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

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Smyth, Patrick, Zhang, Xu, Ning, Zhibin, Mayne, Janice, Moore, Jasmine Isabelle, Walker, Krystal, Lavallée-Adam, Mathieu and Figeys, Daniel (2020) Studying the Temporal Dynamics of the Gut Microbiota Using Metabolic Stable Isotope Labeling and Metaproteomics. Analytical Chemistry, 92 (24). pp. 15711-15718. ISSN 0003-2700

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Abstract

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.

Item Type: Article
Additional Information: MetaProfiler and the bioinformatic pipeline are available at https://github.com/northomics/MetaProfiler.git. The Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/acs.analchem.0c02070.
Uncontrolled Keywords: analytical chemistry ,/dk/atira/pure/subjectarea/asjc/1600/1602
Faculty \ School: Faculty of Medicine and Health Sciences > Norwich Medical School
UEA Research Groups: Faculty of Medicine and Health Sciences > Research Centres > Metabolic Health
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Depositing User: LivePure Connector
Date Deposited: 17 Mar 2026 09:30
Last Modified: 17 Mar 2026 09:30
URI: https://ueaeprints.uea.ac.uk/id/eprint/102357
DOI: 10.1021/acs.analchem.0c02070

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