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Metaproteomics reveals associations between microbiome and intestinal extracellular vesicle proteins in pediatric inflammatory bowel disease

Author

Listed:
  • Xu Zhang

    (Microbiology and Immunology, Faculty of Medicine, University of Ottawa)

  • Shelley A. Deeke

    (Microbiology and Immunology, Faculty of Medicine, University of Ottawa)

  • Zhibin Ning

    (Microbiology and Immunology, Faculty of Medicine, University of Ottawa)

  • Amanda E. Starr

    (Microbiology and Immunology, Faculty of Medicine, University of Ottawa)

  • James Butcher

    (Microbiology and Immunology, Faculty of Medicine, University of Ottawa)

  • Jennifer Li

    (Microbiology and Immunology, Faculty of Medicine, University of Ottawa)

  • Janice Mayne

    (Microbiology and Immunology, Faculty of Medicine, University of Ottawa)

  • Kai Cheng

    (Microbiology and Immunology, Faculty of Medicine, University of Ottawa)

  • Bo Liao

    (Microbiology and Immunology, Faculty of Medicine, University of Ottawa)

  • Leyuan Li

    (Microbiology and Immunology, Faculty of Medicine, University of Ottawa)

  • Ruth Singleton

    (University of Ottawa and Children’s Hospital of Eastern Ontario Inflammatory Bowel Disease Centre and Research Institute)

  • David Mack

    (University of Ottawa and Children’s Hospital of Eastern Ontario Inflammatory Bowel Disease Centre and Research Institute)

  • Alain Stintzi

    (Microbiology and Immunology, Faculty of Medicine, University of Ottawa)

  • Daniel Figeys

    (Microbiology and Immunology, Faculty of Medicine, University of Ottawa
    University of Ottawa, 10 Marie Curie
    661 University Ave)

Abstract

Alterations in gut microbiota have been implicated in the pathogenesis of inflammatory bowel disease (IBD), however factors that mediate the host–microbiota interactions remain largely unknown. Here we collected mucosal-luminal interface samples from a pediatric IBD inception cohort and characterized both the human and microbiota proteins using metaproteomics. We show that microbial proteins related to oxidative stress responses are upregulated in IBD cases compared to controls. In particular, we demonstrate that the expression of human proteins related to oxidative antimicrobial activities is increased in IBD cases and correlates with the alteration of microbial functions. Additionally, we reveal that many of these human proteins are present and show altered abundance in isolated free extracellular vesicles (EVs). Therefore, our study suggests that the alteration of intestinal EV proteomes is associated with the aberrant host–microbiota interactions in IBD.

Suggested Citation

  • Xu Zhang & Shelley A. Deeke & Zhibin Ning & Amanda E. Starr & James Butcher & Jennifer Li & Janice Mayne & Kai Cheng & Bo Liao & Leyuan Li & Ruth Singleton & David Mack & Alain Stintzi & Daniel Figeys, 2018. "Metaproteomics reveals associations between microbiome and intestinal extracellular vesicle proteins in pediatric inflammatory bowel disease," Nature Communications, Nature, vol. 9(1), pages 1-14, December.
  • Handle: RePEc:nat:natcom:v:9:y:2018:i:1:d:10.1038_s41467-018-05357-4
    DOI: 10.1038/s41467-018-05357-4
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    Cited by:

    1. Leyuan Li & Tong Wang & Zhibin Ning & Xu Zhang & James Butcher & Joeselle M. Serrana & Caitlin M. A. Simopoulos & Janice Mayne & Alain Stintzi & David R. Mack & Yang-Yu Liu & Daniel Figeys, 2023. "Revealing proteome-level functional redundancy in the human gut microbiome using ultra-deep metaproteomics," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    2. Shuangshuang Wan & Kepeng Wang & Peihong Huang & Xian Guo & Wurui Liu & Yaocheng Li & Jingjing Zhang & Zhiyang Li & Jiacheng Song & Wenjing Yang & Xianzheng Zhang & Xianguang Ding & David Tai Leong & , 2024. "Mechanoelectronic stimulation of autologous extracellular vesicle biosynthesis implant for gut microbiota modulation," Nature Communications, Nature, vol. 15(1), pages 1-14, December.

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