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

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1Preventative Health National Research Flagship, CSIRO, St. Lucia, Qld, Australia

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1Preventative Health National Research Flagship, CSIRO, St. Lucia, Qld, Australia

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1Preventative Health National Research Flagship, CSIRO, St. Lucia, Qld, Australia

2Ohio State University, Columbus, OH, USA

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2Ohio State University, Columbus, OH, USA

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3Unit for Ecology and Physiology of the Digestive Tract, INRA, Jouy-en-Josas Cedex, France

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3Unit for Ecology and Physiology of the Digestive Tract, INRA, Jouy-en-Josas Cedex, France

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1Preventative Health National Research Flagship, CSIRO, St. Lucia, Qld, Australia

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Received:

20 January 2010

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Seungha Kang, Stuart E. Denman, Mark Morrison, Zhongtang Yu, Joel Dore, Marion Leclerc, Chris S. McSweeney, Dysbiosis of fecal microbiota in Crohn's disease patients as revealed by a custom phylogenetic microarray, Inflammatory Bowel Diseases, Volume 16, Issue 12, 1 December 2010, Pages 2034–2042, https://doi.org/10.1002/ibd.21319
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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. (Inflamm Bowel Dis 2010)

Copyright © 2010 Crohn's & Colitis Foundation of America, Inc.

Topic:

• polymerase chain reaction
• enterococcus
• crohn's disease
• inflammatory bowel disease
• bacteroides fragilis
• clone cells
• recombinant dna
• dna, ribosomal
• eubacterium
• feces
• intestines
• libraries
• listeria
• nurse anesthetists
• oligonucleotide probes
• complementary rna
• ribosomal rna
• rna, ribosomal, 16s
• shigella flexneri
• clostridium difficile
• microbiome
• stool specimen
• quantitative real-time polymerase chain reaction
• verification
• dysbiosis
• firmicutes
• faecalibacterium prausnitzii

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