Digestive Diseases and Sciences

, Volume 55, Issue 2, pp 392–397 | Cite as

A Molecular Analysis of Fecal and Mucosal Bacterial Communities in Irritable Bowel Syndrome

  • Caroline Codling
  • Liam O’Mahony
  • Fergus Shanahan
  • Eamonn M. M. Quigley
  • Julian R. Marchesi
Original Article



The objectives of this study were, firstly, to determine the diversity of the host’s gut microbiota in irritable bowel syndrome (IBS) using a culture-independent method (DGGE of the 16S rRNA gene) and, secondly, to examine mucosal biopsies of IBS patients and compare them to their own fecal microbiota.


The diversity of the dominant microbiota in the fecal material of IBS patients was compared to a healthy control group. In addition, we compared the mucosal and fecal microbiota of IBS patients.


Statistical analysis of the mean similarity data for these groups indicated a significant difference (P < 0.001) between IBS (n = 47) and healthy controls (n = 33) with significantly more variation in the gut microbiota of healthy volunteers than that of IBS patients. The average intra-individual similarity between the mucosa and luminal microbiota was 84%, which indicates that different communities were present at the two sites. This difference, however, is similar to that previously described between these two niches in control subjects. The average inter-individual similarity of the bacterial communities on the mucosa and in the lumen of IBS was not significantly different (P > 0.05).


IBS impacts equally on both bacterial communities in the IBS host and a significant difference in the gut microbiota exists between fecal samples from IBS patients and healthy controls. The reason for this difference is unclear and various possible explanations are available, but much more work is required to determine the underlying reason for this observation.


Irritable bowel syndrome Colonic microbiota Gut flora Fecal flora DGGE Mucosal microbiota 



The authors wish to thank Dr. Pauline Scanlan for help with DGGE. The authors are supported in part by Science Foundation Ireland, Higher Education Authority, and the Health Research Board.

Supplementary material

10620_2009_934_MOESM1_ESM.pdf (38 kb)
Figure S1 DGGE gels of the V1–V3 regions and 5 of the V6–V8 used in this study (PDF 38 kb)


