| MMDBm0000049 | Bacteroides ovatus | Eubacteria | Bacteroidetes | Human Feces | Indirect association between microbiota composition and metabolites measured in host biospecimen | Not Available |
| MMDBm0000054 | Bacteroides thetaiotaomicron | Eubacteria | Bacteroidetes | Human Feces | Indirect association between microbiota composition and metabolites measured in host biospecimen | Not Available |
| MMDBm0000107 | Cloacibacillus evryensis DSM 19522 | Eubacteria | Synergistetes | Human Feces | Metabolic reconstruction | VMH |
| MMDBm0000221 | Ochrobactrum anthropi ATCC 49188 | Eubacteria | Proteobacteria | Human | Metabolic reconstruction | VMH |
| MMDBm0000222 | Ochrobactrum intermedium LMG 3301 | Eubacteria | Proteobacteria | Human Feces | Metabolic reconstruction | VMH |
| MMDBm0000583 | Saccharomyces cerevisiae | Fungi | Ascomycota | Human Feces | Unknown | YMDB |
| MMDBm0000584 | Candida albicans | Fungi | Ascomycota | Human Feces | Not Available | RHEA |
| MMDBm0001126 | Flavonifractor plautii | Eubacteria | Firmicutes | Not Available | Indirect association between microbiota composition and metabolites measured in host biospecimen | Not Available |
| MMDBm0001734 | Lactobacillus plantarum WCFS1 | Eubacteria | Firmicutes | Human | Metabolic reconstruction | VMH |
| MMDBm0001810 | Mesorhizobium loti MAFF303099 | Eubacteria | Proteobacteria | Human Feces | Metabolic reconstruction | VMH |
| MMDBm0001983 | Thermus thermophilus HB27 | Eubacteria | Deinococcus-thermus | Not Available | Not Available | RHEA |
| MMDBm0002403 | Pseudomonas putida F1 | Eubacteria | Proteobacteria | Human Feces | Metabolic reconstruction | VMH |
| MMDBm0002538 | Sinorhizobium meliloti 1021 | Eubacteria | Proteobacteria | Not Available | Not Available | RHEA |
| MMDBm0029062 | Aspergillus nidulans FGSC A4 | Fungi | Ascomycota | Not Available | Not Available | RHEA |
| MMDBm0031170 | Penicillium chrysogenum | Fungi | Ascomycota | Human Feces | Not Available | RHEA |
| MMDBm0070712 | Acremonium chrysogenum | Fungi | Ascomycota | Not Available | Not Available | RHEA |
| MMDBm0098044 | Eremothecium gossypii ATCC 10895 | Fungi | Ascomycota | Not Available | Not Available | RHEA |
| MMDBm0098246 | [Candida] glabrata CBS 138 | Fungi | Ascomycota | Not Available | Not Available | RHEA |
| MMDBm0098378 | Saccharomyces cerevisiae S288C | Fungi | Ascomycota | Not Available | Not Available | RHEA |
| MMDBm0101577 | Schizosaccharomyces pombe 972h- | Fungi | Ascomycota | Not Available | Not Available | RHEA |
| MMDBm0580585 | Pseudomonas monteilii NBRC 103158 = DSM 14164 | Eubacteria | Proteobacteria | Human Feces | Metabolic reconstruction | VMH |
| MMDBm0580586 | Pseudomonas monteilii QM | Eubacteria | Proteobacteria | Human Feces | Metabolic reconstruction | VMH |
| MMDBm0693422 | Amycolatopsis lactamdurans | Bacteria | Actinobacteria | Not Available | Not Available | RHEA |
| MMDBm0696235 | Streptomyces clavuligerus | Bacteria | Actinobacteria | Not Available | Not Available | RHEA |
| MMDBm0881918 | Candidatus Nitrososphaera gargensis Ga9.2 | Archaea | Thaumarchaeota | Not Available | Metabolic reconstruction | VMH |
