Dysbiosis of fecal microbiota in Crohn's disease patients as revealed by a custom phylogenetic microarray

Kang, Seungha, Denman, Stuart E., Morrison, Mark, Yu, Zhongtang, Dore, Joel, Leclerc, Marion and McSweeney, Chris S. (2010) Dysbiosis of fecal microbiota in Crohn's disease patients as revealed by a custom phylogenetic microarray. Inflammatory Bowel Diseases, 16 12: 2034-2042. doi:10.1002/ibd.21319

Author Kang, Seungha
Denman, Stuart E.
Morrison, Mark
Yu, Zhongtang
Dore, Joel
Leclerc, Marion
McSweeney, Chris S.
Title Dysbiosis of fecal microbiota in Crohn's disease patients as revealed by a custom phylogenetic microarray
Journal name Inflammatory Bowel Diseases   Check publisher's open access policy
ISSN 1078-0998
Publication date 2010-01-01
Sub-type Article (original research)
DOI 10.1002/ibd.21319
Open Access Status Not yet assessed
Volume 16
Issue 12
Start page 2034
End page 2042
Total pages 9
Place of publication Philadelphia, PA, United States
Publisher Lippincott Williams & Wilkins
Language eng
Formatted abstract
Background: 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.

Methods: 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.

Results: 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.

Conclusions: 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.  
Keyword 16S rDNA
Crohn's disease
Inflammatory bowel disease
Intestinal microbiology
Microbial diversity
Phylogenetic custom microarray
Real-time PCR
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collection: UQ Diamantina Institute Publications
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