| MMDBm0000039 | Bacteroides clarus YIT 12056 | Eubacteria | Bacteroidetes | Human Feces | Metabolic reconstruction | VMH |
| MMDBm0000054 | Bacteroides thetaiotaomicron | Eubacteria | Bacteroidetes | Human Feces | Microbial culture | Not Available |
| MMDBm0000072 | Bifidobacterium kashiwanohense JCM 15439 = DSM 21854 | Eubacteria | Actinobacteria | Human Feces | Metabolic reconstruction | VMH |
| MMDBm0000074 | Bifidobacterium longum | Eubacteria | Actinobacteria | Human | Microbial culture | Not Available |
| MMDBm0000089 | Bifidobacterium pseudolongum subsp. Pseudolongum DSM 20099 | Eubacteria | Actinobacteria | Human Feces | Metabolic reconstruction | VMH |
| MMDBm0000090 | Bifidobacterium thermophilum RBL67 | Eubacteria | Actinobacteria | Human Feces | Metabolic reconstruction | VMH |
| MMDBm0000105 | Citrobacter freundii ATCC 8090 = MTCC 1658 | Eubacteria | Proteobacteria | Human Feces | Metabolic reconstruction | VMH |
| MMDBm0000107 | Cloacibacillus evryensis DSM 19522 | Eubacteria | Synergistetes | Human Feces | Metabolic reconstruction | VMH |
| MMDBm0000116 | Clostridium beijerinckii NCIMB 8052 | Eubacteria | Firmicutes | Human Feces | Metabolic reconstruction | VMH |
| MMDBm0000125 | Clostridium clostridioforme CM201 | Eubacteria | Firmicutes | Human Feces | Metabolic reconstruction | VMH |
| MMDBm0000132 | Clostridium perfringens ATCC 13124 | Eubacteria | Firmicutes | Human | Metabolic reconstruction | VMH |
| MMDBm0000136 | Clostridium saccharoperbutylacetonicum N1-4(HMT) | Eubacteria | Firmicutes | Human Feces | Metabolic reconstruction | VMH |
| MMDBm0000147 | Dorea formicigenerans ATCC 27755 | Eubacteria | Firmicutes | Human Feces | Metabolic reconstruction | VMH |
| MMDBm0000171 | Eubacterium eligens ATCC 27750 | Eubacteria | Firmicutes | Human | Metabolic reconstruction | VMH |
| MMDBm0000172 | Eubacterium limosum KIST612 | Eubacteria | Firmicutes | Human Feces | Metabolic reconstruction | VMH |
| MMDBm0000181 | Faecalibacterium prausnitzii SL3/3 | Eubacteria | Firmicutes | Human Feces | Metabolic reconstruction | VMH |
| MMDBm0000207 | Lactobacillus reuteri | Eubacteria | Firmicutes | Human | Metabolic reconstruction | VMH |
| MMDBm0000233 | Parabacteroides goldsteinii dnLKV18 | Eubacteria | Bacteroidetes | Human Feces | Metabolic reconstruction | VMH |
| MMDBm0000269 | Stoquefichus massiliensis AP9 | Eubacteria | Firmicutes | Human Feces | Metabolic reconstruction | VMH |
| MMDBm0000306 | Pelobacter carbinolicus | Eubacteria | Proteobacteria | Not Available | Microbial culture | Not Available |
| MMDBm0000472 | Clostridium butyricum | Eubacteria | Firmicutes | Human Feces | Microbial culture | Not Available |
| MMDBm0000492 | Lactobacillus buchneri | Eubacteria | Firmicutes | Human | Microbial culture | Not Available |
| MMDBm0000619 | Thermoanaerobacterium saccharolyticum | Eubacteria | Firmicutes | Not Available | Microbial culture | Not Available |
| MMDBm0000620 | Salmonella enterica | Eubacteria | Proteobacteria | Human | Microbial culture | Not Available |
| MMDBm0000666 | Terrisporobacter glycolicus | Eubacteria | Firmicutes | Human Feces | Microbial culture | Not Available |
