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J Med Microbiol. 1997 Jan;46(1):85-91.

Mucosa-associated bacterial flora of the human colon.

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Department of Medical Microbiology, University of Edinburgh Medical School.


Biopsy samples of mucosa were taken during colonoscopy from the proximal colon and rectum of 12 patients, six with ulcerative colitis (UC) and six with non-inflammatory conditions. After anaerobic transport to the laboratory, biopsy specimens were examined by quantitative bacteriological culture on selective and non-selective media for total aerobic count, total anaerobic count, Bacteroides spp., lactobacilli, bifidobacteria and asaccharolytic, lactic acid producers. Isolates of the genus Bacteroides were identified to species level. Counts from proximal colonic and rectal biopsy samples in the same patient were not significantly different. Viable aerobic counts (aerobes and facultative organisms) ranged from 2.4 x 10(3) to 1.3 x 10(6) cfu/sample biopsy (5.6 mg) and total anaerobic counts were 10-10(2) times higher at (1.4 x 10(5))-(3 x 10(7)) cfu/sample. Bacteroides spp. predominated at both sites (range 8.6 X 10(4) to 1.4 x 10(7) cfu/sample), comprising 66% of total counts from proximal colon (range in individual patients 31-80%) and 68.5% from rectum (range 38-91%). Lactobacilli were isolated from eight biopsy samples from five patients, counts ranging from 3.6 X 10(2) to 1 X 10(5) cfu/sample; bifidobacteria were isolated from both sites from 10 of the 12 patients, counts ranging from 50 to 1.8 x 10(6) cfu/sample. From the 24 biopsy samples, 235 isolates representing 11 species of Bacteroides were identified. For any individual patient, only a few species (2-7; mean 4.4) of Bacteroides were found, with just one or two species predominating. B. vulgatus was cultured from both samples of seven patients (where it was the major isolate in four) and from single samples of two others; B. fragilis was cultured from both sites in six patients, being the major isolate in one patient and second commonest in three, but was not detected in the other six; the majority of other isolates were B. merdae/distasonis, B. ovatus, B. thetaiotaomicron and B. uniformis. B. thetaiotaomicron was isolated from both biopsy samples in all three UC patients with active inflammation (16 of the 60 isolates from these patients) but from only four of the other 18 samples from non-inflamed colonic mucosa (nine of 175 isolates).

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