpern Z, Carmi S, Fu J, Wijmenga C, Zhernakova A, Elinav E, Segal E. |
Environment dominates over host genetics in shaping human gut microbiota. | 10.1038/nature25973 |
| Benno1986 | 1986 |
Benno Y, Suzuki K, Suzuki K, Narisawa K, Bruce WR, Mitsuoka T. |
Comparison of the fecal microflora in rural Japanese and urban Canadians. | 10.1111/j.1348-0421.1986.tb02978.x |
| Taylor1985 | 1985 |
Taylor GR, Kropp KD, Molina TC. |
Nine-year microflora study of an isolator-maintained immunodeficient child. | 10.1128/aem.50.6.1349-1356.1985 |
| Pandey2012 | 2012 |
Pandey PK, Verma P, Kumar H, Bavdekar A, Patole MS, Shouche YS. |
Comparative analysis of fecal microflora of healthy full-term Indian infants born with different methods of delivery (vaginal vs cesarean): Acinetobacter sp. prevalence in vaginally born infants. | 10.1007/s12038-012-9268-5 |
| Wang2005 | 2005 |
Wang M, Ahrné S, Jeppsson B, Molin G. |
Comparison of bacterial diversity along the human intestinal tract by direct cloning and sequencing of 16S rRNA genes. | 10.1016/j.femsec.2005.03.012 |
| PerisBondia2011 | 2011 |
Peris-Bondia F, Latorre A, Artacho A, Moya A, D'Auria G. |
The active human gut microbiota differs from the total microbiota. | 10.1371/journal.pone.0022448 |
| Finegold1977 | 1977 |
Finegold SM, Sutter VL, Sugihara PT, Elder HA, Lehmann SM, Phillips RL. |
Fecal microbial flora in Seventh Day Adventist populations and control subjects. | 10.1093/ajcn/30.11.1781 |
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Favier CF, Vaughan EE, De Vos WM, Akkermans AD. |
Molecular monitoring of succession of bacterial communities in human neonates. | 10.1128/AEM.68.1.219-226.2002 |
| Dubourg2013 | 2013 |
Dubourg G, Lagier JC, Armougom F, Robert C, Hamad I, Brouqui P, Raoult D. |
The gut microbiota of a patient with resistant tuberculosis is more comprehensively studied by culturomics than by metagenomics. | 10.1007/s10096-012-1787-3 |
| Mangin2004 | 2004 |
Mangin I, Bonnet R, Seksik P, Rigottier-Gois L, Sutren M, Bouhnik Y, Neut C, Collins MD, Colombel JF, Marteau P, Doré J. |
Molecular inventory of faecal microflora in patients with Crohn's disease. | 10.1016/j.femsec.2004.05.005 |
| Woodmansey2004 | 2004 |
Woodmansey EJ, McMurdo ME, Macfarlane GT, Macfarlane S. |
Comparison of compositions and metabolic activities of fecal microbiotas in young adults and in antibiotic-treated and non-antibiotic-treated elderly subjects. | 10.1128/AEM.70.10.6113-6122.2004 |
| Frank2007 | 2007 |
Frank DN, St Amand AL, Feldman RA, Boedeker EC, Harpaz N, Pace NR. |
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Fecal microbiota composition differs between children with β-cell autoimmunity and those without. | 10.2337/db12-0526 |
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Margaret L. Zupancic, Brandi L. Cantarel, Zhenqiu Liu, Elliott F. Drabek, Kathleen A. Ryan, Shana Cirimotich, Cheron Jones, Rob Knight, William A. Walters, Daniel Knights, Emmanuel F. Mongodin, Richard B. Horenstein, Braxton D. Mitchell, Nanette Steinle, Soren Snitker, Alan R. Shuldiner, Claire M. Fraser |
Analysis of the Gut Microbiota in the Old Order Amish and Its Relation to the Metabolic Syndrome. | 10.1371/journal.pone.0043052 |
| Nam2008a | 2008 |
Nam YD, Chang HW, Kim KH, Roh SW, Kim MS, Jung MJ, Lee SW, Kim JY, Yoon JH, Bae JW. |
Bacterial, archaeal, and eukaryal diversity in the intestines of Korean people. | 10.1007/s12275-008-0199-7 |
