Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2012-09-26

AUTHORS

Xochitl C Morgan, Timothy L Tickle, Harry Sokol, Dirk Gevers, Kathryn L Devaney, Doyle V Ward, Joshua A Reyes, Samir A Shah, Neal LeLeiko, Scott B Snapper, Athos Bousvaros, Joshua Korzenik, Bruce E Sands, Ramnik J Xavier, Curtis Huttenhower

ABSTRACT

BackgroundThe 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 on 16S data from phylogenetically-related reference genomes, and associated using sparse multivariate linear modeling with medications, environmental factors, and IBD status.ResultsFirmicutes 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.ConclusionsThis inferred functional metagenomic information provides the first insights into community-wide microbial processes and pathways that underpin IBD pathogenesis. More... »

PAGES

r79

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  • Journal

    TITLE

    Genome Biology

    ISSUE

    9

    VOLUME

    13

    Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1186/gb-2012-13-9-r79

    DOI

    http://dx.doi.org/10.1186/gb-2012-13-9-r79

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1029450096

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/23013615


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