Named species · GMrepo v3 · NCBI lineage

Microbes

495 species

Most studiedMost common in healthy guts

Species	Healthy guts	Samples ↓	Products
Faecalibacterium prausnitzii Bacillota · Oscillospiraceae	90%	20,688	0
Bacteroides uniformis Bacteroidota · Bacteroidaceae	87%	20,417	0
Phocaeicola vulgatus Bacteroidota · Bacteroidaceae	82%	19,640	0
Parabacteroides distasonis Bacteroidota · Tannerellaceae	80%	18,684	0
Fusicatenibacter saccharivorans Bacillota · Lachnospiraceae	81%	18,293	0
Bacteroides ovatus Bacteroidota · Bacteroidaceae	76%	17,825	0
Agathobacter rectalis Bacillota · Lachnospiraceae	79%	17,543	0
Bifidobacterium longum Actinomycetota · Bifidobacteriaceae	76%	16,852	1,355
Bacteroides thetaiotaomicron Bacteroidota · Bacteroidaceae	69%	16,618	0
Dorea longicatena Bacillota · Lachnospiraceae	73%	16,441	0
Mediterraneibacter gnavus Bacillota · Lachnospiraceae	62%	16,041	0
Roseburia inulinivorans Bacillota · Lachnospiraceae	70%	15,651	0
Blautia obeum Bacillota · Lachnospiraceae	67%	15,479	0
Blautia massiliensis (ex Durand et al. 2017) Bacillota · Lachnospiraceae	68%	15,176	0
Streptococcus salivarius Bacillota · Streptococcaceae	62%	14,842	34
Roseburia faecis Bacillota · Lachnospiraceae	68%	14,837	0
Lachnospira pectinoschiza Bacillota · Lachnospiraceae	67%	14,692	0
Alistipes onderdonkii Bacteroidota · Rikenellaceae	63%	14,224	0
Parabacteroides merdae Bacteroidota · Tannerellaceae	62%	14,115	0
Bacteroides caccae Bacteroidota · Bacteroidaceae	62%	14,078	0
Collinsella aerofaciens Actinomycetota · Coriobacteriaceae	65%	14,053	0
Ruminococcus bromii Bacillota · Oscillospiraceae	63%	14,012	0
Mediterraneibacter faecis Bacillota · Lachnospiraceae	64%	13,962	0
Roseburia hominis Bacillota · Lachnospiraceae	64%	13,947	0
Coprococcus comes Bacillota · Lachnospiraceae	63%	13,826	0
Bacteroides xylanisolvens Bacteroidota · Bacteroidaceae	59%	13,732	0
Alistipes shahii Bacteroidota · Rikenellaceae	63%	13,514	0
Phocaeicola dorei Bacteroidota · Bacteroidaceae	54%	12,489	0
Bacteroides stercoris Bacteroidota · Bacteroidaceae	50%	12,071	0
Enterocloster bolteae Bacillota · Lachnospiraceae	42%	11,709	0
Ruminococcus bicirculans (ex Wegman et al. 2014) Bacillota · Oscillospiraceae	55%	11,696	0
Roseburia intestinalis Bacillota · Lachnospiraceae	53%	11,670	0
Bacteroides fragilis Bacteroidota · Bacteroidaceae	44%	11,390	0
Streptococcus parasanguinis Bacillota · Streptococcaceae	44%	11,044	0
Faecalibacillus intestinalis Bacillota · Coprobacillaceae	49%	10,685	0
Bifidobacterium adolescentis Actinomycetota · Bifidobacteriaceae	53%	10,367	13
Alistipes communis Bacteroidota · Rikenellaceae	51%	10,222	0
Eubacterium ventriosum Bacillota · Eubacteriaceae	47%	9,921	0
Faecalicatena fissicatena Bacillota · Lachnospiraceae	46%	9,505	0
Hydrogenoanaerobacterium saccharovorans Bacillota · Oscillospiraceae	43%	9,057	0
Segatella copri Bacteroidota · Prevotellaceae	39%	8,908	0
Bacteroides cellulosilyticus Bacteroidota · Bacteroidaceae	35%	8,805	0
[Clostridium] innocuum Bacillota · Clostridiaceae	32%	8,645	0
Bifidobacterium pseudocatenulatum Actinomycetota · Bifidobacteriaceae	37%	8,523	0
Hungatella hathewayi Bacillota · Lachnospiraceae	28%	7,945	0
Phocaeicola massiliensis Bacteroidota · Bacteroidaceae	34%	7,748	0
Coprococcus eutactus Bacillota · Lachnospiraceae	39%	7,725	0
Alistipes indistinctus Bacteroidota · Rikenellaceae	33%	7,331	0
