title: MetaPro-IQ: a universal metaproteomic approach to studying human and mouse gut microbiota.
abstract: The gut microbiota has been shown to be closely associated with human health and disease. While next-generation sequencing can be readily used to profile the microbiota taxonomy and metabolic potential, metaproteomics is better suited for deciphering microbial biological activities. However, the application of gut metaproteomics has largely been limited due to the low efficiency of protein identification. Thus, a high-performance and easy-to-implement gut metaproteomic approach is required.
  
  
  
  In this study, we developed a high-performance and universal workflow for gut metaproteome identification and quantification (named MetaPro-IQ) by using the close-to-complete human or mouse gut microbial gene catalog as database and an iterative database search strategy. An average of 38 and 33 % of the acquired tandem mass spectrometry (MS) spectra was confidently identified for the studied mouse stool and human mucosal-luminal interface samples, respectively. In total, we accurately quantified 30,749 protein groups for the mouse metaproteome and 19,011 protein groups for the human metaproteome. Moreover, the MetaPro-IQ approach enabled comparable identifications with the matched metagenome database search strategy that is widely used but needs prior metagenomic sequencing. The response of gut microbiota to high-fat diet in mice was then assessed, which showed distinct metaproteome patterns for high-fat-fed mice and identified 849 proteins as significant responders to high-fat feeding in comparison to low-fat feeding.
  
  
  
  We present MetaPro-IQ, a metaproteomic approach for highly efficient intestinal microbial protein identification and quantification, which functions as a universal workflow for metaproteomic studies, and will thus facilitate the application of metaproteomics for better understanding the functions of gut microbiota in health and disease.
authors.affiliation: Department of Biochemistry, Ottawa Institute of Systems Biology, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada.
authors.forename: Xu
authors.initials: X
authors.lastname: Zhang
authors.affiliation: Department of Biochemistry, Ottawa Institute of Systems Biology, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada.
authors.forename: Zhibin
authors.initials: Z
authors.lastname: Ning
authors.affiliation: Department of Biochemistry, Ottawa Institute of Systems Biology, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada.
authors.forename: Janice
authors.initials: J
authors.lastname: Mayne
authors.affiliation: Department of Biochemistry, Ottawa Institute of Systems Biology, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada.
authors.forename: Jasmine I
authors.initials: JI
authors.lastname: Moore
authors.affiliation: Department of Biochemistry, Ottawa Institute of Systems Biology, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada.
authors.forename: Jennifer
authors.initials: J
authors.lastname: Li
authors.affiliation: Department of Biochemistry, Ottawa Institute of Systems Biology, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada.
authors.forename: James
authors.initials: J
authors.lastname: Butcher
authors.affiliation: Department of Biochemistry, Ottawa Institute of Systems Biology, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada.
authors.forename: Shelley Ann
authors.initials: SA
authors.lastname: Deeke
authors.affiliation: Department of Biochemistry, Ottawa Institute of Systems Biology, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada.
authors.forename: Rui
authors.initials: R
authors.lastname: Chen
authors.affiliation: Department of Biochemistry, Ottawa Institute of Systems Biology, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada.
authors.forename: Cheng-Kang
authors.initials: CK
authors.lastname: Chiang
authors.affiliation: Department of Biochemistry, Ottawa Institute of Systems Biology, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada.
authors.forename: Ming
authors.initials: M
authors.lastname: Wen
authors.affiliation: Department of Paediatrics, CHEO Inflammatory Bowel Disease Centre and Research Institute, University of Ottawa, Ottawa, ON, Canada. DMack@cheo.on.ca.
authors.forename: David
authors.initials: D
authors.lastname: Mack
authors.affiliation: Department of Biochemistry, Ottawa Institute of Systems Biology, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada. astintzi@uottawa.ca.
authors.forename: Alain
authors.initials: A
authors.lastname: Stintzi
authors.affiliation: Department of Biochemistry, Ottawa Institute of Systems Biology, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada. dfigeys@uottawa.ca.
authors.forename: Daniel
authors.initials: D
authors.lastname: Figeys
mesh_terms: D000818:Animals; D001419:Bacteria / Q000145:classification* / Q000378:metabolism; D001426:Bacterial Proteins / Q000378:metabolism; D019295:Computational Biology / Q000379:methods; D030541:Databases, Genetic; D059305:Diet, High-Fat; D000069196:Gastrointestinal Microbiome / Q000187:drug effects; D015964:Gene Expression Regulation, Bacterial / Q000187:drug effects; D006801:Humans; D056186:Metagenomics / Q000379:methods*; D051379:Mice; D040901:Proteomics / Q000379:methods*; D053719:Tandem Mass Spectrometry
chemical_list: D001426:Bacterial Proteins
keywords: Gene catalog; Gut microbiota; Metagenomics; Metaproteomics; Protein identification; Quantification