Colonic microbiota is associated with inflammation and host epigenomic alterations in inflammatory bowel disease

dc.contributor.authorRyan, Fergal J.
dc.contributor.authorAhern, A. M.
dc.contributor.authorFitzgerald, R. S.
dc.contributor.authorLaserna-Mendieta, E. J.
dc.contributor.authorPower, E. M.
dc.contributor.authorClooney, A. G.
dc.contributor.authorO'Donoghue, K. W.
dc.contributor.authorMcMurdie, P. J.
dc.contributor.authorIwai, S.
dc.contributor.authorCrits-Christoph, A.
dc.contributor.authorSheehan, F.
dc.contributor.authorMoran, C.
dc.contributor.authorFlemer, B.
dc.contributor.authorZomer, A. L.
dc.contributor.authorFanning, A.
dc.contributor.authorO'Callaghan, J.
dc.contributor.authorWalton, Janette
dc.contributor.authorTemko, Andriy
dc.contributor.authorStack, W.
dc.contributor.authorJackson, L.
dc.contributor.authorJoyce, Susan A.
dc.contributor.authorMelgar, Silvia
dc.contributor.authorDeSantis, Todd Z.
dc.contributor.authorBell, Bell, Jordana T.
dc.contributor.authorShanahan, Fergus
dc.contributor.authorClaesson, Marcus J.
dc.contributor.funderScience Foundation Irelanden
dc.contributor.funderHealth Research Boarden
dc.contributor.funderIrish Research Councilen
dc.contributor.funderSecond Genome, Inc., United Statesen
dc.description.abstractStudies of inflammatory bowel disease (IBD) have been inconclusive in relating microbiota with distribution of inflammation. We report microbiota, host transcriptomics, epigenomics and genetics from matched inflamed and non-inflamed colonic mucosa [50 Crohn’s disease (CD); 80 ulcerative colitis (UC); 31 controls]. Changes in community-wide and within-patient microbiota are linked with inflammation, but we find no evidence for a distinct microbial diagnostic signature, probably due to heterogeneous host-microbe interactions, and show only marginal microbiota associations with habitual diet. Epithelial DNA methylation improves disease classification and is associated with both inflammation and microbiota composition. Microbiota sub-groups are driven by dominant Enterbacteriaceae and Bacteroides species, representative strains of which are pro-inflammatory in vitro, are also associated with immune-related epigenetic markers. In conclusion, inflamed and non-inflamed colonic segments in both CD and UC differ in microbiota composition and epigenetic profiles.en
dc.description.sponsorshipHealth Research Board, Ireland (grant number PD/2009/30); Irish Research Council (grant number GOIPG/2017/1573); Second Genome, Inc., South San Francisco, California, USAen
dc.description.statusPeer revieweden
dc.description.versionPublished Versionen
dc.identifier.citationRyan F. J., Ahern, A. M., Fitzgerald, R. S., Laserna-Mendieta, E. J., Power, E. M., Clooney, A.G., O’Donoghue, K.W., McMurdie, P.J., Iwai, S., Crits-Christoph, A., Sheehan, D., Moran C., Flemer, B., Zomer, A. L., Fanning, A., O’Callaghan, J., Walton, J., Temko, A., Stack, W., Jackson L., Joyce, S. A., Melgar, S., DeSantis T. Z., Bell J. T., Shanahan, F. and Claesson, M. J. (2020) 'Colonic microbiota is associated with inflammation and host epigenomic alterations in inflammatory bowel disease'. Nature Communications, 11, 1512, (12 pp). doi: 10.1038/s41467-020-15342-5en
dc.identifier.journaltitleNature Communicationsen
dc.publisherSpringer Natureen
dc.relation.projectinfo:eu-repo/grantAgreement/SFI/SFI Starting Investigator Research Grant (SIRG)/11/SIRG/B2162/IE/Molecular diagnostics and metatranscriptomics of colonic bacteria in inflammatory bowel disease/en
dc.relation.projectinfo:eu-repo/grantAgreement/SFI/SFI Research Centres/12/RC/2273/IE/Alimentary Pharmabiotic Centre (APC) - Interfacing Food & Medicine/en
dc.rights© The Author(s) 2020. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit
dc.subjectInflammatory bowel disease (IBDen
dc.titleColonic microbiota is associated with inflammation and host epigenomic alterations in inflammatory bowel diseaseen
dc.typeArticle (peer-reviewed)en
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