| Bacteria | CD | UC | References |
| Escherichia coli | | | [27, 31, 34] | Pseudomonas | | | [50] | Salmonella | (relapsed) | | [29, 30] | Campylobacter jejuni | (relapsed) | | [29, 30] | Clostridium difficile | (relapsed) | | [29, 30, 47, 48] | Fusobacterium varium | | | [32, 33, 37] | Clostridium cluster IX | | | [37] | Clostridium cluster IV | | | [37] | Faecalibacterium prausnitzii | | | [31, 37, 40–42] | Bifidobacterium adolescentis | | | [40] | Dialister invisus | | | [40] | Ruminococcus gnavus | | | [40] | Enterobacteriaceae | | | [27, 31, 34] | Firmicutes | | | [37, 39, 41, 42] | Bacteroidetes | | | [37, 39, 41, 42] | Proteobacteria | | | [37, 39, 41, 42] | Actinobacteria | | | [37] | Sulphate-reducing bacteria (SRB) | | | [43, 44, 46] |
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