Search for localized dysbiosis in Crohn's disease ulcerations by temporal temperature gradient gel electrophoresis of 16S rRNA - PubMed (original) (raw)

Search for localized dysbiosis in Crohn's disease ulcerations by temporal temperature gradient gel electrophoresis of 16S rRNA

Philippe Seksik et al. J Clin Microbiol. 2005 Sep.

Abstract

The mucosa-associated microbiota lining the gut epithelium might play a central role in the activation and/or perpetuation of mucosal inflammation in Crohn's disease (CD). We sought for localized dysbiosis by comparing the biodiversity and composition of the microbiotas in ulcerated and nonulcerated mucosal samples from patients with CD. Biopsy samples (n = 75) of ulcerated and adjacent nonulcerated mucosa were collected during colonoscopy from 15 patients, from the ileum, right colon, left colon, and rectum. Temporal temperature gradient gel electrophoresis (TTGE) of bacterial 16S rRNAs was used to evaluate the dominant bacterial species. TTGE profiles were compared using software that calculates similarity percentages. For a given patient, average similarity indexes between ulcerated and nonulcerated mucosal TTGE profiles ranged from 95.2% +/- 4.2% to 97.9% +/- 1.7% (means +/- standard deviations) for the different segments. The mean values did not differ significantly. Average interindividual similarity indexes for a given segment among the different patients ranged from 33.6% +/- 15.5% to 42.0% +/- 25.6%. In CD, the dominant microbiotas do not differ qualitatively between ulcerated and nonulcerated mucosae. Biodiversity remains high in ulcerated mucosa. This argues against a pathogenic role of localized qualitative dysbiosis in CD-associated ulceration.

PubMed Disclaimer

Figures

FIG. 1.

FIG. 1.

TTGE of 16S rRNA gene amplicons (obtained using primers for the V6-V8 region) amplified from biopsy samples of ulcerated mucosa (UM) and nonulcerated mucosa (NUM) from the left colons of five CD patients. UM X, TTGE profile for UM of patient X; NUM X, TTGE profile for NUM of patient X. (Center) TTGE profiles ordered by Gel Compar II software. UM and NUM TTGE profiles for a given patient were always more similar than UM and NUM profiles for different patients. (Right) Pearson correlation coefficients yielded the calculated similarity indexes (expressed as percentages) of paired samples. (Left) The dendrogram represents a statistically optimal representation of the similarities between TTGE profiles based on the matrix of Pearson correlation coefficients and applying UPGMA.

FIG. 2.

FIG. 2.

Dendrogram representation of the TTGE profiles of 16S rRNA gene amplicons (obtained using primers for the V6-V8 region) amplified from biopsy samples of ulcerated mucosa (UM) and nonulcerated mucosa (NUM) from 15 CD patients. Biopsy samples were collected from the ileum (I), right colon (RC), left colon (LF), and rectum (R) of each patient. Gray designations, ulcerated mucosa; black designations, nonulcerated mucosa. The dendrogram represents a statistically optimal representation of the similarities between TTGE profiles based on the matrix of Pearson correlation coefficients and applying UPGMA. The vertical dotted line represents the threshold defining a cluster (80%).

Similar articles

Cited by

References

    1. Blaut, M., M. D. Collins, G. W. Welling, J. Dore, J. van Loo, and W. de Vos. 2002. Molecular biological methods for studying the gut microbiota: the EU human gut flora project. Br. J. Nutr. 87(Suppl. 2):S203-S211. - PubMed
    1. Chen, W., D. Li, I. Wilson, and V. S. Chadwick. 2002. Detection of Chlamydia pneumoniae by polymerase chain reaction-enzyme immunoassay in intestinal mucosal biopsies from patients with inflammatory bowel disease and controls. J. Gastroenterol. Hepatol. 17:987-993. - PubMed
    1. Darfeuille-Michaud, A., J. Boudeau, P. Bulois, C. Neut, A. L. Glasser, N. Barnich, M. A. Bringer, A. Swidsinski, L. Beaugerie, and J. F. Colombel. 2004. High prevalence of adherent-invasive Escherichia coli associated with ileal mucosa in Crohn's disease. Gastroenterology 127:412-421. - PubMed
    1. Darfeuille-Michaud, A., C. Neut, N. Barnich, E. Lederman, P. Di Martino, P. Desreumaux, L. Gambiez, B. Joly, A. Cortot, and J. F. Colombel. 1998. Presence of adherent Escherichia coli strains in ileal mucosa of patients with Crohn's disease. Gastroenterology 115:1405-1413. - PubMed
    1. Dore, J., A. Sghir, G. Hannequart-Gramet, G. Corthier, and P. Pochart. 1998. Design and evaluation of a 16S rRNA-targeted oligonucleotide probe for specific detection and quantitation of human faecal Bacteroides populations. Syst. Appl. Microbiol. 21:65-71. - PubMed

MeSH terms

Substances

LinkOut - more resources