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TY - JOUR AU - Ryan, F. J. AU - Ahern, A. M. AU - Fitzgerald, R. S. AU - Laserna-Mendieta, E. J. AU - Power, E. M. AU - Clooney, A. G. AU - O’Donoghue, K. W. AU - McMurdie, P. J. AU - Iwai, S. AU - Crits-Christoph, A. AU - Sheehan, D. AU - Moran, C. AU - Flemer, B. AU - Zomer, A. L. AU - Fanning, A. AU - O’Callaghan, J. AU - Walton, J. AU - Temko, A. AU - Stack, W. AU - Jackson, L. AU - Joyce, S. A. AU - Melgar, S. AU - DeSantis, T. Z. AU - Bell, J. T. AU - Shanahan, F. AU - Claesson, M. J. PY - 2020 DA - 2020/03/23 TI - Colonic microbiota is associated with inflammation and host epigenomic alterations in inflammatory bowel disease JO - Nature Communications SP - 1512 VL - 11 IS - 1 AB - 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. SN - 2041-1723 UR - https://doi.org/10.1038/s41467-020-15342-5 DO - 10.1038/s41467-020-15342-5 ID - Ryan2020 ER -