title: Ribosomal DNA sequence analysis of mucosa-associated bacteria in Crohn's disease.
abstract: BACKGROUND
  Enteric bacteria are implicated in the pathogenesis of Crohn's disease (CD); however, no specific causative organisms have been identified.
  
  
  OBJECTIVE
  This study was undertaken to correlate disease activity with changes in intestinal biota in patients with CD.
  
  
  METHODS
  Ribosomal DNA analysis was used to explore the composition of the intestinal biota in patients with (1) CD undergoing colonoscopy, (2) CD undergoing surgical resection, and (3) no inflammatory bowel disease.
  
  
  METHODS
  Primers targeting bacterial 16S ribosomal DNA (rDNA) were used to amplify bacterial DNA associated with active CD lesions, comparable normal tissue from patients with CD, and normal control tissue. Each amplicon was cloned. Seven hundred thirty-nine rDNA clones were sequenced from 16 biopsies from CD patients, 15 surgical samples, and 10 biopsies from normal control patients.
  
  
  RESULTS
  Known extracellular or intracellular pathogens were not found. No rDNA sequence, phylogenetic group, or subgroup was consistently associated with CD lesions compared with normal tissues from the same patients. Colonic biopsies from CD-afflicted patients compared with biopsies from normal control subjects had an increase in facultative bacteria; in small bowel, CD patients had an increase in the Ruminococcus gnavus subgroup with a decrease in the Clostridium leptum and Prevotella nigrescens subgroups. However, differences in small bowel may have reflected individual variation rather than disease association. Surgical samples showed differences when compared with biopsy-derived samples.
  
  
  CONCLUSIONS
  These findings suggest that CD is not caused by invasive pathogens associated specifically with the sites of lesions but that dysbiosis exists in this condition.
authors.affiliation: Division of Gastroenterology, University of California at Davis, Sacramento, California 95817, USA. tprindiv@mdanderson.org
authors.forename: Tom
authors.initials: T
authors.lastname: Prindiville
authors.forename: Mary
authors.initials: M
authors.lastname: Cantrell
authors.forename: Kenneth H
authors.initials: KH
authors.lastname: Wilson
mesh_terms: D001439:Bacteroides / Q000235:genetics / Q000302:isolation & purification; D016022:Case-Control Studies; D003424:Crohn Disease / Q000382:microbiology*; D004269:DNA, Bacterial / Q000032:analysis; D004275:DNA, Ribosomal / Q000032:analysis*; D016983:Enterococcus / Q000235:genetics / Q000302:isolation & purification; D006801:Humans; D007413:Intestinal Mucosa / Q000382:microbiology; D010802:Phylogeny; D016133:Polymerase Chain Reaction
chemical_list: D004269:DNA, Bacterial; D004275:DNA, Ribosomal