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Macfarlane S, Furrie E, Cummings JH, Macfarlane GT. |
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Holdeman LV, Good IJ, Moore WE. |
Human fecal flora: variation in bacterial composition within individuals and a possible effect of emotional stress. | 10.1128/aem.31.3.359-375.1976 |
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Heilig HG, Zoetendal EG, Vaughan EE, Marteau P, Akkermans AD, de Vos WM. |
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Dal Bello F, Hertel C. |
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Benno Y, Sawada K, Mitsuoka T. |
The intestinal microflora of infants: composition of fecal flora in breast-fed and bottle-fed infants. | 10.1111/j.1348-0421.1984.tb00754.x |
| New2022 | 2022 |
Felicia N. New, Benjamin R. Baer, Andrew G. Clark, Martin T. Wells and Ilana L. Brito |
Collective effects of human genomic variation on microbiome function. | 10.1038/s41598-022-07632-3 |
| Rossi2016 | 2016 |
Rossi M, Martínez-Martínez D, Amaretti A, Ulrici A, Raimondi S, Moya A. |
Mining metagenomic whole genome sequences revealed subdominant but constant Lactobacillus population in the human gut microbiota. | 10.1111/1758-2229.12405 |
| Byrd2020 | 2020 |
Allyson L. Byrd, Menghan Liu, Kei E. Fujimura, Svetlana Lyalina, Deepti R. Nagarkar, Bruno Charbit, Jacob Bergstedt, Etienne Patin, Oliver J. Harrison, Lluís Quintana-Murci, Darragh Duffy, Matthew L. Albert and The Milieu Intérieur Consortium |
Stability and dynamics of the human gut microbiome and its association with systemic immune traits. | 10.1101/2020.01.17.909853 |
| Cassir2015 | 2015 |
Cassir N, Benamar S, Khalil JB, Croce O, Saint-Faust M, Jacquot A, Million M, Azza S, Armstrong N, Henry M, Jardot P, Robert C, Gire C, Lagier JC, Chabrière E, Ghigo E, Marchandin H, Sartor C, Boutte P, Cambonie G, Simeoni U, Raoult D, La Scola B. |
Clostridium butyricum Strains and Dysbiosis Linked to Necrotizing Enterocolitis in Preterm Neonates | 10.1093/cid/civ468 |
| Chen2020 | 2020 |
Chen J, Wang Q, Wang A, Lin Z. |
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Table 3: The 'lived experience' data that doesn't correlate with that of the surveys. The table is sortable.
| Species | Survey Count | Status | Justification for Change |
|---|---|---|---|
| Actinomyces viscosus | 5 | Minor Coloniser | In 17% of Europeans (unseenbio.com). Minor coloniser. |
| Agathobaculum desmolans | 5 | Minor Coloniser | In 39% of Europeans (unseenbio.com). Minor coloniser. |
| Alloscardovia omnicolens | 6 | Minor Coloniser | In 32% of Europeans (unseenbio.com). Minor coloniser. |
| Anaeroglobus geminatus | 5 | Minor Coloniser | In 18% of Europeans (unseenbio.com). Minor coloniser. |
| Bacteroides neonati | 4 | Minor Coloniser | In 63% of Europeans (unseenbio.com). Minor coloniser. |
| Bacteroides pyogenes | 6 | Minor Coloniser | In 58% of Europeans (unseenbio.com). A minor coloniser. |
| Bariatricus massiliensis | 2 | Minor Coloniser | In 41% of Europeans (unseenbio.com). Minor coloniser. |
| Bifidobacterium ruminantium | 2 | Minor Coloniser | In 70% of Europeans (unseenbio.com). Minor coloniser. |
| Bifidobacterium scardovii | 4 | Minor Coloniser | In 27% of Europeans (unseenbio.com). Minor coloniser. |
