Abstract
BackgroundThe 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.ResultsIn 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.ConclusionsWe 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s40168-016-0176-z) contains supplementary material, which is available to authorized users.
Highlights
The gut microbiota has been shown to be closely associated with human health and disease
The first shotgun metaproteomic study of the gut microbiota was reported in 2009 [7], only few follow-up large-scale gut metaproteomic studies have been published. The reasons for this lack of progress have been discussed in several reviews [8,9,10,11,12] and include (1) the inability to detect low abundant proteins with current mass spectrometers coupled to the high diversity of the gut microbiota and, more importantly, (2) the low efficiency in identifying gut microbial peptide or proteins from acquired mass spectrometry (MS) spectra
We subsequently developed a high-performance and universal approach for gut MetaProteome Identification and Quantification (MetaPro-IQ), which led to the quantification of approximately 120,000 peptides corresponding to >30,000 protein groups in a single experiment
Summary
MetaPro-IQ: a universal metaproteomic approach to studying human and mouse gut microbiota. Jennifer Li1, James Butcher, Shelley Ann Deeke, Rui Chen, Cheng-Kang Chiang, Ming Wen, David Mack2*, Alain Stintzi1* and Daniel Figeys1*
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