| MMDBm0000015 | Akkermansia muciniphila ATCC BAA-835 | Eubacteria | Verrucomicrobia | Human | Not Available | RHEA |
| MMDBm0000079 | Bifidobacterium longum subsp. infantis ATCC 15697 = JCM 1222 = DSM 20088 | Eubacteria | Actinobacteria | Human | Metabolic reconstruction | VMH |
| MMDBm0000105 | Citrobacter freundii ATCC 8090 = MTCC 1658 | Eubacteria | Proteobacteria | Human Feces | Metabolic reconstruction | VMH |
| MMDBm0000114 | Clostridium acetobutylicum ATCC 824 | Eubacteria | Firmicutes | Human Feces | Not Available | RHEA |
| MMDBm0000160 | Escherichia coli | Eubacteria | Proteobacteria | Human | Unknown | ECMDB |
| MMDBm0000162 | Escherichia coli CFT073 | Eubacteria | Proteobacteria | Human | Not Available | RHEA |
| MMDBm0000169 | Escherichia coli UTI89 | Eubacteria | Proteobacteria | Human | Not Available | RHEA |
| MMDBm0000194 | Klebsiella aerogenes KCTC 2190 | Eubacteria | Proteobacteria | Human | Metabolic reconstruction | VMH |
| MMDBm0000368 | Shigella flexneri | Eubacteria | Proteobacteria | Human | Not Available | RHEA |
| MMDBm0000464 | Bacillus mycoides | Eubacteria | Firmicutes | Not Available | Metabolic reconstruction | VMH |
| MMDBm0000633 | Staphylococcus capitis | Eubacteria | Firmicutes | Human | Metabolic reconstruction | VMH |
| MMDBm0001052 | Clostridium saccharoperbutylacetonicum | Eubacteria | Firmicutes | Not Available | Metabolic reconstruction | VMH |
| MMDBm0001067 | Klebsiella variicola | Eubacteria | Proteobacteria | Human Feces | Metabolic reconstruction | VMH |
| MMDBm0001213 | Alkaliphilus metalliredigens QYMF | Eubacteria | Firmicutes | Not Available | Not Available | RHEA |
| MMDBm0001312 | Brucella melitensis bv. 1 str. 16M | Eubacteria | Proteobacteria | Human | Not Available | RHEA |
| MMDBm0001313 | Brucella suis 1330 | Eubacteria | Proteobacteria | Human | Not Available | RHEA |
| MMDBm0001314 | Brucella abortus bv. 1 str. 9-941 | Eubacteria | Proteobacteria | Human | Not Available | RHEA |
| MMDBm0001315 | Brucella melitensis biovar Abortus 2308 | Eubacteria | Proteobacteria | Human | Not Available | RHEA |
| MMDBm0001457 | Clostridium thermocellum ATCC 27405 | Eubacteria | Firmicutes | Not Available | Not Available | RHEA |
| MMDBm0001458 | Clostridium kluyveri DSM 555 | Eubacteria | Firmicutes | Not Available | Not Available | RHEA |
| MMDBm0001485 | Corynebacterium glutamicum ATCC 13032 | Eubacteria | Actinobacteria | Not Available | Not Available | RHEA |
| MMDBm0001486 | Corynebacterium efficiens YS-314 | Eubacteria | Actinobacteria | Not Available | Not Available | RHEA |
| MMDBm0001487 | Corynebacterium glutamicum R | Eubacteria | Actinobacteria | Not Available | Not Available | RHEA |
| MMDBm0001501 | Cronobacter sakazakii ATCC BAA-894 | Eubacteria | Proteobacteria | Human | Metabolic reconstruction | VMH |
| MMDBm0001533 | Desulfitobacterium hafniense Y51 | Eubacteria | Firmicutes | Not Available | Not Available | RHEA |
