| MMDBm0000014 | Akkermansia muciniphila | Eubacteria | Verrucomicrobia | Human Feces | Indirect association between microbiota composition and metabolites measured in host biospecimen | Not Available |
| MMDBm0000024 | Bacillus altitudinis 41KF2b | Eubacteria | Firmicutes | Human Feces | Metabolic reconstruction | VMH |
| MMDBm0000090 | Bifidobacterium thermophilum RBL67 | Eubacteria | Actinobacteria | Human Feces | Metabolic reconstruction | VMH |
| MMDBm0000094 | Blautia obeum ATCC 29174 | Eubacteria | Firmicutes | Human Feces | Metabolic reconstruction | VMH |
| MMDBm0000107 | Cloacibacillus evryensis DSM 19522 | Eubacteria | Synergistetes | Human Feces | Metabolic reconstruction | VMH |
| MMDBm0000108 | Clostridioides difficile | Eubacteria | Firmicutes | Human Feces | Microbial culture | Not Available |
| MMDBm0000112 | Clostridioides difficile R20291 | Eubacteria | Firmicutes | Human | Metabolic reconstruction | VMH |
| MMDBm0000119 | Clostridium botulinum | Eubacteria | Firmicutes | Human Feces | Microbial culture | Not Available |
| MMDBm0000120 | Clostridium botulinum A str. ATCC 19397 | Eubacteria | Firmicutes | Human | Metabolic reconstruction | VMH |
| MMDBm0000121 | Clostridium botulinum Bf | Eubacteria | Firmicutes | Human Feces | Metabolic reconstruction | VMH |
| MMDBm0000122 | Clostridium botulinum F str. 230613 | Eubacteria | Firmicutes | Human Feces | Metabolic reconstruction | VMH |
| MMDBm0000157 | Enterococcus hirae ATCC 9790 | Eubacteria | Firmicutes | Human Feces | Metabolic reconstruction | VMH |
| MMDBm0000160 | Escherichia coli | Eubacteria | Proteobacteria | Human | Metabolic reconstruction | VMH |
| MMDBm0000162 | Escherichia coli CFT073 | Eubacteria | Proteobacteria | Human | Not Available | RHEA |
| MMDBm0000167 | Escherichia coli SMS-3-5 | Eubacteria | Proteobacteria | Human | Not Available | RHEA |
| MMDBm0000169 | Escherichia coli UTI89 | Eubacteria | Proteobacteria | Human | Not Available | RHEA |
| MMDBm0000185 | Fusobacterium nucleatum subsp. nucleatum ATCC 25586 | Eubacteria | Fusobacteria | Human | Metabolic reconstruction | VMH |
| MMDBm0000187 | Gemella sanguinis ATCC700632 | Eubacteria | Firmicutes | Human Feces | Metabolic reconstruction | VMH |
| MMDBm0000368 | Shigella flexneri | Eubacteria | Proteobacteria | Human | Not Available | RHEA |
| MMDBm0000432 | Streptococcus sanguinis | Eubacteria | Firmicutes | Human | Indirect association between microbiota composition and metabolites measured in host biospecimen | Not Available |
| MMDBm0000793 | Clostridium hiranonis | Eubacteria | Firmicutes | Human | Metabolic reconstruction | VMH |
| MMDBm0001027 | Acetoanaerobium sticklandii | Eubacteria | Firmicutes | Not Available | Microbial culture | Not Available |
| MMDBm0001116 | Granulicatella | Eubacteria | Firmicutes | Human Feces | Indirect association between microbiota composition and metabolites measured in host biospecimen | Not Available |
| MMDBm0001125 | Subdoligranulum | Eubacteria | Firmicutes | Human Feces | Indirect association between microbiota composition and metabolites measured in host biospecimen | Not Available |
| MMDBm0001450 | Citrobacter koseri ATCC BAA-895 | Eubacteria | Proteobacteria | Human | Not Available | RHEA |
