Skip to main content

Advertisement

SpringerLink
Log in

Comparison of the fecal microbiota profiles between ulcerative colitis and Crohn’s disease using terminal restriction fragment length polymorphism analysis

  • Original Article—Alimentary Tract
  • Published:
Journal of Gastroenterology Aims and scope Submit manuscript

Abstract

Background

Terminal restriction fragment length polymorphism (T-RFLP) analysis is a powerful tool to assess the diversity of a microbial community. In this study, we performed T-RFLP analysis of the fecal microbiota from patients with ulcerative colitis (UC) and those with Crohn’s disease (CD).

Methods

Thirty-one patients with UC, 31 patients with CD, and 30 healthy individuals were enrolled. The polymerase chain reaction (PCR) products obtained from the 16S rRNA genes of fecal samples were digested with BslI, and T-RF lengths were determined.

Results

The fecal microbial communities were classified into 5 clusters. Twenty-eight of the 30 healthy individuals and 17 of the 18 patients with inactive UC were classified into clusters I, II, and III, but these clusters included a small number of patients with active UC and inactive/active CD. In contrast, 8 of the 13 patients with active UC and the majority of CD patients (12 of the 16 patients with inactive CD, and 11 of the 15 patients with active CD) were included in clusters IV and V. Based on the BslI-digested T-RFLP database, the bacteria showed a significant decrease in the Clostridium family in patients with active UC and inactive/active CD. In contrast, Bacteroides were significantly increased in CD patients. No significant differences were observed between patients with active UC and those with active CD.

Conclusion

The fecal microbial communities of IBD patients were different from those of healthy individuals. The gut microbiota of patients with inactive UC tended to be closer to that of healthy individuals, suggesting different roles for the fecal microbiota in the pathophysiology of UC and CD.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1

Similar content being viewed by others

References

  1. Sands BE. Inflammatory bowel disease: past, present, and future. J Gastroenterol. 2007;42:16–25.

    Article  PubMed  Google Scholar 

  2. Mayer L. Evolving paradigms in the pathogenesis of IBD. J Gastroenterol. 2010;45:9–16.

    Article  PubMed  CAS  Google Scholar 

  3. Hibi T, Ogata H. Novel pathophysiological concepts of inflammatory bowel disease. J Gastroenterol. 2006;41:10–6.

    Article  PubMed  Google Scholar 

  4. Podolsky DK. Inflammatory bowel disease. N Engl J Med. 2002;347:417–29.

    Article  PubMed  CAS  Google Scholar 

  5. Mizoguchi A, Mizoguchi E. Inflammatory bowel disease, past, present and future: lessons from animal models. J Gastroenterol. 2008;43:1–17.

    Article  PubMed  Google Scholar 

  6. Sartor RB. Mechanisms of disease: pathogenesis of Crohn’s disease and ulcerative colitis. Nat Clin Pract Gastroenterol Hepatol. 2006;3:390–407.

    Article  PubMed  CAS  Google Scholar 

  7. Wirtz S, Neurath MF. Mouse models of inflammatory bowel disease. Adv Drug Deliv Rev. 2007;59:1073–83.

    Article  PubMed  CAS  Google Scholar 

  8. Braun J, Wei B. Body traffic: ecology, genetics, and immunity in inflammatory bowel disease. Annu Rev Pathol. 2007;2:401–29.

    Article  PubMed  CAS  Google Scholar 

  9. Seksik P, Sokol H, Lepage P, Vasquez N, Manichanh C, Mangin I, et al. Review article: the role of bacteria in onset and perpetuation of inflammatory bowel disease. Aliment Pharmacol Ther. 2006;24(Suppl 3):11–8.

    Article  PubMed  CAS  Google Scholar 

  10. Elson CO, Cong Y, McCracken VJ, Dimmitt RA, Lorenz RG, Weaver CT. Experimental models of inflammatory bowel disease reveal innate, adaptive, and regulatory mechanisms of host dialogue with the microbiota. Immunol Rev. 2005;206:260–76.

