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Open Access Highly Accessed Research article

High-throughput clone library analysis of the mucosa-associated microbiota reveals dysbiosis and differences between inflamed and non-inflamed regions of the intestine in inflammatory bowel disease

Alan W Walker1*, Jeremy D Sanderson2, Carol Churcher1, Gareth C Parkes2, Barry N Hudspith2, Neil Rayment2, Jonathan Brostoff2, Julian Parkhill1, Gordon Dougan1 and Liljana Petrovska23*

Author Affiliations

1 Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK

2 King's College London, Biomedical & Health Sciences, Dept. of Nutrition and Dietetics, Franklin-Wilkins Building, 4th floor, 150 Stamford Street, London, SE1 8NH, UK

3 Department of Bacteriology, Veterinary Laboratories Agency (Weybridge), Woodham Lane, Addlestone, Surrey, KT15 3NB, UK

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BMC Microbiology 2011, 11:7  doi:10.1186/1471-2180-11-7

Published: 10 January 2011

Abstract

Background

The gut microbiota is thought to play a key role in the development of the inflammatory bowel diseases Crohn's disease (CD) and ulcerative colitis (UC). Shifts in the composition of resident bacteria have been postulated to drive the chronic inflammation seen in both diseases (the "dysbiosis" hypothesis). We therefore specifically sought to compare the mucosa-associated microbiota from both inflamed and non-inflamed sites of the colon in CD and UC patients to that from non-IBD controls and to detect disease-specific profiles.

Results

Paired mucosal biopsies of inflamed and non-inflamed intestinal tissue from 6 CD (n = 12) and 6 UC (n = 12) patients were compared to biopsies from 5 healthy controls (n = 5) by in-depth sequencing of over 10,000 near full-length bacterial 16S rRNA genes. The results indicate that mucosal microbial diversity is reduced in IBD, particularly in CD, and that the species composition is disturbed. Firmicutes were reduced in IBD samples and there were concurrent increases in Bacteroidetes, and in CD only, Enterobacteriaceae. There were also significant differences in microbial community structure between inflamed and non-inflamed mucosal sites. However, these differences varied greatly between individuals, meaning there was no obvious bacterial signature that was positively associated with the inflamed gut.

Conclusions

These results may support the hypothesis that the overall dysbiosis observed in inflammatory bowel disease patients relative to non-IBD controls might to some extent be a result of the disturbed gut environment rather than the direct cause of disease. Nonetheless, the observed shifts in microbiota composition may be important factors in disease maintenance and severity.