Abstract
Although the gut microbiome has been associated with dietary patterns linked to health, microbial metabolism is not well characterized. This ancillary study was a proof of principle analysis for a novel application of metaproteomics to study microbial protein expression in a controlled dietary intervention. We measured the response of the microbiome to diet in a randomized crossover dietary intervention of a whole-grain, low glycemic load diet (WG) and a refined-grain, high glycemic load diet (RG). Total proteins in stools from 9 participants at the end of each diet period (n = 18) were analyzed by LC MS/MS and proteins were identified using the Human Microbiome Project (HMP) human gut microbiome database and UniProt human protein databases. T-tests, controlling for false discovery rate (FDR) <10%, were used to compare the Gene Ontology (GO) biological processes and bacterial enzymes between the two interventions. Using shotgun proteomics, more than 53,000 unique peptides were identified including microbial (89%) and human peptides (11%). Forty-eight bacterial enzymes were statistically different between the diets, including those implicated in SCFA production and degradation of fatty acids. Enzymes associated with degradation of human mucin were significantly enriched in the RG diet. These results illustrate that the metaproteomic approach is a valuable tool to study the microbial metabolism of diets that may influence host health.
Highlights
Diet and the microbiome impact health, in part, through the microbial metabolism of dietary components
Participants received two controlled diets: a low glycemic load diet characterized by whole grains, legumes, fruits, vegetables, nuts, and seeds (WG) or a high glycemic load diet, which was high in refined grains and added sugars (RG)
The MS/MS data were converted to mzML format and searched against the Uniprot human protein database (2015-07-23) for human host protein identification and the human gut microbiome database developed by the Human Microbiome Project (HMP) for human gut bacteria identification, respectively
Summary
Diet and the microbiome impact health, in part, through the microbial metabolism of dietary components. Metaproteomics, the measurement of the bacterial proteins in the microbial community, provides a direct measure of gut bacterial activity and metabolism. Complementary to metagenomic and metatranscriptomic methods, metaproteomic analysis of the bacterial proteomes in the microbial community provides a more direct measure of functional status associated with gut bacterial activity and metabolism by globally characterizing proteins and corresponding microbial species in complex and diverse microbiomes [7]. Another study using a metaproteomics approach to study diet induced changes in mouse gut microbiome identified >11,000 protein groups and 167 KEGG pathways in the mouse fecal samples [2]. We present here an integrated shotgun proteomic approach to measure the metaproteomes in fecal specimens We applied this approach to characterize the response of the microbial metaproteome to controlled refined grain, high glycemic load diets versus whole grain, low glycemic load diets
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