Deep Metaproteomics Approach for the Study of Human Microbiomes
- 11 August 2017
- journal article
- research article
- Published by American Chemical Society (ACS) in Analytical Chemistry
- Vol. 89 (17), 9407-9415
- https://doi.org/10.1021/acs.analchem.7b02224
Abstract
Host–microbiome interactions have been shown to play important roles in human health and diseases. Most of the current studies of the microbiome have been performed by genomic approaches through next-generation sequencing. Technologies, such as metaproteomics, for functional analysis of the microbiome are needed to better understand the intricate host–microbiome interactions. However, significant efforts to improve the depth and resolution of gut metaproteomics are still required. In this study, we combined an efficient sample preparation technique, high resolution mass spectrometry, and metaproteomic bioinformatics tools to perform ultradeep metaproteomic analysis of human gut microbiome from stool. We reported the deepest analysis of the microbiome to date with an average of 20 558 protein groups identified per sample analysis. Moreover, strain resolution taxonomic and pathway analysis using deep metaproteomics revealed strain level variations, in particular for Faecalibacterium prausnitzii, in the microbiome from the different individuals. We also reported that the human proteins identified in stool samples are functionally enriched in extracellular region pathways and in particular those proteins involved in defense response against microbial organisms. Deep metaproteomics is a promising approach to perform in-depth microbiome analysis and simultaneously reveals both human and microbial changes that are not readily apparent using the standard genomic approaches.Keywords
Funding Information
- Canadian Institutes of Health Research (GPH-129340, MOP-114872)
- Ministry of Science and Technology of the People's Republic of China (2016YFA0501403)
- Ontario Ministry of Economic Development and Innovation (REG1-4450)
- Canada Research Chairs
- Genome Canada
- Ontario Genomics Institute (OGI-067)
- Natural Sciences and Engineering Research Council of Canada
- National Natural Science Foundation of China (21575057)
- Faculty of Medicine, University of Ottawa
- CHEO Foundation
- Children?s Hospital of Eastern Ontario
- Crohn?s and Colitis Canada
- IBD Foundation
This publication has 50 references indexed in Scilit:
- Integrated multi-omics of the human gut microbiome in a case study of familial type 1 diabetesNature Microbiology, 2016
- Population-level analysis of gut microbiome variationScience, 2016
- An Integrative View of Microbiome-Host Interactions in Inflammatory Bowel DiseasesCell Host & Microbe, 2015
- Relating the metatranscriptome and metagenome of the human gutProceedings of the National Academy of Sciences of the United States of America, 2014
- Diversity, stability and resilience of the human gut microbiotaNature, 2012
- Host-Gut Microbiota Metabolic InteractionsScience, 2012
- Interactions Between the Microbiota and the Immune SystemScience, 2012
- The Impact of the Gut Microbiota on Human Health: An Integrative ViewCell, 2012
- Enterotypes of the human gut microbiomeNature, 2011
- An obesity-associated gut microbiome with increased capacity for energy harvestNature, 2006