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Reduction in diversity of the colonic mucosa associated bacterial microflora in patients with active inflammatory bowel disease
  1. S J Ott1,*,
  2. M Musfeldt1,*,
  3. D F Wenderoth2,
  4. J Hampe1,
  5. O Brant1,
  6. U R Fölsch1,
  7. K N Timmis2,
  8. S Schreiber1
  1. 1Department of General Internal Medicine, University Hospital Schleswig-Holstein, Campus Kiel, Germany
  2. 2German Research Center for Biotechnology (GBF), Department of Microbiology, Braunschweig, Germany
  1. Correspondence to:
    Dr S Schreiber
    I Medical Department, University Hospital Schleswig-Holstein, Campus Kiel, Schittenhelmstr, 12, 24105 Kiel, Germany;


Background and aims: The intestinal bacterial microflora plays an important role in the aetiology of inflammatory bowel disease (IBD). As most of the colonic bacteria cannot be identified by culture techniques, genomic technology can be used for analysis of the composition of the microflora.

Patients and methods: The mucosa associated colonic microflora of 57 patients with active inflammatory bowel disease and 46 controls was investigated using 16S rDNA based single strand conformation polymorphism (SSCP) fingerprint, cloning experiments, and real time polymerase chain reaction (PCR).

Results: Full length sequencing of 1019 clones from 16S rDNA libraries (n = 3) revealed an overall bacterial diversity of 83 non-redundant sequences—among them, only 49 known bacterial species. Molecular epidemiology of the composition of the colonic microflora was investigated by SSCP. Diversity of the microflora in Crohn’s disease was reduced to 50% compared with controls (21.7 v 50.4; p<0.0001) and to 30% in ulcerative colitis (17.2 v 50.4; p<0.0001). The reduction in diversity in inflammatory bowel disease was due to loss of normal anaerobic bacteria such as Bacteroides species, Eubacterium species, and Lactobacillus species, as revealed by direct sequencing of variable bands and confirmed by real time PCR. Bacterial diversity in the Crohn’s group showed no association with CARD15/NOD2 status.

Conclusions: Mucosal inflammation in inflammatory bowel disease is associated with loss of normal anaerobic bacteria. This effect is independent of NOD2/CARD15 status of patients.

  • inflammation
  • Crohn’s disease
  • ulcerative colitis
  • mucosa
  • bacterial microflora
  • inflammatory bowel disease
  • CAI, clinical activity index
  • CD, Crohn’s disease
  • CDAI, Crohn’s disease activity index
  • IBD, inflammatory bowel disease
  • OTU, operational taxonomic unit
  • SNP, single nucleotide polymorphism
  • SSCP, single strand conformation polymorphism
  • ssDNA, single stranded DNA
  • UC, ulcerative colitis
  • UPGMA, unweighted pair group method with arithmetic mean

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  • * S J Ott and M Musfeldt contributed equally to this study