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J. Clin. Microbiol. doi:10.1128/JCM.00312-06
Copyright (c) 2006, American Society for Microbiology and/or the Listed Authors/Institutions. All Rights Reserved.

Culture-independent analyses of the temporal variation of the dominant faecal microbiota and targeted bacterial sub-groups in Crohn's disease

Alimentary Pharmabiotic Centre, National University of Ireland, University College Cork, Cork, Ireland; Department of Microbiology, National University of Ireland, University College Cork, Cork, Ireland

^* To whom correspondence should be addressed. Email: j.marchesi{at}ucc.ie.

	Abstract

Gut microbiota show host-specific diversity, temporal stability and significantly contributes to maintenance of a healthy gut. However, in inflammatory bowel disease (IBD) this microbiota has been implicated as a contributory factor to the illness. This study compared bacterial dynamics in Crohn's disease patients with a control group using a culture independent method to assess the temporal stability, relative diversity and similarity of the dominant fecal microbiota, Clostridia spp., Bacteroides spp., Bifidobacterium spp. and the Lactic Acid Bacteria spp. (LAB) in all individuals. Fecal samples were collected from Crohn's disease individuals over several time points who where in remission (n = 11); from Crohn's disease patients who relapsed into an active Crohn's disease state (n = 5) and a control group (n = 18). Denaturing gradient gel electrophoresis (DGGE) profiles were generated for the different microbial groups by specifically targeting different regions of the 16S rRNA gene and compared on the basis of similarity and diversity. Temporal stability of dominant species in all Crohn's disease patients was significantly lower (P < 0.005) than in the control group. Analysis of group-specific profiles for Bifidobacterium spp. found that they were similar in all samples, while the diversity of the LAB varied significantly between the groups, but temporal stability was not significantly altered. We observed significant changes in two functionally important mutualistic groups of bacteria, viz. members of the Clostridia and Bacteroides, which may have implications for the host's gut health since some genera are involved in short chain fatty acid production e.g. butyrate.

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