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The faecal flora and mucosa-associated flora (MAF) of rectal biopsy material from 12 patients with active Crohn's disease were studied before and during treatment with a combination of metronidazole and cotrimoxazole given orally for at least 2 weeks. The total faecal flora was greater than the MAF although the proportions of bacterial groups were similar. The changes observed during treatment were: obligate anaerobes such as Bacteroides spp. decreased in faeces (p less than 0.05) and in MAF (p less than 0.02); the total count of facultative bacteria increased in the faeces (p less than 0.002) but not in the MAF. Streptococci, predominantly enterococci, increased significantly in faeces (p less than 0.001) and in MAF (p less than 0.02) such that they became predominant components of these florae. Facultative gram-negative bacilli were unaltered in faeces but significantly reduced in the MAF (p less than 0.05). Sporing clostridia were infrequently isolated from the MAF but were significantly reduced in the faeces (p less than 0.01). During the treatment period, eight of the 12 patients showed clinical improvement, but this could not be related to the site or extent of disease or to specific changes in faecal flora or MAF. This combination of antibacterial agents causes profound alterations to the bacterial flora of mucosa and faeces and these changes may help to define the role of bacteria in the pathogenesis of Crohn's disease.

The Microbial Flora of the Rectal Mucosa and Faeces of Patients with Crohn's Disease Before and During Antimicrobial Chemotherapy