Reduced diversity of faecal microbiota in Crohn's disease revealed by a metagenomic approach

Chaysavanh Manichanh ¹, Lionel Rigottier-Gois ¹, Elian Bonnaud ¹, Karine Gloux ¹, Eric Pelletier ², Lionel Frangeul ³, Renaud Nalin ⁴, Cyrille Jarrin ⁴, Patrick Chardon ¹, Phillipe Marteau ⁵, Joaquim Roca ⁶ and Joel Dore ^1*

¹ Institut National de la Recherche Agronomique, France
² Centre National de Séquençage, France
³ Institut Pasteur, France
⁴ LibraGen, France
⁵ Hopital Laennec, France
⁶ CSIC, Spain

^* To whom correspondence should be addressed. E-mail: joel.dore{at}jouy.inra.fr.

Accepted 19 September 2005

Abstract

Background and Aim: A role of the intestinal microbial community (microbiota) in the onset and chronicity of Crohn's disease (CD) is strongly suspected. However, investigation of such a complex ecosystem is difficult, even with culture-independent molecular approaches.

Methods: We used, for the first time, a comprehensive metagenomic approach to investigate the full range of intestinal microbial diversity. We used a fosmid vector to construct two libraries of genomic DNA isolated directly from fecal samples of six healthy donors and six patients with Crohn's disease. Bacterial diversity was analyzed by screening the two DNA libraries, each composed of 25,000 clones, for the 16S rRNA gene by DNA hybridization.

Results: Among 1190 selected clones, we identified 125 non-redundant ribotypes mainly represented by the phyla Bacteroidetes and Firmicutes. Among the Firmicutes, 43 distinct ribotypes were identified in the healthy microbiota, compared to only 13 in CD (p<0.025). Fluorescence in situ hybridization directly targeting 16S rRNA in fecal samples analysed individually (n=12) confirmed the significant reduction in the proportion of bacteria belonging to this phylum in CD patients (p<0.02).

Conclusion: Metagenomic approach allowed us to detect a reduced complexity of the bacterial phylum Firmicutes as a signature of the fecal microbiota in patients with Crohn's disease. It also indicated the presence of new bacterial species.

Keywords: Crohn's disease, firmicutes, metagenome, faecal microbiota, phylogeny

CiteULike    Complore    Connotea    Del.icio.us    Digg    Reddit    Technorati    What's this?

Relevant Articles

Reduced microbial diversity in inflammatory bowel diseases

S J Ott and S Schreiber
Gut 2006 55: 1207. [Extract] [Full Text] [PDF]

This article has been cited by other articles:

