Open AccessUntargeted Stable Isotope Probing of the Gut Microbiota Metabolome Using 13C-Labeled Dietary Fibers
Author(s) -
Pan Deng,
Taylor Valentino,
Michael D. Flythe,
Hunter Moseley,
Jacqueline Leachman,
Andrew J. Morris,
Bernhard Hennig
Publication year - 2021
Publication title -
journal of proteome research
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.644
H-Index - 161
eISSN - 1535-3907
pISSN - 1535-3893
DOI - 10.1021/acs.jproteome.1c00124
Subject(s) - metabolome , metabolomics , gut flora , metabolic pathway , biochemistry , pentose phosphate pathway , inulin , microbiome , metabolism , biology , citric acid cycle , microbial metabolism , chemistry , glycolysis , metabolite , bacteria , bioinformatics , genetics
The gut microbiome generates numerous metabolites that exert local effects and enter the circulation to affect the functions of many organs. Despite extensive sequencing-based characterization of the gut microbiome, there remains a lack of understanding of microbial metabolism. Here, we developed an untargeted stable isotope-resolved metabolomics (SIRM) approach for the holistic study of gut microbial metabolites. Viable microbial cells were extracted from fresh mice feces and incubated anaerobically with 13 C-labeled dietary fibers including inulin or cellulose. High-resolution mass spectrometry was used to monitor 13 C enrichment in metabolites associated with glycolysis, the Krebs cycle, the pentose phosphate pathway, nucleotide synthesis, and pyruvate catabolism in both microbial cells and the culture medium. We observed the differential use of inulin and cellulose as substrates for biosynthesis of essential and non-essential amino acids, neurotransmitters, vitamin B5, and other coenzymes. Specifically, the use of inulin for these biosynthetic pathways was markedly more efficient than the use of cellulose, reflecting distinct metabolic pathways of dietary fibers in the gut microbiome, which could be related with host effects. This technology facilitates deeper and holistic insights into the metabolic function of the gut microbiome (Metabolomic Workbench Study ID: ST001651).