| Butyricimonas synergistica | 5 | Minor Coloniser | In 54% of Europeans (unseenbio.com). A minor coloniser. |
| Christensenella hongkongensis | 6 | Minor Coloniser | In 27% of Europeans (unseenbio.com). Minor coloniser. |
| Christensenella minuta | 5 | Minor Coloniser | In 52% of Europeans (unseenbio.com). A minor coloniser. |
| Christensenella timonensis | 2 | Minor Coloniser | In 15% of Europeans (unseenbio.com). Minor coloniser. |
| Citrobacter farmeri | 3 | Minor Coloniser | In 14% of Europeans (unseenbio.com). Minor coloniser. |
| Citrobacter freundii | 19 | Minor Coloniser | In 6% of Europeans (unseenbio.com), i.e., a minor coloniser. |
| Clostridium saudiense | 4 | Minor Coloniser | In 54% of Europeans (unseenbio.com). Minor coloniser. |
| Collinsella bouchesdurhonensis | 3 | Minor Coloniser | In 26% of Europeans (unseenbio.com). Minor coloniser. |
| Dielma fastidiosa | 6 | Minor Coloniser | In 44% of Europeans (unseenbio.com). Minor coloniser. |
| Duodenibacillus massiliensis | 3 | Minor Coloniser | In 25% of Europeans (unseenbio.com). Minor coloniser. |
| Emergencia timonensis | 2 | Minor Coloniser | In 44% of Europeans (unseenbio.com). Minor coloniser. |
| Enterocloster lavalensis | 5 | Minor Coloniser | In 68% of Europeans (unseenbio.com). Minor coloniser. |
| Eubacterium callanderi | 4 | Minor Coloniser | In 30% of Europeans (unseenbio.com). Minor coloniser. |
| Eubacterium coprostanoligenes | 4 | Minor Coloniser | In 38% of Europeans (unseenbio.com). Minor coloniser. |
| Faecalicatena fissicatena | 2 | Minor Coloniser | In 50% of Europeans (unseenbio.com). Minor coloniser. |
| Faecalicatena glycyrrhizinilyticum | 2 | Minor Coloniser | Isolation and characterisation not yet published. In 69% of Europeans (unseenbio.com). A minor coloniser. |
| Faecalicoccus pleomorphus | 5 | Minor Coloniser | In 13% of Europeans (unseenbio.com). Minor coloniser. |
| Gordonibacter urolithinfaciens | 4 | Minor Coloniser | In 28% of Europeans (unseenbio.com). Minor coloniser. |
| Haemophilus parahaemolyticus | 3 | Minor Coloniser | In 17% of Europeans (unseenbio.com). Minor coloniser. |
| Haemophilus sputorum | 6 | Minor Coloniser | In 11% of Europeans (unseenbio.com). Minor coloniser. |
| Hungatella effluvii | 3 | Minor Coloniser | In 65% of Europeans (unseenbio.com). Minor coloniser. |
| Klebsiella grimontii | 2 | Minor Coloniser | In 11% of Europeans (unseenbio.com). Minor coloniser. |
| Klebsiella michiganensis | 4 | Minor Coloniser | In 12% of Europeans (unseenbio.com). Minor coloniser. |
| Klebsiella quasipneumoniae subsp. quasipneumoniae | 2 | Minor Coloniser | In 10% of Europeans (unseenbio.com). Minor coloniser. |
| Kluyvera ascorbata | 6 | Minor Coloniser | Kluyvera ascorbata in 8% of Europeans, Kluyvera ascorbata_B also with 8% (unseenbio.com). Minor coloniser. |
| Kosakonia cowanii | 2 | Minor Coloniser | In 10% of Europeans (unseenbio.com). Minor coloniser. |
| Lachnoclostridium edouardi | 2 | Minor Coloniser | In 59% of Europeans (unseenbio.com). Minor coloniser. |
| Lachnoclostridium phytofermentans | 5 | Minor Coloniser | In 14% of Europeans (unseenbio.com). Minor coloniser. |
| Lacticaseibacillus paracasei | 15 | Minor Coloniser | In 17% of Europeans (unseenbio.com). Produces GABA (Sahad2020). |
| Lactobacillus delbrueckii subsp. delbrueckii | 16 | Minor Coloniser | In 12% of Europeans (unseenbio.com). Minor coloniser. |