  1. 1.
    Agrawal A, Whorwell PJ. Irritable bowel syndrome: diagnosis and management. Br Med J. 2006;332:280–283.CrossRefGoogle Scholar
  2. 2.
    Balsari A, Ceccarelli A, Dubini F, Fesce E, Poli G. The fecal microbial population in the irritable bowel syndrome. Microbiologica. 1982;5:185–194.PubMedGoogle Scholar
  3. 3.
    Bayliss CE, Bradley HK, Jones VA, Hunter JO. Some aspects of colonic microbial activity in irritable bowel syndrome associated with food intolerance. Ann Ist Super Sanita. 1986;22:959–963.PubMedGoogle Scholar
  4. 4.
    Dubini F, Balsari A. Midecamycin activity against aerobic and anaerobic bacteria. G Ital Chemioter. 1985;32:539–544.PubMedGoogle Scholar
  5. 5.
    Eckburg PB, Bik EM, Bernstein CN, et al. Diversity of the human intestinal microbial flora. Science. 2005;308:1635–1638.CrossRefPubMedGoogle Scholar
  6. 6.
    Green GL, Brostoff J, Hudspith B, et al. Molecular characterization of the bacteria adherent to human colorectal mucosa. J Appl Microbiol. 2006;100:460–469.CrossRefPubMedGoogle Scholar
  7. 7.
    Kang JY. Systematic review: the influence of geography and ethnicity in irritable bowel syndrome. Aliment Pharmacol Ther. 2005;21:663–676.CrossRefPubMedGoogle Scholar
  8. 8.
    Kassinen A, Krogius-Kurikka L, Makivuokko H, et al. The fecal microbiota of irritable bowel syndrome patients differs significantly from that of healthy subjects. Gastroenterol. 2007;133:24–33.CrossRefGoogle Scholar
  9. 9.
    King TS, Elia M, Hunter JO. Abnormal colonic fermentation in irritable bowel syndrome. Lancet. 1998;352:1187–1189.CrossRefPubMedGoogle Scholar
  10. 10.
    Lane DJ. 16S/23S rRNA Sequencing. In: Stackebrandt E, Goodfellow M, eds. Nucleic acids techniques in bacterial systematics. Chichester: Wiley; 1991:115–175.Google Scholar
  11. 11.
    Lepage P, Seksik P, Sutren M, et al. Biodiversity of the mucosa-associated microbiota is stable along the distal digestive tract in healthy individuals and patients with IBD. Inflamm Bowel Dis. 2005;11:473–480.CrossRefPubMedGoogle Scholar
  12. 12.
    Madden JA, Hunter JO. A review of the role of the gut microflora in irritable bowel syndrome and the effects of probiotics. Br J Nutr. 2002;88(suppl 1):S67–S72.CrossRefPubMedGoogle Scholar
  13. 13.
    Malinen E, Rinttila T, Kajander K, et al. Analysis of the fecal microbiota of irritable bowel syndrome patients and healthy controls with real-time PCR. Am J Gastroenterol. 2005;100:373–382.CrossRefPubMedGoogle Scholar
  14. 14.
    Mangin I, Bonnet R, Seksik P, et al. Molecular inventory of faecal microflora in patients with Crohn’s disease. FEMS Microbiol Ecol. 2004;50:25–36.CrossRefPubMedGoogle Scholar
  15. 15.
    Manichanh C, Rigottier-Gois L, Bonnaud E, et al. Reduced diversity of faecal microbiota in Crohn’s disease revealed by a metagenomic approach. Gut. 2006;55:205–211.CrossRefPubMedGoogle Scholar
  16. 16.
    Matto J, Maunuksela L, Kajander K, et al. Composition and temporal stability of gastrointestinal microbiota in irritable bowel syndrome—a longitudinal study in IBS and control subjects. FEMS Immunol Med Microbiol. 2005;43:213–222.CrossRefPubMedGoogle Scholar
  17. 17.
    Maukonen J, Satokari R, Matto J, Soderlund H, Mattila-Sandholm T, Saarela M. Prevalence and temporal stability of selected clostridial groups in irritable bowel syndrome in relation to predominant faecal bacteria. J Med Microbiol. 2006;55:625–633.CrossRefPubMedGoogle Scholar
  18. 18.
    Nandi R, Sengupta S. Microbial production of hydrogen: an overview. Crit Rev Microbiol. 1998;24:61–84.CrossRefPubMedGoogle Scholar
  19. 19.
    Nubel U, Engelen B, Felske A, et al. Sequence heterogeneities of genes encoding 16S rRNAs in Paenibacillus polymyxa detected by temperature gradient gel electrophoresis. J Bacteriol. 1996;178:5636–5643.PubMedGoogle Scholar
  20. 20.
    O’Mahony L, McCarthy J, Kelly P, et al. Lactobacillus and Bifidobacterium in irritable bowel syndrome: symptom responses and relationship to cytokine profiles. Gastroenterol. 2005;128:541–551.CrossRefGoogle Scholar
  21. 21.
    Pimentel M, Chow EJ, Lin HC. Eradication of small intestinal bacterial overgrowth reduces symptoms of irritable bowel syndrome. Am J Gastroenterol. 2000;95:3503–3506.CrossRefPubMedGoogle Scholar