    Article  PubMed  Google Scholar 

  11. Sartor RB. Microbial influences in inflammatory bowel diseases. Gastroenterology. 2008;134:577–94.

    Article  PubMed  CAS  Google Scholar 

  12. Hooper LV, Wong MH, Thelin A, Hansson L, Falk PG, Gordon JI. Molecular analysis of commensal host-microbial relationships in the intestine. Science. 2001;291:881–4.

    Article  PubMed  CAS  Google Scholar 

  13. Guarner F, Malagelada JR. Gut flora in health and disease. Lancet. 2003;361:512–9.

    Article  PubMed  Google Scholar 

  14. Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, Sargent M, et al. Diversity of the human intestinal microbial flora. Science. 2005;308:1635–8.

    Article  PubMed  Google Scholar 

  15. Mahida YR, Rolfe VE. Host-bacterial interactions in inflammatory bowel disease. Clin Sci (Lond). 2004;107:331–41.

    Article  CAS  Google Scholar 

  16. Hayashi H, Sakamoto M, Kitahara M, Benno Y. Molecular analysis of fecal microbiota in elderly individuals using 16S rDNA library and T-RFLP. Microbiol Immunol. 2003;47:557–70.

    PubMed  CAS  Google Scholar 

  17. Sakamoto M, Hayashi H, Benno Y. Terminal restriction fragment length polymorphism analysis for human fecal microbiota and its application for analysis of complex bifidobacterial communities. Microbiol Immunol. 2003;47:133–42.

    PubMed  CAS  Google Scholar 

  18. Sakamoto M, Takeuchi Y, Umeda M, Ishikawa I, Benno Y. Application of terminal RFLP analysis to characterize oral bacterial flora in saliva of healthy subjects and patients with periodontitis. J Med Microbiol. 2003;52(Pt 1):79–89.

    Article  PubMed  CAS  Google Scholar 

  19. Li F, Hullar MA, Lampe JW. Optimization of terminal restriction fragment polymorphism (TRFLP) analysis of human gut microbiota. J Microbiol Methods. 2007;68:303–11.

    Article  PubMed  CAS  Google Scholar 

  20. Schutte UM, Abdo Z, Bent SJ, Shyu C, Williams CJ, Pierson JD, et al. Advances in the use of terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA genes to characterize microbial communities. Appl Microbiol Biotechnol. 2008;80:365–80.

    Article  PubMed  CAS  Google Scholar 

  21. Hayashi H, Takahashi R, Nishi T, Sakamoto M, Benno Y. Molecular analysis of jejunal, ileal, caecal and recto-sigmoidal human colonic microbiota using 16S rRNA gene libraries and terminal restriction fragment length polymorphism. J Med Microbiol. 2005;54(Pt 11):1093–101.

    Article  PubMed  CAS  Google Scholar 

  22. Andoh A, Benno Y, Kanauchi O, Fujiyama Y. Recent advances in molecular approaches to gut microbiota in inflammatory bowel disease. Curr Pharm Des. 2009;15:2066–73.

    Article  PubMed  CAS  Google Scholar 

  23. Marsh TL, Saxman P, Cole J, Tiedje J. Terminal restriction fragment length polymorphism analysis program, a web-based research tool for microbial community analysis. Appl Environ Microbiol. 2000;66:3616–20.

    Article  PubMed  CAS  Google Scholar 

  24. Andoh A, Sakata S, Koizumi Y, Mitsuyama K, Fujiyama Y, Benno Y. Terminal restriction fragment length polymorphism analysis of the diversity of fecal microbiota in patients with ulcerative colitis. Inflamm Bowel Dis. 2007;13:955–62.

    Article  PubMed  Google Scholar 

  25. Andoh A, Tsujikawa T, Sasaki M, Mitsuyama K, Suzuki Y, Matsui T, et al. Fecal microbiota profile of Crohn’s disease determined by terminal restriction fragment length polymorphism (t-rflp) analysis. Aliment Pharmacol Ther. 2009;29:75–82.