| Lactobacillus kalixensis | 3 | Minor Coloniser | In 24% of Europeans (unseenbio.com). Minor coloniser. |
| Lactococcus raffinolactis | 5 | Minor Coloniser | In 13% of Europeans (unseenbio.com). Minor coloniser. |
| Lactonifactor longoviformis | 6 | Minor Coloniser | In 56% of Europeans (unseenbio.com). Minor coloniser. |
| Lancefieldella rimae | 5 | Minor Coloniser | In 11% of Europeans (unseenbio.com). Minor coloniser. |
| Mitsuokella jalaludinii | 6 | Minor Coloniser | In 16% of Europeans (unseenbio.com). Minor coloniser. |
| Monoglobus pectinilyticus | 4 | Minor Coloniser | In 34% of Europeans (unseenbio.com). Minor coloniser. |
| Muribaculum intestinale | 2 | Minor Coloniser | In 31% of Europeans (unseenbio.com). Minor coloniser. |
| Negativibacillus massiliensis | 2 | Minor Coloniser | In 53% of Europeans (unseenbio.com). Minor coloniser. |
| Phocaeicola salanitronis | 6 | Minor Coloniser | In 34% of Europeans (unseenbio.com). Minor coloniser. |
| Phocea massiliensis | 3 | Minor Coloniser | In 61% of Europeans (unseenbio.com). Minor coloniser. |
| Prevotella multisaccharivorax | 5 | Minor Coloniser | In 14% of Europeans (unseenbio.com). Minor coloniser. |
| Prevotellamassilia timonensis | 4 | Minor Coloniser | In 50% of Europeans (unseenbio.com). Minor coloniser. |
| Ruminococcus gauvreauii | 6 | Minor Coloniser | In 19% of Europeans (unseenbio.com). Minor coloniser. |
| Scardovia wiggsiae | 3 | Minor Coloniser | In 15% of Europeans (unseenbio.com). Minor coloniser. |
| Sellimonas intestinalis | 4 | Minor Coloniser | In 44% of Europeans (unseenbio.com). Minor coloniser. |
| Stomatobaculum longum | 4 | Minor Coloniser | In 27% of Europeans (unseenbio.com). Minor coloniser. |
| Streptococcus infantarius subsp. infantarius | 3 | Minor Coloniser | In 15% of Europeans (unseenbio.com). Minor coloniser. |
| Streptococcus timonensis | 2 | Minor Coloniser | In 16% of Europeans (unseenbio.com). Minor coloniser. |
| Thermophilibacter provencensis | 2 | Minor Coloniser | In 19% of Europeans (unseenbio.com). Minor coloniser. |
| Veillonella rogosae | 2 | Minor Coloniser | In 43% of Europeans (unseenbio.com). Minor coloniser. |
| Weissella viridescens | 3 | Minor Coloniser | In 48% of Europeans (unseenbio.com). Minor coloniser. |
| Absiella innocuum | 1 | Moderate Coloniser | In 94% of Europeans (unseenbio.com). |
| Agathobaculum butyriciproducens | 3 | Moderate Coloniser | In 99% of Europeans (unseenbio.com). |
| Alistipes ihumii | 4 | Moderate Coloniser | In 92% of Europeans (unseenbio.com). |
| Alistipes obesi | 5 | Moderate Coloniser | In 97% of Europeans (unseenbio.com). |
| Alistipes senegalensis | 9 | Moderate Coloniser | In 97% of Europeans (unseenbio.com). |
| Alistipes timonensis | 5 | Moderate Coloniser | In 89% of Europeans (unseenbio.com). |
| Anaerotignum lactatifermentans | 8 | Moderate Coloniser | In 95% of Europeans (unseenbio.com). |
| Anaerotruncus rubiinfantis | 3 | Moderate Coloniser | In 75% of Europeans (unseenbio.com). |
| Bacteroides acidifaciens | 5 | Moderate Coloniser | In 100% of Europeans (unseenbio.com). |
| Bacteroides bouchesdurhonensis | 2 | Moderate Coloniser | In 96% of Europeans (unseenbio.com). Reported attributes are confusing and have been added to a limited extent. |
| Bacteroides congonensis | 3 | Moderate Coloniser | High salt required for optimum growth. In 99% of Europeans (unseenbio.com). |
