Studies of mucosal microbiota in CD where isolated colonic disease was separately identified
| Author/ref | Year | Specimen type | Number of cases CD | Ileal CD | Ileocolonic CD | Isolated colonic CD | UC | Healthy controls | Conclusions |
|---|---|---|---|---|---|---|---|---|---|
| Naftali et al131 | 2016 | Ileum and colon | 31 | 15 Increased abundance of Escherichia and reduced Faecalibacterium; disease activity correlated with abundance of Fusobacterium | 8* Similar to colonic CD apart from Faecalibacterium abundance 2.7-fold lower than in isolated colonic CD (not significant) | 8* Higher levels of Faecalibacterium and 2 unidentified genera of the Clostridiales and Ruminococceaea; lower levels of Enterobacteriaceae compared with ileal | NA | NA | Ileal CD and colonic CD microbiomes distinct |
| Haberman et al132 | 2015 | Ileal biopsy | 243 (Paediatric) | 180 Persistent reduction in Lachnospiraceae, Bifidobacteriaceae, Clostridiales and Erysipelotrichaceae in all forms of CD, with expansion of Veillonellaceae, Pasteurellaceae, Neisseriaceae, Gemellaceae, Fusobacteriaceae and Enterobacteriaceae | 63 Persistent reduction in Lachnospiraceae, Bifidobacteriaceae, Clostridiales and Erysipelotrichaceae in all forms of CD, with expansion of Veillonellaceae, Pasteurellaceae, Neisseriaceae, Gemellaceae, Fusobacteriaceae and Enterobacteriaceae | 73 Increased abundance of Firmicutes phyla | 43 | No difference between ileal/ileocolonic CD and colonic CD microbiome | |
| Lopez-Siles et al130 | 2014 | Ileum and colon | 45 | 19 Reduction in Faecalibacterium prausnitzii, Escherichia coli moderately increased. | 13 Reduction in F. prausnitzii | 13 F. prausnitzii comparable to UC; E. coli commoner than UC particularly in ulcerated zones | 28 F. prausnitzii abundance intermediate between CD and HC | 28 | F. prausnitzii/ E. coli (FE index)‡ allowed differentiation between ileal CD and other CD phenotypes. Microbiota changes in colonic CD intermediate between ileal CD and UC |
| Willing et al128 129† | 2009, 2010 | Ileum and colon | 14 | 6 Increased Enterobacteriaceae and Ruminococcus gnavus; decreased Faecalibacterium and Roseburia and compared with healthy controls. Increased E. coli | 8 No reduction in Faecalibacterium or Roseburia. Some increase in E. coli but less marked than ileocolonic | 6 | Colonic CD microbiome intermediate between ileal CD and healthy controls | ||
| Baumgart et al127 | 2007 | Ileum | 29 | 13 Increased abundance of Enterobacteriaceae, (E. coli, Shigella) reduction in Lachnospiraceae, (Ruminococci, Roseburia and Coprococci) and Clostridiales (Faecalibacterium and Subdoligranula) | 8 Results not presented separately | 8 Enterobacteriaceae not increased and Faecalibacterium not reduced | NA | 7 | Ileal CD and colonic CD microbiome were distinct. Colonic CD more closely resembled healthy controls |
*Although the study included patients with isolated colonic CD, results were pooled for patients with colonic involvement.
†Willing et al128, similar patient cohort to Willing et al129, but sequencing methodology compared with terminal-restriction fragment length polymorphism in Willing et al129.
‡FE index was calculated as: log10 (F/HC) − log10 (E/HC)/log10 (TB/HC), F being the 16S rRNA gene copies of F. prausnitzii, E the 16S rRNA gene copies of E. coli, HC a million of human cells and TB a million of 16S rRNA gene copies of total bacteria.
CD, Crohn's disease.