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

被引：199

作者：

Ryan, F. J. ^{[1
,2
]}

Ahern, A. M. ^{[1
,2
]}

Fitzgerald, R. S. ^{[1
,2
]}

Laserna-Mendieta, E. J. ^{[1
,2
]}

Power, E. M. ^{[1
,2
]}

Clooney, A. G. ^{[1
,2
,3
]}

O'Donoghue, K. W. ^{[1
,2
]}

McMurdie, P. J. ^{[4
]}

Iwai, S. ^{[4
]}

Crits-Christoph, A. ^{[2
,5
]}

Sheehan, D. ^{[2
,5
]}

Moran, C. ^{[2
,5
]}

Flemer, B. ^{[1
,2
]}

Zomer, A. L. ^{[6
]}

Fanning, A. ^{[2
]}

O'Callaghan, J. ^{[1
]}

Walton, J. ^{[7
]}

Temko, A. ^{[8
]}

Stack, W. ^{[9
]}

Jackson, L. ^{[9
]}

Joyce, S. A. ^{[2
,10
]}

Melgar, S. ^{[2
]}

DeSantis, T. Z. ^{[4
]}

Bell, J. T. ^{[11
]}

Shanahan, F. ^{[2
,5
]}

Claesson, M. J. ^{[1
,2
]}

机构：

[1] Univ Coll Cork, Sch Microbiol, Cork, Ireland

[2] Univ Coll Cork, APC Microbiome Ireland, Cork, Ireland

[3] Cork Inst Technol, Dept Biol Sci, Cork, Ireland

[4] Second Genome, San Francisco, CA 94080 USA

[5] Univ Coll Cork, Dept Med, Cork, Ireland

[6] Radboud Univ Nijmegen, Lab Pediat Infect Dis, Med Ctr, Nijmegen, Netherlands

[7] Univ Coll Cork, Sch Food & Nutr Sci, Cork, Ireland

[8] Univ Coll Cork, Irish Ctr Fetal & Neonatal Translat Res, Dept Elect & Elect Engn, Cork, Ireland

[9] Bon Secours Hosp, Cork, Ireland

[10] Univ Coll Cork, Sch Biochem & Cell Biol, Cork, Ireland

[11] Kings Coll London, Dept Twin Res & Genet Epidemiol, London, England

来源：

NATURE COMMUNICATIONS | 2020年 / 11卷 / 01期

基金：

爱尔兰科学基金会;

关键词：

CROHNS-DISEASE; DNA METHYLATION; ULCERATIVE-COLITIS; GENE-EXPRESSION; GUT MICROBIOTA; SUSCEPTIBILITY; MUCOSA; POLYMORPHISM; DIET; RISK;

D O I：

10.1038/s41467-020-15342-5

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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.

引用

页数：12

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