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

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 () and Daniel Figeys ()
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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

Nature Communications, 2018, vol. 9, issue 1, 1-14

Abstract: 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.

Date: 2018
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DOI: 10.1038/s41467-018-05357-4

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