The Landscape and Perspectives of the Human Gut Metaproteomics

Abstract

The human gut microbiome is closely associated with human health and diseases. Metaproteomics has emerged as a valuable tool for studying the functionality of the gut microbiome by analyzing the entire proteins present in microbial communities. Recent advancements in liquid chromatography and tandem mass spectrometry (LC-MS/MS) techniques have expanded the detection range of metaproteomics. However, the overall coverage of the proteome in metaproteomics is still limited. While metagenomics studies have revealed substantial microbial diversity and functional potential of the human gut microbiome, few studies have summarized and studied the human gut microbiome landscape revealed with metaproteomics. In this article, we present the current landscape of human gut metaproteomics studies by re-analyzing the identification results from 15 published studies. We quantified the limited proteome coverage in metaproteomics and revealed a high proportion of annotation coverage of metaproteomics-identified proteins. We conducted a preliminary comparison between the metaproteomics view and the metagenomics view of the human gut microbiome, identifying key areas of consistency and divergence. Based on the current landscape of human gut metaproteomics, we discuss the feasibility of using metaproteomics to study functionally unknown proteins and propose a whole workflow peptide-centric analysis. Additionally, we suggest enhancing metaproteomics analysis by refining taxonomic classification and calculating confidence scores, as well as developing tools for analyzing the interaction between taxonomy and function.

Keywords: functional annotation; human gut; metaproteomics; microbiome; proteome coverage.

Graphical abstract

Fig. 1

Phylogenetic distribution of identified peptides in metaproteomics studies. The innermost is the phylogenetic tree of 4716 bacterial species extracted from the UHGG dataset. From the inner to the outer circle, 3 bar plots show the number of genome-distinct peptides, peptides assigned to genus-level lowest common ancestors (LCA), and peptides assigned to family-level LCA for each node/clade. Dashed lines serve as references for the number of peptides: red dash line (1000 peptides), purple dash line (10,000 peptides). Phylum-level taxonomy is indicated by different colors in both the phylogenetic tree and the color strip on the outermost ring.

Fig. 2

Phylogenetic distribution of identified proteins in metaproteomics studies. The innermost is the phylogenetic tree of 4716 bacterial species extracted from the UHGG dataset. The bar plot shows the number of identified proteins from each bacterial species. Dashed lines serve as references for the number of proteins: red dash line (100 proteins), purple dash line (1000 proteins). Phylum-level taxonomy is indicated by different colors in both the phylogenetic tree and the color strip on the outermost ring.

Fig. 3

Comparison of taxonomic composition of bacterial species identified in metaproteomic studies and the species in the metagenomics reference database, UHGG.A, taxonomic affiliation of the bacterial species collected in the UHGG at different taxonomic ranks. B, taxonomic affiliation of the metaproteomics-identified peptides (peptides compiled in MetaPep) at different taxonomic ranks. The legend only depicts the five most highly represented taxa per rank.