• Clavel, T., Charrier, C., Braune, A., Wenning, M., Blaut, M., Haller, D. (2009). Isolation of bacteria from the ileal mucosa of TNFdeltaARE mice and description of Enterorhabdus mucosicola gen. nov., sp. nov.. Int. J. Syst. Evol. Microbiol. 59: 1805-1812 [Abstract] [Full Text]  
• Petrosino, J. F., Highlander, S., Luna, R. A., Gibbs, R. A., Versalovic, J. (2009). Metagenomic Pyrosequencing and Microbial Identification. Clin. Chem. 55: 856-866 [Abstract] [Full Text]  
• Matsuda, K., Tsuji, H., Asahara, T., Matsumoto, K., Takada, T., Nomoto, K. (2009). Establishment of an Analytical System for the Human Fecal Microbiota, Based on Reverse Transcription-Quantitative PCR Targeting of Multicopy rRNA Molecules. Appl. Environ. Microbiol. 75: 1961-1969 [Abstract] [Full Text]  
• Hattori, M., Taylor, T. D. (2009). The Human Intestinal Microbiome: A New Frontier of Human Biology. DNA Res 16: 1-12 [Abstract] [Full Text]  
• Kuehbacher, T., Rehman, A., Lepage, P., Hellmig, S., Folsch, U. R., Schreiber, S., Ott, S. J. (2008). Intestinal TM7 bacterial phylogenies in active inflammatory bowel disease. J Med Microbiol 57: 1569-1576 [Abstract] [Full Text]  
• Zoetendal, E G, Rajilic-Stojanovic, M, de Vos, W M (2008). High-throughput diversity and functionality analysis of the gastrointestinal tract microbiota. Gut 57: 1605-1615 [Abstract] [Full Text]  
• Sokol, H., Pigneur, B., Watterlot, L., Lakhdari, O., Bermudez-Humaran, L. G., Gratadoux, J.-J., Blugeon, S., Bridonneau, C., Furet, J.-P., Corthier, G., Grangette, C., Vasquez, N., Pochart, P., Trugnan, G., Thomas, G., Blottiere, H. M., Dore, J., Marteau, P., Seksik, P., Langella, P. (2008). From the Cover: Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients. Proc. Natl. Acad. Sci. USA 105: 16731-16736 [Abstract] [Full Text]  
• Sartor, R. B. (2008). Therapeutic correction of bacterial dysbiosis discovered by molecular techniques. Proc. Natl. Acad. Sci. USA 105: 16413-16414 [Full Text]  
• Ott, S. J., Plamondon, S., Hart, A., Begun, A., Rehman, A., Kamm, M. A., Schreiber, S. (2008). Dynamics of the Mucosa-Associated Flora in Ulcerative Colitis Patients during Remission and Clinical Relapse. J. Clin. Microbiol. 46: 3510-3513 [Abstract] [Full Text]  
• Manichanh, C., Chapple, C. E., Frangeul, L., Gloux, K., Guigo, R., Dore, J. (2008). A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library. Nucleic Acids Res 36: 5180-5188 [Abstract] [Full Text]  
• Lewis, K., Caldwell, J., Phan, V., Prescott, D., Nazli, A., Wang, A., Soderholm, J. D., Perdue, M. H., Sherman, P. M., McKay, D. M. (2008). Decreased epithelial barrier function evoked by exposure to metabolic stress and nonpathogenic E. coli is enhanced by TNF-{alpha}. Am. J. Physiol. Gastrointest. Liver Physiol. 294: G669-G678 [Abstract] [Full Text]  
• Kurokawa, K., Itoh, T., Kuwahara, T., Oshima, K., Toh, H., Toyoda, A., Takami, H., Morita, H., Sharma, V. K., Srivastava, T. P., Taylor, T. D., Noguchi, H., Mori, H., Ogura, Y., Ehrlich, D. S., Itoh, K., Takagi, T., Sakaki, Y., Hayashi, T., Hattori, M. (2007). Comparative Metagenomics Revealed Commonly Enriched Gene Sets in Human Gut Microbiomes. DNA Res 0: dsm018v2-13 [Abstract] [Full Text]  
• LeLeiko, N. S. (2007). GI Flora in IBS. AAP Grand Rounds 18: 41-42 [Full Text]  
• Frank, D. N., St. Amand, A. L., Feldman, R. A., Boedeker, E. C., Harpaz, N., Pace, N. R. (2007). Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc. Natl. Acad. Sci. USA 104: 13780-13785 [Abstract] [Full Text]  
• Gloux, K., Leclerc, M., Iliozer, H., L'Haridon, R., Manichanh, C., Corthier, G., Nalin, R., Blottiere, H. M., Dore, J. (2007). Development of High-Throughput Phenotyping of Metagenomic Clones from the Human Gut Microbiome for Modulation of Eukaryotic Cell Growth. Appl. Environ. Microbiol. 73: 3734-3737 [Abstract] [Full Text]  
• Hall, N. (2007). Advanced sequencing technologies and their wider impact in microbiology. J. Exp. Biol. 210: 1518-1525 [Abstract] [Full Text]  
• Klaassens, E. S., de Vos, W. M., Vaughan, E. E. (2007). Metaproteomics Approach To Study the Functionality of the Microbiota in the Human Infant Gastrointestinal Tract. Appl. Environ. Microbiol. 73: 1388-1392 [Abstract] [Full Text]  
• Zhang, M., Liu, B., Zhang, Y., Wei, H., Lei, Y., Zhao, L. (2007). Structural Shifts of Mucosa-Associated Lactobacilli and Clostridium leptum Subgroup in Patients with Ulcerative Colitis. J. Clin. Microbiol. 45: 496-500 [Abstract] [Full Text]  
• Mai, V, Greenwald, B, Glenn Morris, J Jr, Raufman, J-P, Stine, O C (2006). Effect of bowel preparation and colonoscopy on post-procedure intestinal microbiota composition.. Gut 55: 1822-1823 [Full Text]  
• Mai, V., Braden, C. R., Heckendorf, J., Pironis, B., Hirshon, J. M. (2006). Monitoring of Stool Microbiota in Subjects with Diarrhea Indicates Distortions in Composition. J. Clin. Microbiol. 44: 4550-4552 [Abstract] [Full Text]  
• Scanlan, P. D., Shanahan, F., O'Mahony, C., Marchesi, J. R. (2006). Culture-Independent Analyses of Temporal Variation of the Dominant Fecal Microbiota and Targeted Bacterial Subgroups in Crohn's Disease. J. Clin. Microbiol. 44: 3980-3988 [Abstract] [Full Text]  
• Gophna, U., Sommerfeld, K., Gophna, S., Doolittle, W. F., Veldhuyzen van Zanten, S. J. O. (2006). Differences between Tissue-Associated Intestinal Microfloras of Patients with Crohn's Disease and Ulcerative Colitis. J. Clin. Microbiol. 44: 4136-4141 [Abstract] [Full Text]  
• Furrie, E (2006). A molecular revolution in the study of intestinal microflora. Gut 55: 141-143 [Abstract] [Full Text]