Dysbiosis of fecal microbiota in Crohn's disease patients as revealed by a custom phylogenetic microarray
Version of Record online: 28 JUN 2010
Copyright © 2010 Crohn's & Colitis Foundation of America, Inc.
Inflammatory Bowel Diseases
Volume 16, Issue 12, pages 2034–2042, December 2010
How to Cite
Kang, S., Denman, S. E., Morrison, M., Yu, Z., Dore, J., Leclerc, M. and McSweeney, C. S. (2010), Dysbiosis of fecal microbiota in Crohn's disease patients as revealed by a custom phylogenetic microarray. Inflamm Bowel Dis, 16: 2034–2042. doi: 10.1002/ibd.21319
- Issue online: 19 NOV 2010
- Version of Record online: 28 JUN 2010
- Manuscript Accepted: 9 MAR 2010
- Manuscript Received: 20 JAN 2010
- Crohn's disease;
- inflammatory bowel disease;
- phylogenetic custom microarray;
- microbial diversity;
- 16S rDNA;
- intestinal microbiology;
- real-time PCR
A custom phylogenetic microarray composed of small subunit ribosomal RNA probes, representing ≈500 bacterial species from the human and animal gut, was developed and evaluated for analysis of gut microbial diversity using fecal samples from healthy subjects and Crohn's disease (CD) patients.
Oligonucleotide probes (≈40 mer) used on the microarray were selected from published articles or designed with the “GoArray” microarray probe design program using selected bacterial 16S rRNA sequences. Fecal 16S rDNA from individual samples of six healthy subjects and six CD patients were used as template to generate fluorescently labeled cRNA that was hybridized to the microarray. Differences revealed by the microarray in relative abundance of microbial populations between healthy and diseased patients were verified using quantitative real-time polymerase chain reaction (PCR) with species-specific primer sets.
The microarray analyses showed that Eubacterium rectale, Bacteroides fragilis group, B. vulgatus, Ruminococcus albus, R. callidus, R. bromii, and Faecalibacterium prausnitzii were 5–10-fold more abundant in the healthy subjects than in the CD patients, while Enterococcus sp., Clostridium difficile, Escherichia coli, Shigella flexneri, and Listeria sp. were more abundant in the CD group.
The microarray detected differences in abundance of bacterial populations within the phylum Firmicutes that had been reported previously for the same samples based on phylogenetic analysis of metagenomic clone libraries. In addition, the microarray showed that Enterococcus sp. was in higher abundance in the CD patients. This microarray should be another useful tool to examine the diversity and abundance of human intestinal microbiota. (Inflamm Bowel Dis 2010)