Since genetically engineered animal models of inflammatory bowel disease (IBD) do not develop colitis under germ-free conditions, the intestinal microflora is thought to be one of the most important environmental factors associated with IBD. To understand the involvement of intestinal microflora in the pathogenesis of IBD, we analyzed the constituents of intestinal microflora in IBD. Faecal samples from 73 patients with ulcerative colitis (UC) and 23 patients with Crohn's disease (CD) were analyzed by quantitative PCR using 16S rRNA gene-targeted group-specific primers for Bacteroides fragilis group, Bifidobacterium, Clostridium coccoides groups, Clostridium leptum subgroup, Atopobium cluster, and seven species of Bacteroides. We analyzed the distribution of the predominant microflora by fluorescence in situ hybridization (FISH) using group-specific probes. We also examined the concentration of faecal organic acids produced by intestinal microflora. Contrary to previous reports, we found that the B. fragilis group was significantly decreased in the faeces of patients with IBD. Moreover, B. vulgatus was the predominant microflora in healthy controls and relatively decreased among IBD patients. Most of the microflora adhering to the colonic mucosa surrounding the mucus layer comprised C. coccoides group and Bifidobacterium. B. fragilis group mainly inhabited the faeces, but did not adhere to or invade the mucosa. The concentrations of propionic and butyric acids in the faeces were significantly decreased in patients with IBD. These findings indicate that IBD is not caused by a specific intestinal bacterial cluster or species and that disordered intestinal microflora could be involved in the pathogenesis of IBD.
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