Studying the Temporal Dynamics of the Gut Microbiota Using Metabolic Stable Isotope Labeling and Metaproteomics

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/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 microbiome
dynamics. From the stool sample of five mice that were fed with 15N hydrolysate from Ralstonia eutropha, we identified 12 326 nonredundant unlabeled peptides, of
which 8256 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). Our study helps unravel the complex dynamics of protein
synthesis and bacterial dynamics in the mouse microbiome. MetaProfiler
and the bioinformatic pipeline are available at https://github.com/northomics/MetaProfiler.git.