Comparison of altered taxa in patients with Crohn's disease (CD) compared with healthy controls: family level and above
| Gut microbiota alterations in patients with CD (current study: FDR<0.05) | |||||
|---|---|---|---|---|---|
| Taxon (family and above) | Phylum (or kingdom) | Current study* | Gevers et al† | Morgan et al‡ | Willing et al§ |
| f__Methanobacteriaceae | Archea (kingdom) | Down | Not reported | Not reported | Not reported |
| p__Actinobacteria | Down | Down | Not reported | Up in colonic CD | |
| c__Actinobacteria | Actinobacteria | Down | Down | Not reported | Up in colonic CD |
| f__Micrococcaceae | Actinobacteria | Not reported | Up | Not reported | Not reported |
| f__Bifidobacteriaceae | Actinobacteria | Down | Down | Down, in lower taxonomic levels | Up in colonic CD |
| f__Coriobacteriaceae | Actinobacteria | Down | Down | Not reported | Up in colonic CD |
| p__Bacteroidetes | Up | Down | Not reported | Not reported | |
| o__Bacteroidales | Bacteriodetes | Up | Down | Not reported | Not reported |
| f__Porphyromonadaceae | Bacteriodetes | Up | Down | Down, in lower taxonomic levels | Unknown genus in this family: down in ileal CD |
| p__Firmicutes | Down, in lower taxonomic levels | Down | Down | Up in colonic CD | |
| c__Bacilli | Firmicutes | Up, in lower taxonomic levels | Up | Associated to ileal involvement | Up in ileal CD |
| f__Aerococcaceae | Firmicutes | Up | Not reported | Not reported | Not reported |
| f__Enterococcaceae | Firmicutes | Up | Not reported | Not reported | Not reported |
| o__Gemellales | Firmicutes | Not reported | Up | Not reported | Not reported |
| f__Gemellaceae | Firmicutes | Not reported | Up | Not reported | Not reported |
| f__Streptococcaceae | Firmicutes | Not reported | Up | Not reported | Not reported |
| c__Clostridia | Firmicutes | Down | Down | Down | Down in ileal CD |
| o__Clostridiales | Firmicutes | Down | Down | Down | Down in ileal CD |
| f__Mogibacteriaceae | Firmicutes | Down | Not reported | Not reported | Not reported |
| f__Christensenellaceae | Firmicutes | Down | Down | Not reported | Not reported |
| f__Clostridiaceae | Firmicutes | Down | Down | Not reported | Not reported |
| f__Dehalobacteriaceae | Firmicutes | Down | Not reported | Not reported | Not reported |
| f__Lachnospiraceae | Firmicutes | Up, but genera in lower levels both going up and down | Down | Down, in lower taxonomic levels | Down, in lower taxonomic levels |
| f__Peptococcaceae | Firmicutes | Down | Not reported | Not reported | Down in ileal CD |
| f__Peptostreptococcaceae | Firmicutes | Down | Not reported | Not reported | |
| f__Ruminococcaceae | Firmicutes | Down | Down | Down | Down in ileal CD |
| f__Veillonellaceae | Firmicutes | Not reported | Up | Up | Up in lower taxonomic levels in ileal CD |
| f__Erysipelotrichaceae | Firmicutes | Down | Down | Associated to ileal involvement | Not reported |
| p__Fusobacteria | Not reported | Not reported | Not reported | Up in ileal CD | |
| o__Fusobacteriales | Fusobacteria | Not reported | Up | Not reported | Up in ileal CD |
| f__Fusobacteriaceae | Fusobacteria | Not reported | Up | Not reported | Up in ileal CD |
| p__Proteobacteria | Up | Up | Up | Up in ileal CD | |
| c__Betaproteobacteria | Proteobacteria | Up | Up | Not reported | Not reported |
| o__Burkholderiales | Proteobacteria | Up | Up | Not reported | Not reported |
| f__ Neisseriaceae | Proteobacteria | Not reported | Up | Not reported | Not reported |
| c__Gammaproteobacteria | Proteobacteria | Up | Up | Up | Up in ileal CD |
| f__Aeromonadaceae | Proteobacteria | Not reported | Not reported | Not reported | Up in ileal CD |
| o__Campylobacterales | Proteobacteria | Not reported | Up | Not reported | Not reported |
| f__Enterobacteriaceae | Proteobacteria | Up | Up | Up | Up in ileal CD |
| f__Pasteurellaceae | Proteobacteria | Not reported | Up | Not reported | |
| p__Tenericutes | Down | Not reported | Not reported | ||
| c__Mollicutes | Tenericutes | Down | Not reported | Not reported | Down in ileal CD, up in colonic CD |
| f__Anaeroplasmataceae | Tenericutes | Not reported | Not reported | Not reported | Down in ileal CD, up in colonic CD |
| f__Verrucomicrobiaceae | Verrucomicrobia | Not reported | Down | Not reported | Not reported |
k__, kingdom; p__; phylum; c__ , class; o__ , order; f__, family.
*313 patients with IBD including 188 patients with CD; 582 healthy controls; stool only.
†Cell Host Microbe 2014; 447 patients with CD; 221 controls; stool and biopsy.
‡Genome Biology 2012; 204 patients with IBD including 121 patients with CD and 27 controls; stool and biopsy.
§Gastroenterology 2010; 40 twin pairs concordant or discordant for CD/UC (23 CD pairs, 15 UC pairs, 2 healthy pairs).
FDR, false discovery rate.