    Article  PubMed  CAS  Google Scholar 

  26. Rachmilewitz D. Coated mesalazine (5-aminosalicylic acid) versus sulphasalazine in the treatment of active ulcerative colitis: a randomised trial. BMJ. 1989;298:82–6.

    Article  PubMed  CAS  Google Scholar 

  27. Best WR, Becktel JM, Singleton JW, Kern F Jr. Development of a Crohn’s disease activity index. National Cooperative Crohn’s Disease Study. Gastroenterology. 1976;70:439–44.

    PubMed  CAS  Google Scholar 

  28. Hayashi H, Sakamoto M, Kitahara M, Benno Y. Diversity of the Clostridium coccoides group in human fecal microbiota as determined by 16S rRNA gene library. FEMS Microbiol Lett. 2006;257:202–7.

    Article  PubMed  CAS  Google Scholar 

  29. Nagashima K, Hisada T, Sato M, Mochizuki J. Application of new primer–enzyme combinations to terminal restriction fragment length polymorphism profiling of bacterial populations in human feces. Appl Environ Microbiol. 2003;69:1251–62.

    Article  PubMed  CAS  Google Scholar 

  30. Frank DN, St Amand AL, Feldman RA, Boedeker EC, Harpaz N, Pace NR. Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc Natl Acad Sci USA. 2007;104:13780–5.

    Article  PubMed  CAS  Google Scholar 

  31. Matsuda H, Fujiyama Y, Andoh A, Ushijima T, Kajinami T, Bamba T. Characterization of antibody responses against rectal mucosa-associated bacterial flora in patients with ulcerative colitis. J Gastroenterol Hepatol. 2000;15:61–8.

    Article  PubMed  CAS  Google Scholar 

  32. Lucke K, Miehlke S, Jacobs E, Schuppler M. Prevalence of Bacteroides and Prevotella spp. in ulcerative colitis. J Med Microbiol. 2006;55(Pt 5):617–24.

    Article  PubMed  CAS  Google Scholar 

  33. Swidsinski A, Ladhoff A, Pernthaler A, Swidsinski S, Loening-Baucke V, Ortner M, et al. Mucosal flora in inflammatory bowel disease. Gastroenterology. 2002;122:44–54.

    Article  PubMed  Google Scholar 

  34. Hayashi H, Sakamoto M, Benno Y. Phylogenetic analysis of the human gut microbiota using 16S rDNA clone libraries and strictly anaerobic culture-based methods. Microbiol Immunol. 2002;46:535–48.

    PubMed  CAS  Google Scholar 

  35. Langendijk PS, Schut F, Jansen GJ, Raangs GC, Kamphuis GR, Wilkinson MH, et al. Quantitative fluorescence in situ hybridization of Bifidobacterium spp. with genus-specific 16S rRNA-targeted probes and its application in fecal samples. Appl Environ Microbiol. 1995;61:3069–75.

    PubMed  CAS  Google Scholar 

  36. Suau A, Bonnet R, Sutren M, Godon JJ, Gibson GR, Collins MD, et al. Direct analysis of genes encoding 16S rRNA from complex communities reveals many novel molecular species within the human gut. Appl Environ Microbiol. 1999;65:4799–807.

    PubMed  CAS  Google Scholar 

  37. Baumgart M, Dogan B, Rishniw M, Weitzman G, Bosworth B, Yantiss R, et al. Culture independent analysis of ileal mucosa reveals a selective increase in invasive Escherichia coli of novel phylogeny relative to depletion of Clostridiales in Crohn’s disease involving the ileum. ISME J. 2007;1:403–18.

    Article  PubMed  CAS  Google Scholar 

  38. Martinez-Medina M, Aldeguer X, Gonzalez-Huix F, Acero D, Garcia-Gil LJ. Abnormal microbiota composition in the ileocolonic mucosa of Crohn’s disease patients as revealed by polymerase chain reaction-denaturing gradient gel electrophoresis. Inflamm Bowel Dis. 2006;12:1136–45.

