Studying the dynamics of the gut microbiota using metabolically stable isotopic labeling and metaproteomics.

Abstract

Background: The gut microbiome and its metabolic processes are dynamic systems. Surprisingly, our understanding of gut microbiome dynamics is limited. Here we report a metaproteomic workflow that involves protein stable isotope probing (protein-SIP) and identification and quantification of partially labeled peptides. We also developed a package, which we call MetaProfiler, that corrects for false identifications and performs phylogenetic and time series analysis for the study of gut microbiome functional dynamics. Results: From the stool sample of five mice that were fed with \ensuremath{^{15}}N hydrolysate from \textit{Ralstonia eutropha}, we identified 15,297 non-redundant unlabeled peptides of which 10,839 of their heavy counterparts were quantified. These peptides revealed incorporation profiles over time that were different between and within taxa, as well as between and within clusters of orthologous groups (COGs). Conclusions: Our study helps unravel the complex dynamics of protein synthesis and bacterial dynamics in the mouse microbiome. Availability: MetaProfiler and the bioinformatic pipeline are available at https://github.com/psmyth94/MetaProfiler.git.

Five key aspects of metaproteomics as a tool to understand functional interactions in host-associated microbiomes

“…Recently developed approaches make use of this to (1) link microbial species in communities to the environmental carbon sources that they consume by protein stable isotope fingerprinting (Protein-SIF) [ 17 ]; and (2) to follow incorporation and interspecies transfer of isotopically labeled substrates in microbial communities by protein-based stable isotope probing (Protein-SIP) [ 18 ]. Protein-SIP was recently used to detect differential incorporation of 15 N labeled dietary protein in members of the mouse microbiota [ 19 ].…”