| MMDBm0000014 | Akkermansia muciniphila | Bacteria | Verrucomicrobia | Human Feces | Indirect association between microbiota composition and metabolites measured in host biospecimen | Not Available |
| MMDBm0000049 | Bacteroides ovatus | Bacteria | Bacteroidetes | Human Feces | Indirect association between microbiota composition and metabolites measured in host biospecimen | Not Available |
| MMDBm0000056 | Bacteroides vulgatus | Bacteria | Bacteroidetes | Human Feces | Indirect association between microbiota composition and metabolites measured in host biospecimen | Not Available |
| MMDBm0000105 | Citrobacter freundii ATCC 8090 = MTCC 1658 | Bacteria | Proteobacteria | Human Feces | Metabolic reconstruction | VMH |
| MMDBm0000112 | Clostridioides difficile R20291 | Bacteria | Firmicutes | Human | Metabolic reconstruction | VMH |
| MMDBm0000116 | Clostridium beijerinckii NCIMB 8052 | Bacteria | Firmicutes | Human Feces | Metabolic reconstruction | VMH |
| MMDBm0000132 | Clostridium perfringens ATCC 13124 | Bacteria | Firmicutes | Human | Metabolic reconstruction | VMH |
| MMDBm0000207 | Lactobacillus reuteri | Bacteria | Firmicutes | Human | Metabolic reconstruction | VMH |
| MMDBm0000306 | Pelobacter carbinolicus | Bacteria | Proteobacteria | Not Available | Microbial culture | Not Available |
| MMDBm0000306 | Pelobacter carbinolicus | Bacteria | Proteobacteria | Not Available | Microbial culture | Not Available |
| MMDBm0000474 | Clostridium pasteurianum | Bacteria | Firmicutes | Not Available | Microbial culture | Not Available |
| MMDBm0000583 | Saccharomyces cerevisiae | Fungi | Ascomycota | Human Feces | Unknown | YMDB |
| MMDBm0000814 | Pelotomaculum thermopropionicum | Bacteria | Firmicutes | Not Available | Microbial culture | Not Available |
| MMDBm0000861 | Ilyobacter polytropus | Bacteria | Fusobacteria | Not Available | Microbial culture | Not Available |
| MMDBm0000948 | Roseburia inulinivorans | Bacteria | Firmicutes | Human Stool | Indirect association between microbiota composition and metabolites measured in host biospecimen | Not Available |
| MMDBm0001053 | Coprococcus catus | Bacteria | Firmicutes | Human Stool | Indirect association between microbiota composition and metabolites measured in host biospecimen | Not Available |
| MMDBm0001061 | Eubacterium rectale | Bacteria | Firmicutes | Human Stool | Indirect association between microbiota composition and metabolites measured in host biospecimen | Not Available |
| MMDBm0001066 | Klebsiella pneumoniae | Bacteria | Proteobacteria | Human | Microbial culture | Not Available |
| MMDBm0001067 | Klebsiella variicola | Bacteria | Proteobacteria | Human Feces | Metabolic reconstruction | VMH |
| MMDBm0001090 | Veillonella parvula | Bacteria | Firmicutes | Human | Indirect association between microbiota composition and metabolites measured in host biospecimen | Not Available |
| MMDBm0001098 | Methanobrevibacter | Archaea | Euryarchaeota | Human Feces | Indirect association between microbiota composition and metabolites measured in host biospecimen | Not Available |
| MMDBm0001104 | Eubacterium hallii | Bacteria | Firmicutes | Not Available | Metabolic reconstruction | VMH |
| MMDBm0001450 | Citrobacter koseri ATCC BAA-895 | Bacteria | Proteobacteria | Human | Metabolic reconstruction | VMH |
| MMDBm0001470 | Clostridium difficile CD196 | Bacteria | Firmicutes | Human | Metabolic reconstruction | VMH |
| MMDBm0001734 | Lactobacillus plantarum WCFS1 | Bacteria | Firmicutes | Human | Metabolic reconstruction | VMH |