  22. 22.
    Pimentel M, Chow EJ, Lin HC. Normalization of lactulose breath testing correlates with symptom improvement in irritable bowel syndrome. A double-blind, randomized, placebo-controlled study. Am J Gastroenterol. 2003;98:412–419.PubMedGoogle Scholar
  23. 23.
    Pimentel M, Lin HC, Enayati P, et al. Methane, a gas produced by enteric bacteria, slows intestinal transit and augments small intestinal contractile activity. Am J Physiol Gastrointest Liver Physiol. 2005;290:G1089–G1095.CrossRefPubMedGoogle Scholar
  24. 24.
    Posserud I, Stotzer PO, Bjornsson E, Abrahamsson H, Simren M. Small intestinal bacterial overgrowth in patients with irritable bowel syndrome. Gut. 2006;56:802–808.CrossRefPubMedGoogle Scholar
  25. 25.
    Quigley EM. Changing face of irritable bowel syndrome. World J Gastroenterol. 2006;12:1–5.PubMedGoogle Scholar
  26. 26.
    Rinttila T, Kassinen A, Malinen E, Krogius L, Palva A. Development of an extensive set of 16S rDNA-targeted primers for quantification of pathogenic and indigenous bacteria in faecal samples by real-time PCR. J Appl Microbiol. 2004;97:1166–1177.CrossRefPubMedGoogle Scholar
  27. 27.
    Savage DC. Microbial ecology of the gastrointestinal tract. Annu Rev Microbiol. 1977;31:107–133.CrossRefPubMedGoogle Scholar
  28. 28.
    Scanlan PD, Shanahan F, O’Mahony C, Marchesi JR. Culture-independent analyses of the temporal variation of the dominant faecal microbiota and targeted bacterial sub-groups in Crohn’s disease. J Clin Microbiol. 2006;44:3980–3988.CrossRefPubMedGoogle Scholar
  29. 29.
    Seksik P, Lepage P, de la Cochetiere MF, et al. Search for localized dysbiosis in Crohn’s disease ulcerations by temporal temperature gradient gel electrophoresis of 16S rRNA. J Clin Microbiol. 2005;43:4654–4658.CrossRefPubMedGoogle Scholar
  30. 30.
    Shanahan F. Host-flora interactions in inflammatory bowel disease. Inflamm Bowel Dis. 2004;10:S16–S24.CrossRefPubMedGoogle Scholar
  31. 31.
    Si JM, Yu YC, Fan YJ, Chen SJ. Intestinal microecology and quality of life in irritable bowel syndrome patients. World J Gastroenterol. 2004;10:1802–1805.PubMedGoogle Scholar
  32. 32.
    Swidsinski A, Weber J, Loening-Baucke V, Hale LP, Lochs H. Spatial organization and composition of the mucosal flora in patients with inflammatory bowel disease. J Clin Microbiol. 2005;43:3380–3389.CrossRefPubMedGoogle Scholar
  33. 33.
    Thompson WG, Longstreth GF, Drossman DA, Heaton KW, Irvine EJ, Muller-Lissner SA. Functional bowel disorders and functional abdominal pain. Gut. 1999;45:43ii–47.Google Scholar
  34. 34.
    van de Peer Y, Chapelle S, Dewachter R. A quantitative map of nucleotide substitution rates in bacterial rRNA. Nucl Acid Res. 1996;24:3381–3391.CrossRefGoogle Scholar
  35. 35.
    Vanhoutte T, Huys G, De Brandt E, Swings J. Temporal stability analysis of the microbiota in human feces by denaturing gradient gel electrophoresis using universal and group-specific 16S rRNA gene primers. FEMS Microbiol Ecol. 2004;48:437–446.CrossRefPubMedGoogle Scholar
  36. 36.
    Zhang M, Liu B, Zhang Y, Wei H, Lei Y, Zhao L. Structural shifts of mucosa-associated Lactobacilli and Clostridium leptum subgroup in patients with ulcerative colitis. J Clin Microbiol. 2007;45:496–500.CrossRefPubMedGoogle Scholar
  37. 37.
    Zoetendal EG, von Wright A, Vilpponen-Salmela T, Ben Amor K, Akkermans AD, de Vos WM. Mucosa-associated bacteria in the human gastrointestinal tract are uniformly distributed along the colon and differ from the community recovered from feces. Appl Environ Microbiol. 2002;68:3401–3407.CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2009

Authors and Affiliations

  • Caroline Codling
    • 1
    • 2
  • Liam O’Mahony
    • 1
  • Fergus Shanahan
    • 1
  • Eamonn M. M. Quigley
    • 1
    • 3
  • Julian R. Marchesi
    • 1
    • 2
    • 4
  1. 1.Alimentary Pharmabiotic Centre, Department of MedicineCork University HospitalCorkIreland
  2. 2.Department of MicrobiologyNational University of Ireland, CorkCorkIreland
  3. 3.Department of MedicineCork University HospitalCorkIreland
  4. 4.School of BiosciencesCardiff UniversityCardiffUK

Personalised recommendations