Enterocloster citroniae Bacillota · Lachnospiraceae	28%	7,304	0
Alistipes ihumii Bacteroidota · Rikenellaceae	36%	7,246	0
Thomasclavelia ramosa Bacillota · Coprobacillaceae	24%	7,172	0
Bacteroides finegoldii Bacteroidota · Bacteroidaceae	27%	6,205	0
Anaerotruncus colihominis Bacillota · Oscillospiraceae	25%	6,169	0
Phocaeicola plebeius Bacteroidota · Bacteroidaceae	25%	6,067	0
Paraprevotella clara Bacteroidota · Prevotellaceae	27%	5,834	0
Bifidobacterium bifidum Actinomycetota · Bifidobacteriaceae	28%	5,813	1,272
Bacteroides eggerthii Bacteroidota · Bacteroidaceae	24%	5,593	0
Bacteroides nordii Bacteroidota · Bacteroidaceae	21%	5,434	0
Sellimonas intestinalis Bacillota · Lachnospiraceae	21%	5,299	0
Bacteroides intestinalis Bacteroidota · Bacteroidaceae	21%	5,257	0
Faecalicatena contorta Bacillota · Lachnospiraceae	21%	5,231	0
Ruminococcus callidus Bacillota · Oscillospiraceae	25%	5,144	0
Klebsiella pneumoniae Pseudomonadota · Enterobacteriaceae	16%	4,821	0
Phocaeicola coprocola Bacteroidota · Bacteroidaceae	19%	4,676	0
Blautia luti Bacillota · Lachnospiraceae	22%	4,637	0
Parabacteroides goldsteinii Bacteroidota · Tannerellaceae	18%	4,504	0
Streptococcus mitis Bacillota · Streptococcaceae	19%	4,478	0
Bacteroides salyersiae Bacteroidota · Bacteroidaceae	18%	4,433	0
Coprobacter fastidiosus Bacteroidota · Barnesiellaceae	21%	4,432	0
Megamonas funiformis Bacillota · Selenomonadaceae	17%	4,235	0
[Clostridium] nexile Bacillota · Lachnospiraceae	14%	4,085	0
Intestinimonas massiliensis (ex Afouda et al. 2020) Bacillota	18%	4,081	0
Blautia producta Bacillota · Lachnospiraceae	14%	3,888	0
Bacteroides faecis Bacteroidota · Bacteroidaceae	17%	3,706	0
Bacteroides clarus Bacteroidota · Bacteroidaceae	15%	3,529	0
Schaalia odontolytica Actinomycetota · Actinomycetaceae	15%	3,497	0
Faecalimonas umbilicata Bacillota · Lachnospiraceae	10%	3,489	0
Blautia hansenii Bacillota · Lachnospiraceae	11%	3,453	0
Monoglobus pectinilyticus Bacillota · Monoglobaceae	14%	3,279	0
Leyella stercorea Bacteroidota · Prevotellaceae	13%	3,175	0
Anaerostipes caccae Bacillota · Lachnospiraceae	12%	2,997	0
Faecalibacillus faecis Bacillota · Coprobacillaceae	13%	2,832	0
Bifidobacterium dentium Actinomycetota · Bifidobacteriaceae	9.8%	2,771	0
Streptococcus gordonii Bacillota · Streptococcaceae	9.4%	2,720	0
Candidatus Borkfalkia ceftriaxoniphila Bacillota · Christensenellaceae	13%	2,676	0
Bifidobacterium catenulatum Actinomycetota · Bifidobacteriaceae	15%	2,651	0
Bifidobacterium breve Actinomycetota · Bifidobacteriaceae	11%	2,645	713
Blautia hydrogenotrophica Bacillota · Lachnospiraceae	10%	2,513	0
Lactococcus lactis Bacillota · Streptococcaceae	11%	2,510	219
Actinomyces oris Actinomycetota · Actinomycetaceae	9.7%	2,494	0
Streptococcus oralis Bacillota · Streptococcaceae	8.1%	2,444	0
Enterococcus faecium Bacillota · Enterococcaceae	5.4%	2,414	49
Parabacteroides johnsonii Bacteroidota · Tannerellaceae	10%	2,353	0
Allofournierella massiliensis Bacillota · Oscillospiraceae	11%	2,308	0
Enterococcus faecalis Bacillota · Enterococcaceae	6.5%	2,243	13
Gemella sanguinis Bacillota · Gemellaceae	9.7%	2,206	0
Bifidobacterium animalis Actinomycetota · Bifidobacteriaceae	7.4%	1,915	1,443
Lactonifactor longoviformis Bacillota · Clostridiaceae	7.4%	1,722	0
Clostridium perfringens Bacillota · Clostridiaceae	5.9%	1,710	0
Enterobacter hormaechei Pseudomonadota · Enterobacteriaceae	6.5%	1,649	0
