Skip to Main content Skip to Navigation
Journal articles

Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment.

Abstract : ABSTRACT: BACKGROUND: The inflammatory bowel diseases (IBD) Crohn's disease and ulcerative colitis result from alterations in intestinal microbes and the immune system. However, the precise dysfunctions of microbial metabolism in the gastrointestinal microbiome during IBD remain unclear. We analyzed the microbiota of intestinal biopsies and stool samples from 231 IBD and healthy subjects by 16S gene pyrosequencing and followed up a subset using shotgun metagenomics. Gene and pathway composition were assessed, based in 16S data on phylogenetically-related reference genomes, and associated using sparse multivariate linear modeling with medications, environmental factors, and IBD status. RESULTS: Firmicutes and Enterobacteriaceae abundances were associated with disease status as expected, but also with treatment and subject characteristics. Microbial function, though, was more consistently perturbed than composition, with 12% of analyzed pathways changed compared with 2% of genera. We identified major shifts in oxidative stress pathways, as well as decreased carbohydrate metabolism and amino acid biosynthesis in favor of nutrient transport and uptake. The microbiome of ileal Crohn's disease was notable for increases in virulence and secretion pathways. CONCLUSIONS: This inferred functional metagenomic information provides the first insights into community-wide microbial processes and pathways that underpin IBD pathogenesis.
Complete list of metadatas

https://hal.archives-ouvertes.fr/hal-00736429
Contributor : -
Submitted on : Friday, September 28, 2012 - 11:13:19 AM
Last modification on : Tuesday, February 26, 2019 - 10:12:45 AM

Links full text

Identifiers

Collections

Citation

Xochitl C Morgan, Timothy L Tickle, Harry Sokol, Dirk Gevers, Kathryn L Devaney, et al.. Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment.. Genome Biology, BioMed Central, 2012, 13 ((9)), pp.R79. ⟨10.1186/gb-2012-13-9-r79⟩. ⟨hal-00736429⟩

Share

Metrics

Record views

207