| MMDBm0000012 | Agrobacterium tumefaciens F2 | Eubacteria | Proteobacteria | Human Feces | Metabolic reconstruction | VMH |
| MMDBm0000028 | Bacillus halodurans C-125 | Eubacteria | Firmicutes | Human Feces | Not Available | RHEA |
| MMDBm0000033 | Bacillus vallismortis DV1-F-3 | Eubacteria | Firmicutes | Human Feces | Metabolic reconstruction | VMH |
| MMDBm0000064 | Bifidobacterium adolescentis ATCC 15703 | Eubacteria | Actinobacteria | Human | Metabolic reconstruction | VMH |
| MMDBm0000072 | Bifidobacterium kashiwanohense JCM 15439 = DSM 21854 | Eubacteria | Actinobacteria | Human Feces | Metabolic reconstruction | VMH |
| MMDBm0000075 | Bifidobacterium longum DJO10A | Eubacteria | Actinobacteria | Human | Metabolic reconstruction | VMH |
| MMDBm0000187 | Gemella sanguinis ATCC700632 | Eubacteria | Firmicutes | Human Feces | Metabolic reconstruction | VMH |
| MMDBm0000310 | Treponema bryantii | Eubacteria | Spirochaetes | Not Available | Microbial culture | Not Available |
| MMDBm0000433 | Streptococcus mutans | Eubacteria | Firmicutes | Human | Microbial culture | Not Available |
| MMDBm0000525 | Mycolicibacterium smegmatis | Eubacteria | Actinobacteria | Not Available | Microbial culture | Not Available |
| MMDBm0000583 | Saccharomyces cerevisiae | Fungi | Ascomycota | Human Feces | Microbial culture | Not Available |
| MMDBm0000583 | Saccharomyces cerevisiae | Fungi | Ascomycota | Human Feces | Unknown | YMDB |
| MMDBm0000584 | Candida albicans | Fungi | Ascomycota | Human Feces | Microbial culture | Not Available |
| MMDBm0000585 | Candida tropicalis | Fungi | Ascomycota | Human Feces | Microbial culture | Not Available |
| MMDBm0000619 | Thermoanaerobacterium saccharolyticum | Eubacteria | Firmicutes | Not Available | Microbial culture | Not Available |
| MMDBm0000626 | Thermoanaerobacterium xylanolyticum | Eubacteria | Firmicutes | Not Available | Microbial culture | Not Available |
| MMDBm0000633 | Staphylococcus capitis | Eubacteria | Firmicutes | Human | Metabolic reconstruction | VMH |
| MMDBm0000692 | Staphylococcus lentus | Eubacteria | Firmicutes | Not Available | Microbial culture | Not Available |
| MMDBm0000707 | Staphylococcus pasteuri | Eubacteria | Firmicutes | Human | Microbial culture | Not Available |
| MMDBm0000790 | Thermus igniterrae | Eubacteria | Deinococcus-thermus | Not Available | Microbial culture | Not Available |
| MMDBm0000815 | Enterococcus villorum | Eubacteria | Firmicutes | Not Available | Microbial culture | Not Available |
| MMDBm0000848 | Enterococcus haemoperoxidus | Eubacteria | Firmicutes | Not Available | Microbial culture | Not Available |
| MMDBm0000889 | Bacteroides massiliensis | Eubacteria | Bacteroidetes | Human Stool | Microbial culture | Not Available |
| MMDBm0000931 | Emticicia oligotrophica | Eubacteria | Bacteroidetes | Not Available | Microbial culture | Not Available |
| MMDBm0001089 | Treponema succinifaciens | Eubacteria | Spirochaetes | Not Available | Microbial culture | Not Available |
