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Bowel commensals appear to be an important source of antigens that drive the chronic immune inflammation characteristic of Crohn's disease and ulcerative colitis [inflammatory bowel diseases (IBD)]. Biopsy-associated bacteria are assumed to be particularly relevant in bacteriological investigations of IBD because they are assumed to be located on the mucosal surface and hence close to immunological cells. This investigation analysed the bacterial collections associated with bowel biopsies, aspirates of residual fluid after bowel cleansing and faeces from IBD patients and non-IBD subjects in Edmonton, Canada, and Mexico City, Mexico. Temporal temperature gradient gel electrophoresis of 16S rRNA gene sequences produced profiles of the bacterial collections and their similarities were compared. Similarity analysis showed that the profiles did not cluster according to disease status, but that Canadian and Mexican profiles could be differentiated by this method. Comparison of biopsy, aspirate and faecal samples obtained from the same subject showed that, on average, the profiles were highly similar. Therefore, biopsy-associated bacteria are likely to represent, at least in part, contaminants from the fluid, which resembles a faecal solution, that pools in the bowel after cleansing prior to endoscopy.

Differential clustering of bowel biopsy-associated bacterial profiles of specimens collected in Mexico and Canada: what do these profiles represent?