| Bacteroides cutis | 1 | Moderate Coloniser | In 76% of Europeans (unseenbio.com). |
| Bacteroides faecis | 13 | Moderate Coloniser | In 100% of Europeans (unseenbio.com). |
| Bacteroides fluxus | 11 | Moderate Coloniser | In 95% of Europeans (unseenbio.com). |
| Bacteroides gallinarum | 4 | Moderate Coloniser | In 88% of Europeans (unseenbio.com). |
| Bacteroides mediterraneensis | 2 | Moderate Coloniser | In 87% of Europeans (unseenbio.com). |
| Bacteroides oleiciplenus | 9 | Moderate Coloniser | In 97% of Europeans (unseenbio.com). |
| Bacteroides stercorirosoris | 4 | Moderate Coloniser | In 98% of Europeans (unseenbio.com). |
| Bifidobacterium longum subsp. infantis | 14 | Moderate Coloniser | In 83% of Europeans (unseenbio.com). |
| Bittarella massiliensis | 2 | Moderate Coloniser | In 90% of Europeans (unseenbio.com). |
| Blautia massiliensis | 5 | Moderate Coloniser | In 100% of Europeans (unseenbio.com). |
| Blautia wexlerae | 13 | Moderate Coloniser | In 100% of Europeans (unseenbio.com). |
| Butyricimonas virosa | 9 | Moderate Coloniser | In 81% of Europeans (unseenbio.com). |
| Clostridium methylpentosum | 11 | Moderate Coloniser | Seen in 83% of subjects in study by Qin2010, but at low levels. Moderate coloniser. |
| Coprobacter fastidiosus | 10 | Moderate Coloniser | In 87% of Europeans (unseenbio.com). |
| Coprobacter secundus | 2 | Moderate Coloniser | In 73% of Europeans (unseenbio.com). |
| Dysosmobacter welbionis | 1 | Moderate Coloniser | Recently discovered but reported to be widespread ("up to 70% of the population"). |
| Eisenbergiella massiliensis | 3 | Moderate Coloniser | In 74% of Europeans (unseenbio.com). |
| Eisenbergiella tayi | 5 | Moderate Coloniser | In 97% of Europeans (unseenbio.com). |
| Enterocloster asparagiformis | 13 | Moderate Coloniser | In 51% of Europeans (unseenbio.com), but in 95% of subjects in study by Qin2010. Moderate coloniser. |
| Enterococcus devriesei | 2 | Moderate Coloniser | In 79% of Europeans (unseenbio.com). |
| Faecalicatena faecis | 1 | Moderate Coloniser | Isolation and characterisation not yet published. In 99% of Europeans (unseenbio.com). A moderate coloniser. |
| Faecalicatena gnavus | 1 | Moderate Coloniser | Isolation and characterisation not yet published. In 85% of Europeans (unseenbio.com). A moderate coloniser. |
| Faecalicatena lactaris | 1 | Moderate Coloniser | Isolation and characterisation not yet published. In 98% of Europeans (unseenbio.com). A moderate coloniser. |
| Faecalicatena torques | 1 | Moderate Coloniser | Isolation and characterisation not yet published. In 97% of Europeans (unseenbio.com). A moderate coloniser. |
| Fournierella massiliensis | 2 | Moderate Coloniser | In 90% of Europeans (unseenbio.com). |
| Fusicatenibacter saccharivorans | 9 | Moderate Coloniser | In 100% of Europeans (unseenbio.com). |
| Gemmiger formicilis | 8 | Moderate Coloniser | In 97% of Europeans (unseenbio.com). |
| Gemmiger variabile | 1 | Moderate Coloniser | No record in the NCBI database for this organism. In 77% of Europeans (unseenbio.com). A moderate coloniser. |
| Intestinimonas butyriciproducens | 11 | Moderate Coloniser | In 94% of Europeans (unseenbio.com). |
| Intestinimonas massiliensis | 3 | Moderate Coloniser | In 94% of Europeans (unseenbio.com). |
| Lachnospira rogosae | 1 | Moderate Coloniser | No record in the NCBI database for this organism. In 99% of Europeans (unseenbio.com). A moderate coloniser. |
