Faecal Metaproteomic Analysis Reveals a Personalized and Stable Functional Microbiome and Limited Effects of a Probiotic Intervention in Adults

Recent metagenomic studies have demonstrated that the overall functional potential of the intestinal microbiome is rather conserved between healthy individuals. Here we assessed the biological processes undertaken in-vivo by microbes and the host in the intestinal tract by conducting a metaproteome...

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Published in:PLoS One
Main Authors: Kolmeder, Carolin A., Salojärvi, Jarkko, Ritari, Jarmo, de Been, Mark, Raes, Jeroen, Falony, Gwen, Vieira-Silva, Sara, Kekkonen, Riina A., Corthals, Garry L., Palva, Airi, Salonen, Anne, de Vos, Willem M.
Format: Artigo
Language:Inglês
Published: Public Library of Science 2016
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Research Article
Online Access:https://ncbi.nlm.nih.gov/pmc/articles/PMC4829149/
https://ncbi.nlm.nih.gov/pubmed/27070903
https://ncbi.nlm.nih.govhttp://dx.doi.org/10.1371/journal.pone.0153294
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spelling pubmed-48291492016-04-22 Faecal Metaproteomic Analysis Reveals a Personalized and Stable Functional Microbiome and Limited Effects of a Probiotic Intervention in Adults Kolmeder, Carolin A. Salojärvi, Jarkko Ritari, Jarmo de Been, Mark Raes, Jeroen Falony, Gwen Vieira-Silva, Sara Kekkonen, Riina A. Corthals, Garry L. Palva, Airi Salonen, Anne de Vos, Willem M. PLoS One Research Article Recent metagenomic studies have demonstrated that the overall functional potential of the intestinal microbiome is rather conserved between healthy individuals. Here we assessed the biological processes undertaken in-vivo by microbes and the host in the intestinal tract by conducting a metaproteome analysis from a total of 48 faecal samples of 16 healthy adults participating in a placebo-controlled probiotic intervention trial. Half of the subjects received placebo and the other half consumed Lactobacillus rhamnosus GG for three weeks (10(10) cfu per day). Faecal samples were collected just before and at the end of the consumption phase as well as after a three-week follow-up period, and were processed for microbial composition and metaproteome analysis. A common core of shared microbial protein functions could be identified in all subjects. Furthermore, we observed marked differences in expressed proteins between subjects that resulted in the definition of a stable and personalized microbiome both at the mass-spectrometry-based proteome level and the functional level based on the KEGG pathway analysis. No significant changes in the metaproteome were attributable to the probiotic intervention. A detailed taxonomic assignment of peptides and comparison to phylogenetic microarray data made it possible to evaluate the activity of the main phyla as well as key species, including Faecalibacterium prausnitzii. Several correlations were identified between human and bacterial proteins. Proteins of the human host accounted for approximately 14% of the identified metaproteome and displayed variations both between and within individuals. The individually different human intestinal proteomes point to personalized host-microbiota interactions. Our findings indicate that analysis of the intestinal metaproteome can complement gene-based analysis and contributes to a thorough understanding of the activities of the microbiome and the relevant pathways in health and disease. Public Library of Science 2016-04-12 /pmc/articles/PMC4829149/ /pubmed/27070903 http://dx.doi.org/10.1371/journal.pone.0153294 Text en © 2016 Kolmeder et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
institution US NLM
collection PubMed Central
language Inglês
format Artigo
topic Research Article
spellingShingle Research Article
Kolmeder, Carolin A.
Salojärvi, Jarkko
Ritari, Jarmo
de Been, Mark
Raes, Jeroen
Falony, Gwen
Vieira-Silva, Sara
Kekkonen, Riina A.
Corthals, Garry L.
Palva, Airi
Salonen, Anne
de Vos, Willem M.
Faecal Metaproteomic Analysis Reveals a Personalized and Stable Functional Microbiome and Limited Effects of a Probiotic Intervention in Adults
description Recent metagenomic studies have demonstrated that the overall functional potential of the intestinal microbiome is rather conserved between healthy individuals. Here we assessed the biological processes undertaken in-vivo by microbes and the host in the intestinal tract by conducting a metaproteome analysis from a total of 48 faecal samples of 16 healthy adults participating in a placebo-controlled probiotic intervention trial. Half of the subjects received placebo and the other half consumed Lactobacillus rhamnosus GG for three weeks (10(10) cfu per day). Faecal samples were collected just before and at the end of the consumption phase as well as after a three-week follow-up period, and were processed for microbial composition and metaproteome analysis. A common core of shared microbial protein functions could be identified in all subjects. Furthermore, we observed marked differences in expressed proteins between subjects that resulted in the definition of a stable and personalized microbiome both at the mass-spectrometry-based proteome level and the functional level based on the KEGG pathway analysis. No significant changes in the metaproteome were attributable to the probiotic intervention. A detailed taxonomic assignment of peptides and comparison to phylogenetic microarray data made it possible to evaluate the activity of the main phyla as well as key species, including Faecalibacterium prausnitzii. Several correlations were identified between human and bacterial proteins. Proteins of the human host accounted for approximately 14% of the identified metaproteome and displayed variations both between and within individuals. The individually different human intestinal proteomes point to personalized host-microbiota interactions. Our findings indicate that analysis of the intestinal metaproteome can complement gene-based analysis and contributes to a thorough understanding of the activities of the microbiome and the relevant pathways in health and disease.
author Kolmeder, Carolin A.
Salojärvi, Jarkko
Ritari, Jarmo
de Been, Mark
Raes, Jeroen
Falony, Gwen
Vieira-Silva, Sara
Kekkonen, Riina A.
Corthals, Garry L.
Palva, Airi
Salonen, Anne
de Vos, Willem M.
author_facet Kolmeder, Carolin A.
Salojärvi, Jarkko
Ritari, Jarmo
de Been, Mark
Raes, Jeroen
Falony, Gwen
Vieira-Silva, Sara
Kekkonen, Riina A.
Corthals, Garry L.
Palva, Airi
Salonen, Anne
de Vos, Willem M.
author_sort Kolmeder, Carolin A.
title Faecal Metaproteomic Analysis Reveals a Personalized and Stable Functional Microbiome and Limited Effects of a Probiotic Intervention in Adults
title_short Faecal Metaproteomic Analysis Reveals a Personalized and Stable Functional Microbiome and Limited Effects of a Probiotic Intervention in Adults
title_full Faecal Metaproteomic Analysis Reveals a Personalized and Stable Functional Microbiome and Limited Effects of a Probiotic Intervention in Adults
title_fullStr Faecal Metaproteomic Analysis Reveals a Personalized and Stable Functional Microbiome and Limited Effects of a Probiotic Intervention in Adults
title_full_unstemmed Faecal Metaproteomic Analysis Reveals a Personalized and Stable Functional Microbiome and Limited Effects of a Probiotic Intervention in Adults
title_sort faecal metaproteomic analysis reveals a personalized and stable functional microbiome and limited effects of a probiotic intervention in adults
publisher Public Library of Science
container_title PLoS One
publishDate 2016
url https://ncbi.nlm.nih.gov/pmc/articles/PMC4829149/
https://ncbi.nlm.nih.gov/pubmed/27070903
https://ncbi.nlm.nih.govhttp://dx.doi.org/10.1371/journal.pone.0153294
_version_ 1814798809613467648

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