Gut Microbial Protein Expression in Response to Dietary Patterns in a Controlled Feeding Study: A Metaproteomic Approach

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.

Metaproteomics—An Advantageous Option in Studies of Host-Microbiota Interaction

“…Although metaproteomics is a very powerful method, issues within the bioinformatics evaluation impede its success. There will be more studies of gut microbial protein expression in response to dietary patterns that would lead to new heights in understanding microbiome behavior [ 32 ].…”

Co-interventions withClostridium butyricumand soluble dietary fiber targeting the gut microbiota improve MAFLDviathe Acly/Nrf2/NF-κB signaling pathway

“…24 Furthermore, CB fermentation of SDF results in the production of short-chain fatty acids (butyrate, propionate, and acetate), which are important determinants of gut homeostasis and have been strongly associated with host lipid metabolism. 25 However, the role of CB and SDF in the crosstalk of hepatic steatosis, oxidative stress, and hepatic inflammation in MAFLD remains unclear.…”

Analysis of Human Faecal Host Proteins: Responsiveness to 10-Week Dietary Intervention Modifying Dietary Protein Intake in Elderly Males

“…To date, high throughput methods to comprehensively profile the genes and proteins from the microbiota have been applied to the analysis of the biological functioning of the human GIT. These techniques have been used to comprehensively describe the taxonomy and functional attributes of the microbiome population ( 6 , 7 ). Fewer studies have addressed the inherent expression and abundance of self-derived genetic material or proteins.…”