| Phylum | Family/species | Disease | References |
|---|
| Proteobacteria | Campylobacter concisus | CD/UC | [87] |
| Invasive Escherichia coli | CD | [86, 89] |
| Pseudomonas spp. | CD | [104] |
| Helicobacter spp. | CD | [146] |
| Desulfovibrio spp. | UC | [88] |
| Actinobacteria | Atopobium parvulum | CD | [107] |
| Collinsella spp. | UC | [119] |
| Mycobacterium avium spp. | CD | [106] |
| Pasteurellaceae | CD | [106] |
| Firmicutes | Clostridium difficile | CD/UC | [117] |
| Ruminococcus gnavus | CD/UC | [110] |
| Veillonellaceae | CD | [119, 120] |
| Streptococcus spp. | CD/UC | [119] |
| Fusobacteria | Fucobacterium spp. | CD | [108] |
| Ascomycota | Clavispora lusitaniae | CD | [118, 128] |
| Kluyveromyces marxianus | CD | [118] |
| Candida albicans | CD | [118, 129] |
| Saccharomyces cerevisiae | | [118] |
| Cyberlindnera jadinii | CD | [124] |
| Bacteriophage | Caudovirales | CD | [130, 131] |
