There Is a Shift of Luminal Flora to the Mucosal Surface in Inflammatory Bowel Disease

Abstract

Purpose: While clinical observations and animal models of inflammatory bowel disease (IBD) suggest that a dysbiosis may exist in IBD, the changes in the mucosal microflora of IBD patients are largely unknown. Amplicon length heterogeneity (ALH) is a sophisticated technology that examines the 16s ribosomal DNA of bacteria. We hypothesized that ALH is a tool to study the changes in the mucosal microflora in IBD. We also hypothesized that ALH can aid in selection of samples for costly cloning and sequencing, in an effort to identify the nature of the much suspected dysbiosis in IBD. Methods: We have collected colonoscopic stool & mucosal tissue samples of patients with inactive and active IBD {n = 19 for Crohn's disease (CD) and n = 18 for ulcerative colitis(UC)} and healthy controls {n = 9}. The samples were fingerprinted for bacterial patterns using ALH. We selected samples that were diverse on the basis of ALH patterns and cloned and sequenced pooled samples of CD (n = 4), UC (n = 2)patients and healthy controls (n = 4).Table: Cloning results.Results: An overview shows that the flora found on the mucosal surface of CD and UC tissue resemble the floral composition of fecal mater in healthy individuals, which is significantly different than the mucosal composition of bacteria in these healthy individuals. When the data are examined at RDP phylotype level 4, there is a decrease in the Bacteroides group in UC more than CD. Clostridium & Enteroccoci groups are associated with the mucosal surface of UC and Cytophagia group I seems to be associated with CD mucosal surface and stool samples. Conclusions: Our results suggest that there may be a loss of a “protective biofilm” in IBD that results in easy attachment of luminal bacteria to the tissues. Larger number of cloning experiments are needed in IBD to confirm these results.