| MMDBm0000012 | Agrobacterium tumefaciens F2 | Eubacteria | Proteobacteria | Human Feces | Metabolic reconstruction | VMH |
| MMDBm0000160 | Escherichia coli | Eubacteria | Proteobacteria | Human | Unknown | ECMDB |
| MMDBm0000778 | Clostridium methylpentosum | Eubacteria | Firmicutes | Human | Metabolic reconstruction | VMH |
| MMDBm0001191 | Actinobacillus pleuropneumoniae serovar 5b str. L20 | Eubacteria | Proteobacteria | Pig | Metabolic reconstruction | VMH |
| MMDBm0001501 | Cronobacter sakazakii ATCC BAA-894 | Eubacteria | Proteobacteria | Human | Metabolic reconstruction | VMH |
| MMDBm0001574 | Enterobacter asburiae LF7a | Eubacteria | Proteobacteria | Human Feces | Metabolic reconstruction | VMH |
| MMDBm0001596 | Escherichia fergusonii ATCC 35469 | Eubacteria | Proteobacteria | Human | Metabolic reconstruction | VMH |
| MMDBm0001658 | Haemophilus influenzae Rd KW20 | Eubacteria | Proteobacteria | Human | Not Available | RHEA |
| MMDBm0001810 | Mesorhizobium loti MAFF303099 | Eubacteria | Proteobacteria | Human Feces | Not Available | RHEA |
| MMDBm0001963 | Thermotoga maritima MSB8 | Eubacteria | Thermotogae | Not Available | Not Available | RHEA |
| MMDBm0002345 | Pasteurella multocida subsp. multocida str. Pm70 | Eubacteria | Proteobacteria | Chicken | Not Available | RHEA |
| MMDBm0028951 | Aspergillus niger ATCC 1015 | Fungi | Ascomycota | Not Available | Not Available | RHEA |
| MMDBm0028954 | Aspergillus niger CBS 513.88 | Fungi | Ascomycota | Not Available | Not Available | RHEA |
| MMDBm0028973 | Aspergillus oryzae | Fungi | Ascomycota | Human Feces | Not Available | RHEA |
| MMDBm0031184 | Penicillium rubens Wisconsin 54-1255 | Fungi | Ascomycota | Not Available | Not Available | RHEA |
| MMDBm0035525 | Rasamsonia emersonii | Fungi | Ascomycota | Human Feces | Not Available | RHEA |
| MMDBm0060570 | Trichoderma reesei | Fungi | Ascomycota | Human Feces | Not Available | RHEA |
| MMDBm0060571 | Trichoderma reesei QM6a | Fungi | Ascomycota | Not Available | Not Available | RHEA |
| MMDBm0082117 | Neurospora crassa OR74A | Fungi | Ascomycota | Not Available | Not Available | RHEA |
| MMDBm0099639 | Ambrosiozyma monospora | Fungi | Ascomycota | Not Available | Not Available | RHEA |
| MMDBm0483496 | Burkholderia cepacia GG4 | Eubacteria | Proteobacteria | Human Feces | Metabolic reconstruction | VMH |
| MMDBm0534800 | Enterobacter hormaechei YT2 | Eubacteria | Proteobacteria | Human Feces | Metabolic reconstruction | VMH |
| MMDBm0534801 | Enterobacter hormaechei YT3 | Eubacteria | Proteobacteria | Human Feces | Metabolic reconstruction | VMH |
| MMDBm0540122 | Escherichia albertii TW07627 | Eubacteria | Proteobacteria | Human Feces | Metabolic reconstruction | VMH |
| MMDBm0544444 | Klebsiella michiganensis KCTC 1686 | Bacteria | Proteobacteria | Human Feces | Metabolic reconstruction | VMH |
