Highlighting new phylogenetic specificities of Crohn's disease microbiota

Mondot, S., Kang, S., Furet, J.P., Aguirre De Carcer, D., McSweeney, C., Morrison, M., Marteau, P., Dore, J. and Leclerc, M. (2011) Highlighting new phylogenetic specificities of Crohn's disease microbiota. Inflammatory Bowel Diseases, 17 1: 185-192. doi:10.1002/ibd.21436

Author Mondot, S.
Kang, S.
Furet, J.P.
Aguirre De Carcer, D.
McSweeney, C.
Morrison, M.
Marteau, P.
Dore, J.
Leclerc, M.
Title Highlighting new phylogenetic specificities of Crohn's disease microbiota
Journal name Inflammatory Bowel Diseases   Check publisher's open access policy
ISSN 1078-0998
Publication date 2011
Sub-type Article (original research)
DOI 10.1002/ibd.21436
Open Access Status
Volume 17
Issue 1
Start page 185
End page 192
Total pages 8
Place of publication Philadelphia, PA, United States
Publisher Lippincott Williams & Wilkins
Language eng
Formatted abstract
Background: Recent studies suggest that gastrointestinal (GI) microbes play a part in the pathogenesis of Crohn's disease (CD).

Methods: Fecal samples were collected from 16 healthy individuals and 16 CD patients (age- and sex-matched). The DNA extracted from these samples were subjected to two different methods of microbiome analysis. Specific bacterial groups were quantified by real-time polymerase chain reaction (PCR) methods using primers designed using a high-throughput in-house bioinformatics pipeline. The same DNA extracts were also used to produce fluorescently labeled cRNA amplicons to interrogate a custom-designed phylogenetic microarray for intestinal bacteria.

Results: Even though the intersubject variability was high, differences in the fecal microbiomes of healthy and CD patients were detected. Faecalibacterium prausnitzii and Escherichia coli were more represented in healthy and ileal CD patients, respectively. Additionally, probes specific for Ruminococcus bromii, Oscillibacter valericigenes, Bifidobacterium bifidum, and Eubacterium rectale produced stronger hybridization signals with the DNA samples from healthy subjects. Conversely, species overrepresented in CD patients were E. coli, Enterococcus faecium, and species from the Proteobacteria not normally found in the healthy human GI tract. Furthermore, we detected "healthy specific" molecular species or operational taxonomic units (OTUs) that are not closely related to any known species (Faecalibacterium, Subdoligranulum, and Oscillospora species), indicating that the phylogenetic dysbiosis is broader than at strain or species level.

Conclusions: These two techniques of microbiome analysis provided a statistically robust new picture of the dysbiosis in fecal microbiota from ileal CD patients. Specifically, we identified a set of six species discriminant for CD, which provides a preliminary diagnostic tool. 
Keyword 16S rRNA
Crohn's disease
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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