Gut 55:1760-1767 doi:10.1136/gut.2005.078824
  • Inflammatory bowel disease

Gut-associated bacterial microbiota in paediatric patients with inflammatory bowel disease

  1. M P Conte1,
  2. S Schippa1,
  3. I Zamboni1,
  4. M Penta1,
  5. F Chiarini1,
  6. L Seganti1,
  7. J Osborn1,
  8. P Falconieri2,
  9. O Borrelli2,
  10. S Cucchiara2
  1. 1Department of Public Health Sciences, University of Rome, La Sapienza, University Hospital Umberto I, Rome, Italy
  2. 2Department of Paediatrics, University of Rome, La Sapienza, University Hospital Umberto I, Rome, Italy
  1. Correspondence to:
    S Cucchiara
    Paediatric Gastroenterology Unit, University of Rome La Sapienza, Viale Regina Elena 324, Rome 00161, Italy;salvatore.cucchiara{at}
  • Accepted 5 April 2006
  • Revised 17 March 2006
  • Published Online First 28 April 2006


Background: Clinical and experimental observations in animal models indicate that intestinal commensal bacteria are involved in the initiation and amplification of inflammatory bowel disease (IBD). No paediatric reports are available on intestinal endogenous microflora in IBD.

Aims: To investigate and characterise the predominant composition of the mucosa-associated intestinal microflora in colonoscopic biopsy specimens of paediatric patients with newly diagnosed IBD.

Methods: Mucosa-associated bacteria were quantified and isolated from biopsy specimens of the ileum, caecum and rectum obtained at colonoscopy in 12 patients with Crohn’s disease, 7 with ulcerative colitis, 6 with indeterminate colitis, 10 with lymphonodular hyperplasia of the distal ileum and in 7 controls. Isolation and characterisation were carried out by conventional culture techniques for aerobic and facultative-anaerobic microorganisms, and molecular analysis (16S rRNA-based amplification and real-time polymerase chain reaction assays) for the detection of anaerobic bacterial groups or species.

Results: A higher number of mucosa-associated aerobic and facultative-anaerobic bacteria were found in biopsy specimens of children with IBD than in controls. An overall decrease in some bacterial species or groups belonging to the normal anaerobic intestinal flora was suggested by molecular approaches; in particular, occurrence of Bacteroides vulgatus was low in Crohn’s disease, ulcerative colitis and indeterminate colitis specimens.

Conclusion: This is the first paediatric report investigating the intestinal mucosa-associated microflora in patients of the IBD spectrum. These results, although limited by the sample size, allow a better understanding of changes in mucosa-associated bacterial flora in these patients, showing either a predominance of some potentially harmful bacterial groups or a decrease in beneficial bacterial species. These data underline the central role of mucosa-adherent bacteria in IBD.


  • Published Online First 28 April 2006

  • Funding: This work was supported by MIUR grants to MPC and SS.

  • Competing interests: None.