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

Author

Listed:
  • F. J. Ryan

    (University College Cork
    University College Cork)

  • A. M. Ahern

    (University College Cork
    University College Cork)

  • R. S. Fitzgerald

    (University College Cork
    University College Cork)

  • E. J. Laserna-Mendieta

    (University College Cork
    University College Cork)

  • E. M. Power

    (University College Cork
    University College Cork)

  • A. G. Clooney

    (University College Cork
    University College Cork
    Department of Biological Sciences Cork Institute of Technology)

  • K. W. O’Donoghue

    (University College Cork
    University College Cork)

  • P. J. McMurdie

    (Second Genome)

  • S. Iwai

    (Second Genome)

  • A. Crits-Christoph

    (Second Genome)

  • D. Sheehan

    (University College Cork
    University College Cork)

  • C. Moran

    (University College Cork
    University College Cork)

  • B. Flemer

    (University College Cork
    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
    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
    University College Cork)

  • M. J. Claesson

    (University College Cork
    University College Cork)

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.

Suggested Citation

  • 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. Fleme, 2020. "Colonic microbiota is associated with inflammation and host epigenomic alterations in inflammatory bowel disease," Nature Communications, Nature, vol. 11(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-15342-5
    DOI: 10.1038/s41467-020-15342-5
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    Cited by:

    1. Manina M. Etter & Tomás A. Martins & Laila Kulsvehagen & Elisabeth Pössnecker & Wandrille Duchemin & Sabrina Hogan & Gretel Sanabria-Diaz & Jannis Müller & Alessio Chiappini & Jonathan Rychen & Noëmi , 2022. "Severe Neuro-COVID is associated with peripheral immune signatures, autoimmunity and neurodegeneration: a prospective cross-sectional study," Nature Communications, Nature, vol. 13(1), pages 1-21, December.

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