    Article  PubMed  Google Scholar 

  39. Gophna U, Sommerfeld K, Gophna S, Doolittle WF, Veldhuyzen van Zanten SJ. Differences between tissue-associated intestinal microfloras of patients with Crohn’s disease and ulcerative colitis. J Clin Microbiol. 2006;44:4136–41.

    Article  PubMed  CAS  Google Scholar 

  40. Manichanh C, Rigottier-Gois L, Bonnaud E, Gloux K, Pelletier E, Frangeul L, et al. Reduced diversity of faecal microbiota in Crohn’s disease revealed by a metagenomic approach. Gut. 2006;55:205–11.

    Article  PubMed  CAS  Google Scholar 

  41. Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature. 2010;464:59–65.

    Article  PubMed  CAS  Google Scholar 

  42. Sokol H, Pigneur B, Watterlot L, Lakhdari O, Bermu dez-Humara n LG, Gratadoux JJ, et al. Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients. Proc Natl Acad Sci USA. 2008;105:16731–6.

    Article  PubMed  CAS  Google Scholar 

  43. Dicksved J, Halfvarson J, Rosenquist M, Jarnerot G, Tysk C, Apajalahti J, et al. Molecular analysis of the gut microbiota of identical twins with Crohn’s disease. ISME J. 2008;2:716–27.

    Article  PubMed  CAS  Google Scholar 

  44. Andoh A, Fujiyama Y, Hata K, Araki Y, Takaya H, Shimada M, et al. Counter-regulatory effect of sodium butyrate on tumour necrosis factor-alpha (TNF-alpha)-induced complement C3 and factor B biosynthesis in human intestinal epithelial cells. Clin Exp Immunol. 1999;118:23–9.

    Article  PubMed  CAS  Google Scholar 

  45. Kawamura T, Andoh A, Nishida A, Shioya M, Yagi Y, Nishimura T, et al. Inhibitory effects of short-chain fatty acids on matrix metalloproteinase secretion from human colonic subepithelial myofibroblasts. Dig Dis Sci. 2009;54:238–45.

    Article  PubMed  CAS  Google Scholar 

  46. Marchesi JR, Holmes E, Khan F, Kochhar S, Scanlan P, Shanahan F, et al. Rapid and noninvasive metabonomic characterization of inflammatory bowel disease. J Proteome Res. 2007;6:546–51.

    Article  PubMed  CAS  Google Scholar 

  47. Ley RE, Turnbaugh PJ, Klein S, Gordon JI. Microbial ecology: human gut microbes associated with obesity. Nature. 2006;444:1022–3.

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Division of Mucosal Immunology, Graduate School of Medicine, Shiga University of Medical Science, Seta Tsukinowa, Otsu, 520-2192, Japan

    Akira Andoh

  2. Department of Medicine, Shiga University of Medical Science, Seta Tsukinowa, Otsu, 520-2192, Japan

    Hirotsugu Imaeda, Tomoki Aomatsu, Osamu Inatomi, Shigeki Bamba, Masaya Sasaki, Yasuharu Saito, Tomoyuki Tsujikawa & Yoshihide Fujiyama

Authors
  1. Akira Andoh
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Hirotsugu Imaeda
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Tomoki Aomatsu
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Osamu Inatomi
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Shigeki Bamba
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Masaya Sasaki
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Yasuharu Saito
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Tomoyuki Tsujikawa
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Yoshihide Fujiyama
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Akira Andoh.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Andoh, A., Imaeda, H., Aomatsu, T. et al. Comparison of the fecal microbiota profiles between ulcerative colitis and Crohn’s disease using terminal restriction fragment length polymorphism analysis. J Gastroenterol 46, 479–486 (2011). https://doi.org/10.1007/s00535-010-0368-4

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00535-010-0368-4

Keywords

Search

Navigation