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

F. J. Ryan, A. M. Ahern, R. S. Fitzgerald, E. J. Laserna-Mendieta, E. M. Power, A. G. Clooney, K. W. O’Donoghue, P. J. McMurdie, S. Iwai, A. Crits-Christoph, D. Sheehan, C. Moran, B. Flemer, A. L. Zomer, A. Fanning, J. O’Callaghan, J. Walton, A. Temko, W. Stack, L. Jackson, S. A. Joyce, S. Melgar, T. Z. DeSantis, J. T. Bell, F. Shanahan and M. J. Claesson ()
Additional contact information
F. J. Ryan: University College Cork
A. M. Ahern: University College Cork
R. S. Fitzgerald: University College Cork
E. J. Laserna-Mendieta: University College Cork
E. M. Power: University College Cork
A. G. Clooney: University College Cork
K. W. O’Donoghue: University College Cork
P. J. McMurdie: Second Genome
S. Iwai: Second Genome
A. Crits-Christoph: Second Genome
D. Sheehan: University College Cork
C. Moran: University College Cork
B. Flemer: University College Cork
A. L. Zomer: Radboud University Medical Center, Laboratory of Pediatric Infectious Diseases
A. Fanning: University College Cork
J. O’Callaghan: University College Cork
J. Walton: University College Cork
A. Temko: University College Cork
W. Stack: Bon Secours Hospital
L. Jackson: Bon Secours Hospital
S. A. Joyce: University College Cork
S. Melgar: University College Cork
T. Z. DeSantis: Second Genome
J. T. Bell: King’s College London
F. Shanahan: University College Cork
M. J. Claesson: University College Cork

Nature Communications, 2020, vol. 11, issue 1, 1-12

Abstract: 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.

Date: 2020
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DOI: 10.1038/s41467-020-15342-5

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