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An optimised faecal microRNA sequencing pipeline reveals fibrosis in Trichuris muris infection

Author

Listed:
  • Emma Layton

    (University of Manchester
    University of Manchester
    Agency for Science, Technology and Research)

  • Sian Goldsworthy

    (University of Manchester)

  • EnJun Yang

    (Agency for Science, Technology and Research)

  • Wei Yee Ong

    (Agency for Science, Technology and Research
    National University of Singapore)

  • Tara E. Sutherland

    (University of Aberdeen)

  • Allison J. Bancroft

    (University of Manchester
    University of Manchester
    University of Manchester)

  • Seona Thompson

    (University of Manchester
    University of Manchester
    University of Manchester)

  • Veonice Bijin Au

    (Agency for Science, Technology and Research)

  • Sam Griffiths-Jones

    (University of Manchester)

  • Richard K. Grencis

    (University of Manchester
    University of Manchester
    University of Manchester)

  • Anna-Marie Fairhurst

    (Agency for Science, Technology and Research
    Agency for Science, Technology and Research)

  • Ian S. Roberts

    (University of Manchester
    University of Manchester)

Abstract

The intestine is a site of diverse functions including digestion, nutrient absorption, immune surveillance, and microbial symbiosis. Intestinal microRNAs (miRNAs) are detectable in faeces and regulate barrier integrity, host-microbe interactions and the immune response, potentially offering valuable non-invasive tools to study intestinal health. However, current experimental methods are suboptimal and heterogeneity in study design limits the utility of faecal miRNA data. Here, we develop an optimised protocol for faecal miRNA detection and report a reproducible murine faecal miRNA profile in healthy mice. We use this pipeline to study faecal miRNAs during infection with the gastrointestinal helminth, Trichuris muris, revealing roles for miRNAs in fibrosis and wound healing. Intestinal fibrosis was confirmed in vivo using Hyperion® imaging mass cytometry, demonstrating the efficacy of this approach. Further applications of this optimised pipeline to study host-microbe interactions and intestinal disease will enable the generation of hypotheses and therapeutic strategies in diverse contexts.

Suggested Citation

  • Emma Layton & Sian Goldsworthy & EnJun Yang & Wei Yee Ong & Tara E. Sutherland & Allison J. Bancroft & Seona Thompson & Veonice Bijin Au & Sam Griffiths-Jones & Richard K. Grencis & Anna-Marie Fairhur, 2025. "An optimised faecal microRNA sequencing pipeline reveals fibrosis in Trichuris muris infection," Nature Communications, Nature, vol. 16(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-56698-w
    DOI: 10.1038/s41467-025-56698-w
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    References listed on IDEAS

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    1. Amy H. Buck & Gillian Coakley & Fabio Simbari & Henry J. McSorley & Juan F. Quintana & Thierry Le Bihan & Sujai Kumar & Cei Abreu-Goodger & Marissa Lear & Yvonne Harcus & Alessandro Ceroni & Simon A. , 2014. "Exosomes secreted by nematode parasites transfer small RNAs to mammalian cells and modulate innate immunity," Nature Communications, Nature, vol. 5(1), pages 1-12, December.
    2. Dionysios V Chartoumpekis & Apostolos Zaravinos & Panos G Ziros & Ralitsa P Iskrenova & Agathoklis I Psyrogiannis & Venetsana E Kyriazopoulou & Ioannis G Habeos, 2012. "Differential Expression of MicroRNAs in Adipose Tissue after Long-Term High-Fat Diet-Induced Obesity in Mice," PLOS ONE, Public Library of Science, vol. 7(4), pages 1-13, April.
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