title: Molecular characterization of rectal mucosa-associated bacterial flora in inflammatory bowel disease.
abstract: BACKGROUND
  Colorectal bacteria may play a role in the pathogenesis of inflammatory bowel disease (IBD). To test the hypothesis that, in affected patients, the numbers of potentially protective mucosal bacteria might be reduced and pathogenic species increased, we compared rectal mucosa-associated flora in patients with IBD and normal controls.
  
  
  METHODS
  Snap-frozen rectal biopsies taken at routine diagnostic colonoscopy from 33 patients with ulcerative colitis, 6 patients with Crohn's disease, and 14 controls with normal colonoscopy were processed, and individual bacterial groups were counted using fluorescent in situ hybridization.
  
  
  RESULTS
  Bacteria were mostly found apposed to the epithelial surface and within crypts. Epithelium-associated counts of bifidobacteria in active [median 15/mm of epithelial surface (range, 4-56), n = 14] and quiescent ulcerative colitis [26/mm (range, 11-140), n = 19] were lower than in controls [56/mm (range, 0-144), n = 14; P = 0.006 and P = 0.03, respectively]. Conversely, epithelium-associated Escherichia coli counts were higher in active [82/mm (range, 56-136)] than inactive ulcerative colitis [6/mm (range, 0-136), P = 0.0001] or controls [0/mm (range, 0-16), P < 0.0001]. Epithelium-associated clostridia counts were also higher in active [3/mm (range, 0-9)] than inactive colitis [0/mm (range, 0-9), P = 0.03] or controls [0/mm (range, 0-1); P = 0.0007]. Epithelium-associated E. coli counts were higher in Crohn's disease [42/mm (range, 3-90), n = 6] than controls (P = 0.0006). E. coli were also found as individual bacteria and in clusters in the lamina propria in ulcerative colitis and Crohn's disease but in none of the controls (P < 0.01). Numbers of Lactobacillus and Bacteroides showed no differences between patient groups.
  
  
  CONCLUSIONS
  The reduction in mucosa-associated bifidobacteria and increase in E. coli and clostridia in patients with IBD supports the hypothesis that an imbalance between potentially beneficial and pathogenic bacteria may contribute to its pathogenesis.
authors.affiliation: Academic Department of Adult and Paediatric Gastroenterology, Barts and the London School of Medicine and Dentistry, UK.
authors.forename: Maria
authors.initials: M
authors.lastname: Mylonaki
authors.forename: Neil B
authors.initials: NB
authors.lastname: Rayment
authors.forename: David S
authors.initials: DS
authors.lastname: Rampton
authors.forename: Barry N
authors.initials: BN
authors.lastname: Hudspith
authors.forename: Jonathan
authors.initials: J
authors.lastname: Brostoff
mesh_terms: D000328:Adult; D000368:Aged; D001439:Bacteroides / Q000235:genetics / Q000302:isolation & purification; D001644:Bifidobacterium / Q000235:genetics / Q000302:isolation & purification; D016022:Case-Control Studies; D003013:Clostridium / Q000235:genetics / Q000302:isolation & purification; D003093:Colitis, Ulcerative / Q000382:microbiology* / Q000473:pathology; D003113:Colonoscopy; D003424:Crohn Disease / Q000382:microbiology* / Q000473:pathology; D004926:Escherichia coli / Q000235:genetics / Q000302:isolation & purification; D005260:Female; D006801:Humans; D017404:In Situ Hybridization, Fluorescence; D007413:Intestinal Mucosa / Q000382:microbiology*; D007778:Lactobacillus / Q000235:genetics / Q000302:isolation & purification; D008297:Male; D008875:Middle Aged; D012313:RNA / Q000032:analysis; D012007:Rectum / Q000382:microbiology*
chemical_list: D012313:RNA