Streptococcus mutans Bacillota · Streptococcaceae	5.4%	1,639	0
Klebsiella variicola Pseudomonadota · Enterobacteriaceae	5.9%	1,602	0
Lancefieldella parvula Actinomycetota · Atopobiaceae	4.7%	1,523	0
Streptococcus rubneri Bacillota · Streptococcaceae	6.9%	1,496	0
Phocaeicola coprophilus Bacteroidota · Bacteroidaceae	6.0%	1,462	0
Lactobacillus gasseri Bacillota · Lactobacillaceae	4.2%	1,410	377
Megasphaera micronuciformis Bacillota · Veillonellaceae	3.6%	1,362	0
Ligilactobacillus salivarius Bacillota · Lactobacillaceae	3.7%	1,353	754
Citrobacter freundii Pseudomonadota · Enterobacteriaceae	4.7%	1,313	0
Enterobacter roggenkampii Pseudomonadota · Enterobacteriaceae	5.2%	1,271	0
Actinomyces naeslundii Actinomycetota · Actinomycetaceae	4.8%	1,226	0
Lacticaseibacillus paracasei Bacillota · Lactobacillaceae	4.6%	1,159	747
Limosilactobacillus fermentum Bacillota · Lactobacillaceae	2.7%	1,150	177
Streptococcus gallolyticus Bacillota · Streptococcaceae	3.6%	1,113	0
Limosilactobacillus mucosae Bacillota · Lactobacillaceae	3.4%	1,108	0
Citrobacter portucalensis Pseudomonadota · Enterobacteriaceae	4.1%	1,068	0
Lactobacillus delbrueckii Bacillota · Lactobacillaceae	5.3%	1,044	604
Gemella morbillorum Bacillota · Gemellaceae	2.5%	1,021	0
Lacticaseibacillus rhamnosus Bacillota · Lactobacillaceae	2.9%	1,004	1,504
Enterobacter kobei Pseudomonadota · Enterobacteriaceae	4.4%	996	0
Ligilactobacillus ruminis Bacillota · Lactobacillaceae	4.6%	974	0
Actinomyces dentalis Actinomycetota · Actinomycetaceae	2.9%	923	0
Parabacteroides gordonii Bacteroidota · Tannerellaceae	3.0%	917	0
Klebsiella michiganensis Pseudomonadota · Enterobacteriaceae	3.4%	833	0
Alistipes provencensis Bacteroidota · Rikenellaceae	3.1%	793	0
Raoultella ornithinolytica Pseudomonadota · Enterobacteriaceae	3.4%	786	0
Cuneatibacter caecimuris Bacillota · Lachnospiraceae	3.0%	777	0
Streptococcus lutetiensis Bacillota · Streptococcaceae	2.5%	768	0
Prevotella dentalis Bacteroidota · Prevotellaceae	3.5%	764	0
Scardovia wiggsiae Actinomycetota · Bifidobacteriaceae	1.6%	742	0
Enorma massiliensis Actinomycetota · Coriobacteriaceae	2.7%	723	0
Enterobacter asburiae Pseudomonadota · Enterobacteriaceae	3.2%	695	0
Bacillus subtilis Bacillota · Bacillaceae	4.8%	691	458
Mitsuokella jalaludinii Bacillota · Selenomonadaceae	3.6%	689	0
Enterobacter ludwigii Pseudomonadota · Enterobacteriaceae	3.1%	686	0
Lactococcus cremoris Bacillota · Streptococcaceae	3.0%	679	0
Clostridioides difficile Bacillota · Peptostreptococcaceae	1.6%	668	0
Enterococcus gallinarum Bacillota · Enterococcaceae	1.9%	645	0
Hoylesella buccalis Bacteroidota · Prevotellaceae	2.3%	645	0
Leuconostoc lactis Bacillota · Lactobacillaceae	2.7%	640	11
Paraprevotella xylaniphila Bacteroidota · Prevotellaceae	3.0%	625	0
Bifidobacterium angulatum Actinomycetota · Bifidobacteriaceae	3.8%	604	0
Faecalicatena orotica Bacillota · Lachnospiraceae	1.9%	601	0
Klebsiella aerogenes Pseudomonadota · Enterobacteriaceae	2.3%	586	0
Enterococcus casseliflavus Bacillota · Enterococcaceae	2.1%	578	0
Clostridium neonatale Bacillota · Clostridiaceae	2.3%	566	0
Mitsuokella multacida Bacillota · Selenomonadaceae	2.8%	564	0
Alloscardovia omnicolens Actinomycetota · Bifidobacteriaceae	1.6%	554	0
Lactobacillus acidophilus Bacillota · Lactobacillaceae	2.0%	552	2,602
Lactobacillus crispatus Bacillota · Lactobacillaceae	1.6%	508	28

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