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

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Date
2020-03-23
Authors
Ryan, Fergal 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.
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Publisher
Springer Nature
Published Version
10.1038/s41467-020-15342-5
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Abstract
Studies 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.
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Keywords
Inflammatory bowel disease (IBD , Microbiota
Citation
Ryan 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/s41467-020-15342-5
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https://www.nature.com/articles/s41467-020-15342-5
URI
https://hdl.handle.net/10468/9819
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Biochemistry and Cell Biology - Journal Articles
APC Microbiome Ireland - Journal Articles
Food and Nutritional Sciences - Journal Articles
INFANT Research Centre - Journal Articles
Medicine - Journal Articles
Microbiology - Journal Articles
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© 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 http://creativecommons.org/licenses/by/4.0/.