Journal Article

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

Laserna-Mendieta, E. J., Fanning, A., Crits-Christoph, A., O’Callaghan, J., Ahern, A. M., Melgar, S., Stack, W., Ryan, F. J., McMurdie, P. J., Joyce, S. A., Clooney, A. G., Power, E. M., Flemer, B., O’Donoghue, K. W., Zomer, A. L., Claesson, M. J., Fitzgerald, R. S., Walton, J., Shanahan, F., Jackson, L., Iwai, S., Temko, A., Moran, C., Sheehan, D., DeSantis, T. Z., Bell, J. T.

2020

Overview

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. Inflammatory bowel disease (IBD) has been linked to host-microbiota interactions. Here, the authors investigate mucosa-associated microbiota using endoscopically-targeted biopsies from inflamed and non-inflamed colon in patients with Crohn’s disease and ulcerative colitis, finding associations with inflammation and host epigenomic alterations.

• Publisher: Nature Publishing Group UK,Nature Publishing Group,Nature Portfolio
• Subject: 13 / 38 / 38/91 / 45 / 45/23 / 631/114/1314 / 631/208/177 / Adult / Aged / Astrophysics / Bacteroides - genetics / Bacteroides - immunology / Bacteroides - isolation & purification / Biopsy / Caco-2 Cells / Case-Control Studies / Cohort Studies / Colitis, Ulcerative - genetics / Colitis, Ulcerative - immunology / Colitis, Ulcerative - microbiology / Colitis, Ulcerative - pathology / Colon / Colon - diagnostic imaging / Colon - immunology / Colon - microbiology / Colon - pathology / Colonoscopy / Composition / Crohn Disease - genetics / Crohn Disease - immunology / Crohn Disease - microbiology / Crohn Disease - pathology / Crohn's disease / Deoxyribonucleic acid / Diagnostic systems / DNA / DNA methylation / DNA, Bacterial - isolation & purification / Enterobacteriaceae - genetics / Enterobacteriaceae - immunology / Enterobacteriaceae - isolation & purification / Epigenesis, Genetic - immunology / Epigenetics / Epigenomics / Female / Gastrointestinal Microbiome - genetics / Gastrointestinal Microbiome - immunology / Genetics / Host Microbial Interactions - genetics / Host Microbial Interactions - immunology / Humanities and Social Sciences / Humans / Inflammation / Inflammatory bowel disease / Inflammatory bowel diseases / Intestinal Mucosa - diagnostic imaging / Intestinal Mucosa - immunology / Intestinal Mucosa - microbiology / Intestinal Mucosa - pathology / Intestine / Male / Microbiota / Microorganisms / Middle Aged / Mucosa / multidisciplinary / Physics / RNA, Ribosomal, 16S - genetics / RNA-Seq / Science / Science (multidisciplinary) / Ulcerative colitis / Young Adult