The etiology of inflammatory bowel disease (IBD) is thought to involve a shift in bacterial balance favoring pro-inflammatory microbiota. However, why inflammation develops in certain parts of the intestine and not in others is unknown.
Aim: To identify differences in the microbiota of individuals with different locations and types of IBD.
Methods: Biopsies from IBD patients undergoing ileocolonoscopy were processed for 16S rRNA gene amplicon pyrosequencing. Unifrac matrices and OTU tables were generated by Qiime pipeline and the effect of various parameters on community structure was assessed by ANOSIM probability test. LDA Effect Size algorithm (LefSE) was used for identification of particular taxa that discriminate between groups.
Results: 133 samples from 31 Crohn's disease (CD) and 38 Ulcerative colitis (UC) patients were analyzed. Highly significant separation was observed between bacterial composition in ileal CD compared to colonic involvement CD (Bray Curtis p=0.0006 R=22%) and to UC (Bray-Curtis p=0.0048, R=15.5%). The microbiota was unaffected by samples origin, inflammatory state, disease activity (remission or relapse) or medical treatment.
Fecalibacterium and three genera belonging to the Lachnospiraceae were strongly reduced in ileal CD compared to CD with colonic involvement, whereas Enterobacteriaceae and Erysipelotrichaceae were more abundant in ileal CD. Additionally, Faecalibacterium , Sutterella, Ruminococcus and Dorea were all reduced in Ulcerative Colitis when compared to colonic involvement CD.
Conclusion: Ileal Crohn's disease has a distinct bacterial composition, unaffected by tissue inflammation, sampling site or disease activity. These results support the possibility that bacterial composition precedes inflammation, and suggests a different etiology, with distinct bacterial effects, in the different manifestations of IBD.
