Gut Microbial Protein Expression in Response to Dietary Patterns in a Controlled Feeding Study: A Metaproteomic Approach
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 inter...
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doaj-7c410c7c3d94433ebe846f03bf43f8fc2020-11-25T03:03:25ZengMDPI AGMicroorganisms2076-26072020-03-018337910.3390/microorganisms8030379microorganisms8030379Gut Microbial Protein Expression in Response to Dietary Patterns in a Controlled Feeding Study: A Metaproteomic ApproachSheng Pan0Meredith A. J. Hullar1Lisa A. Lai2Hong Peng3Damon H. May4William S. Noble5Daniel Raftery6Sandi L. Navarro7Marian L. Neuhouser8Paul D. Lampe9Johanna W. Lampe10Ru Chen11Institute of Molecular Medicine, the University of Texas Health Science Center at Houston, Houston, TX 77030, USAFred Hutchinson Cancer Research Center, Division of Public Health Sciences, Seattle, WA 98109, USADepartment of Medicine, University of Washington, Seattle, WA 98105, USAInstitute of Molecular Medicine, the University of Texas Health Science Center at Houston, Houston, TX 77030, USADepartment of Genome Sciences, University of Washington, Seattle, WA 98105, USADepartment of Genome Sciences, University of Washington, Seattle, WA 98105, USAFred Hutchinson Cancer Research Center, Division of Public Health Sciences, Seattle, WA 98109, USAFred Hutchinson Cancer Research Center, Division of Public Health Sciences, Seattle, WA 98109, USAFred Hutchinson Cancer Research Center, Division of Public Health Sciences, Seattle, WA 98109, USAFred Hutchinson Cancer Research Center, Division of Public Health Sciences, Seattle, WA 98109, USAFred Hutchinson Cancer Research Center, Division of Public Health Sciences, Seattle, WA 98109, USADivision of Gastroenterology and Hepatology, Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USAAlthough 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 (<i>n</i> = 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.https://www.mdpi.com/2076-2607/8/3/379microbiomeproteomicsdietary interventionscfafatty acid metabolismdysbiosismucin-degrading enzymes |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Sheng Pan Meredith A. J. Hullar Lisa A. Lai Hong Peng Damon H. May William S. Noble Daniel Raftery Sandi L. Navarro Marian L. Neuhouser Paul D. Lampe Johanna W. Lampe Ru Chen |
spellingShingle |
Sheng Pan Meredith A. J. Hullar Lisa A. Lai Hong Peng Damon H. May William S. Noble Daniel Raftery Sandi L. Navarro Marian L. Neuhouser Paul D. Lampe Johanna W. Lampe Ru Chen Gut Microbial Protein Expression in Response to Dietary Patterns in a Controlled Feeding Study: A Metaproteomic Approach Microorganisms microbiome proteomics dietary intervention scfa fatty acid metabolism dysbiosis mucin-degrading enzymes |
author_facet |
Sheng Pan Meredith A. J. Hullar Lisa A. Lai Hong Peng Damon H. May William S. Noble Daniel Raftery Sandi L. Navarro Marian L. Neuhouser Paul D. Lampe Johanna W. Lampe Ru Chen |
author_sort |
Sheng Pan |
title |
Gut Microbial Protein Expression in Response to Dietary Patterns in a Controlled Feeding Study: A Metaproteomic Approach |
title_short |
Gut Microbial Protein Expression in Response to Dietary Patterns in a Controlled Feeding Study: A Metaproteomic Approach |
title_full |
Gut Microbial Protein Expression in Response to Dietary Patterns in a Controlled Feeding Study: A Metaproteomic Approach |
title_fullStr |
Gut Microbial Protein Expression in Response to Dietary Patterns in a Controlled Feeding Study: A Metaproteomic Approach |
title_full_unstemmed |
Gut Microbial Protein Expression in Response to Dietary Patterns in a Controlled Feeding Study: A Metaproteomic Approach |
title_sort |
gut microbial protein expression in response to dietary patterns in a controlled feeding study: a metaproteomic approach |
publisher |
MDPI AG |
series |
Microorganisms |
issn |
2076-2607 |
publishDate |
2020-03-01 |
description |
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 (<i>n</i> = 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. |
topic |
microbiome proteomics dietary intervention scfa fatty acid metabolism dysbiosis mucin-degrading enzymes |
url |
https://www.mdpi.com/2076-2607/8/3/379 |
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