| Lacrimispora saccharolytica | 9 | Moderate Coloniser | In 99% of Europeans (unseenbio.com). |
| Lawsonibacter asaccharolyticus | 1 | Moderate Coloniser | In 97% of Europeans (unseenbio.com). |
| Massilimicrobiota timonensis | 2 | Moderate Coloniser | In 98% of Europeans (unseenbio.com). |
| Massilioclostridium coli | 2 | Moderate Coloniser | In 98% of Europeans (unseenbio.com). |
| Parabacteroides goldsteinii | 14 | Moderate Coloniser | In 69% of Europeans (unseenbio.com). |
| Paraprevotella clara | 11 | Moderate Coloniser | In 91% of Europeans (unseenbio.com). |
| Phocaeicola barnesiae | 7 | Moderate Coloniser | In 79% of Europeans (unseenbio.com). |
| Phocaeicola sartorii | 4 | Moderate Coloniser | In 99% of Europeans (unseenbio.com). |
| Prevotella bergensis | 5 | Moderate Coloniser | In 86% of Europeans (unseenbio.com). |
| Prevotella corporis | 6 | Moderate Coloniser | In 99% of Europeans (unseenbio.com). |
| Prevotella melaninogenica | 13 | Moderate Coloniser | In 86% of Europeans (unseenbio.com). |
| Prevotella oris | 8 | Moderate Coloniser | In 94% of Europeans (unseenbio.com). |
| Provencibacterium massiliense | 1 | Moderate Coloniser | In 75% of Europeans (unseenbio.com). |
| Romboutsia timonensis | 2 | Moderate Coloniser | In 78% of Europeans (unseenbio.com). |
| Ruminococcus bicirculans | 10 | Moderate Coloniser | In 94% of Europeans (unseenbio.com). |
| Ruminococcus champanellensis | 13 | Moderate Coloniser | In 72% of Europeans (unseenbio.com). |
| Ruthenibacterium lactatiformans | 5 | Moderate Coloniser | In 99% of Europeans (unseenbio.com). |
| Tidjanibacter inops | 1 | Moderate Coloniser | Isolation and characterisation not yet published. In 83% of Europeans (unseenbio.com). A moderate coloniser. |
| Phocaeicola coprocola | 22 | Widespread Coloniser | In 95% of Europeans (unseenbio.com). |
| Phocaeicola coprophilus | 21 | Widespread Coloniser | In 87% of Europeans (unseenbio.com). |
| Roseburia faecis | 16 | Widespread Coloniser | In 99% of Europeans (unseenbio.com). |
| Acinetobacter johnsonii | 8 | Rare Coloniser | 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 | 10 | Rare Coloniser | In 1% of Europeans (unseenbio.com). Rare coloniser. |
| Enterococcus gallinarum | 12 | Rare Coloniser | In 1% of Europeans (unseenbio.com). |
| Fusobacterium ulcerans | 13 | Rare Coloniser | Few Europeans have it (unseenbio.com). |
| Lacticaseibacillus casei | 13 | Rare Coloniser | An unlikely permanent inhabitant of the colon. Found in human breast milk (Jeurink2013). |
| Lactobacillus helveticus | 11 | Rare Coloniser | A probiotic, but only present in the faeces of 3% of Europeans (unseenbio.com). Found in human breast milk (Jeurink2013). |
| Lactobacillus iners | 11 | Rare Coloniser | Rare coloniser. |
| Limosilactobacillus mucosae | 13 | Rare Coloniser | In 4% of Europeans (unseenbio.com), i.e., a rare coloniser. |
| Limosilactobacillus vaginalis | 13 | Rare Coloniser | In 3% of Europeans, so a rare coloniser. Found in human breast milk (Jeurink2013). |
| Neisseria subflava | 12 | Rare Coloniser | In 6% of Europeans (unseenbio.com). Rare coloniser. |
| Pediococcus acidilactici | 10 | Rare Coloniser | In 1% of Europeans (unseenbio.com). Rare coloniser. A probiotic. |
| Pseudomonas aeruginosa | 15 | Rare Coloniser | In 7% of Europeans (unseenbio.com). Rare coloniser. |