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Summary. Commonly cited in human gut microbiome research as influencing - or serving as markers of - intestinal health, metabolism, and immune function.
Gut Barrier Integrity
Summary. Bacteria that produce short-chain fatty acids (SCFAs) - such as butyrate, propionate, and acetate - break down dietary fibers and other complex carbohydrates that human digestive mechanisms cannot digest, converting them into SCFAs.
Canonical Designation | GTDB Designation (R220) | Branchpoint Reference Strain |
Faecalibacterium prausnitzii | Faecalibacterium prausnitzii | DSM 107838 |
n/a | Faecalibacterium prausnitzii_A | n/a |
n/a | Faecalibacterium prausnitzii_C | n/a |
n/a | Faecalibacterium prausnitzii_D | n/a |
n/a | Faecalibacterium prausnitzii_E | n/a |
n/a | Faecalibacterium prausnitzii_F | n/a |
n/a | Faecalibacterium prausnitzii_G | n/a |
n/a | Faecalibacterium prausnitzii_H | n/a |
n/a | Faecalibacterium prausnitzii_I | n/a |
n/a | Faecalibacterium prausnitzii_J | n/a |
n/a | Faecalibacterium prausnitzii_K | n/a |
n/a | Faecalibacterium prausnitzii_L | n/a |
Bifidobacterium adolescentis | Bifidobacterium adolescentis | DSM 20087 |
Bifidobacterium bifidum | Bifidobacterium bifidum | DSM 20456 |
Bifidobacterium catenulatum | Bifidobacterium catenulatum | DSM 16992 |
Bifidobacterium longum subsp. infantis | Bifidobacterium infantis | DSM 20088 |
Bifidobacterium longum subsp. longum | Bifidobacterium longum | DSM 20219 |
Bifidobacterium pseudocatenulatum | Bifidobacterium pseudocatenulatum | DSM 20438 |
Bifidobacterium vaginale_G | Bifidobacterium swidsinskii | n/a |
Bifidobacterium sp002884815 | Bifidobacterium piotii | n/a |
Eubacterium hallii | Anaerobutyricum hallii | DSM 3353 |
Anaerostipes hadrus | Anaerostipes hadrus | DSM 3319 |
n/a | Anaerostipes hadrus_A | n/a |
Roseburia hominis | Roseburia hominis | DSM 16839 |
Roseburia inulinivorans | Roseburia inulinivorans | DSM 16841 |
Coprococcus catus | Coprococcus_A catus | n/a |
Dorea longicatena | Dorea_A longicatena | DSM 13814 |
n/a | Dorea_A longicatena_B | n/a |
Dorea formicigenerans | Dorea formicigenerans | DSM 3992 |
Eubacterium ramulus | Eubacterium_I ramulus | ATCC 29099 |
Eubacterium eligens | Lachnospira eligens | ATCC 27750 |
Summary. Hydrogen sulfide (H2S)-producing bacteria in the gut can play a complicated role in gut health. At low, physiologically normal levels, hydrogen sulfide can have some signaling or regulatory functions. However, when these organisms become overly abundant, they can increase H2S concentrations to levels that may cause or exacerbate intestinal inflammation and epithelial damage.
Canonical Designation | GTDB Designation (R220) | Branchpoint Reference Strain |
Bilophila wadsworthia | Bilophila wadsworthia | DSM 11045 |
Desulfovibrio piger | Desulfovibrio piger | DSM 749 |
n/a | Desulfovibrio piger_A | n/a |
Summary. Mucin-degrading bacteria help maintain a healthy turnover of the mucus layer. This process allows for the production of fresh mucus, which helps keep the barrier robust. However, if these bacteria become overabundant then degradation can outpace replenishment. The result is a thinned mucus layer, exposing the intestinal epithelium to potential pathogens and increasing the risk of “leaky gut” or inflammatory conditions.
Canonical Designation | GTDB Designation (R220) | Branchpoint Reference Strain |
Akkermansia muciniphila | Akkermansia muciniphila | DSM 26127 |
n/a | Akkermansia muciniphila_A | n/a |
n/a | Akkermansia muciniphila_B | n/a |
n/a | Akkermansia muciniphila_C | n/a |
n/a | Akkermansia muciniphila_D | n/a |
Ruminococcus gnavus | Ruminococcus_B gnavus | ATCC 29149 |
Ruminococcus bromii | Ruminococcus_E bromii | ATCC 27255 |
n/a | Ruminococcus_E bromii_A | n/a |
n/a | Ruminococcus_E bromii_B | n/a |
Health Status
Summary. Many microbes in the gut do not have a single, well-defined function. These microbes appear consistently in healthy microbiomes, where they are presumed beneficial or at least neutral. Their precise metabolic activities remain unclear, and they may shift between positive and negative roles depending on factors such as the broader microbiome composition, diet, host genetics, or overall health status. These organisms remain important but mysterious members of the microbiome whose significance often lies in helping maintain the overall balance and stability of the gut ecosystem rather than performing a single, clearly defined task.
Canonical Designation | GTDB Designation (R220) | Branchpoint Reference Strain |
Bacteroides fragilis | Bacteroides fragilis | DSM 2151 |
n/a | Bacteroides fragilis_A | n/a |
Bacteroides ovatus | Bacteroides ovatus | DSM 1896 |
Bacteroides thetaiotaomicron | Bacteroides thetaiotaomicron | DSM 2079 |
Bacteroides uniformis | Bacteroides uniformis | DSM 6597 |
Bacteroides xylanisolvens | Bacteroides xylanisolvens | DSM 18836 |
Bacteroides dorei | Phocaeicola dorei | DSM 17855 |
Bacteroides vulgatus | Phocaeicola vulgatus | ATCC 8482 |
Alistipes putredinis | Alistipes putredinis | DSM 17216 |
Alistipes shahii | Alistipes shahii | DSM 19121 |
Barnesiella intestinihominis | Barnesiella intestinihominis | DSM 21032 |
Parabacteroides distasonis | Parabacteroides distasonis | DSM 20701 |
n/a | Parabacteroides distasonis_A | n/a |
n/a | Parabacteroides distasonis_B | n/a |
Collinsella aerofaciens | Collinsella aerofaciens | DSM 3979 |
Clostridium asparagiforme | Enterocloster asparagiformis | DSM 15981 |
Clostridium bolteae | Enterocloster bolteae | ATCC BAA-613 |
Flavonifractor plautii | Flavonifractor plautii | DSM 6740 |
Clostridium hathewayi | Hungatella hathewayi | DSM 13479 |
Methanobrevibacter smithii | Methanobrevibacter_A smithii | DSM 861 |