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Title: Divergent responses of viral and bacterial communities in the gut microbiome to dietary disturbances in mice

Abstract

To improve our understanding of the stability of mammalian intestinal communities, we characterized the responses of both bacterial and viral communities in murine fecal samples to dietary changes between high- and low-fat (LF) diets. Targeted DNA extraction methods for bacteria, virus-like particles and induced prophages were used to generate bacterial and viral metagenomes as well as 16S ribosomal RNA amplicons. Gut microbiome communities from two cohorts of C57BL/6 mice were characterized in a 6-week diet perturbation study in response to high fiber, LF and high-refined sugar, milkfat (MF) diets. The resulting metagenomes from induced bacterial prophages and extracellular viruses showed significant overlap, supporting a largely temperate viral lifestyle within these gut microbiomes. The resistance of baseline communities to dietary disturbances was evaluated, and we observed contrasting responses of baseline LF and MF bacterial and viral communities. In contrast to baseline LF viral communities and bacterial communities in both diet treatments, baseline MF viral communities were sensitive to dietary disturbances as reflected in their non-recovery during the washout period. Finally, the contrasting responses of bacterial and viral communities suggest that these communities can respond to perturbations independently of each other and highlight the potentially unique role of viruses in gut health.

Authors:
 [1];  [2];  [3];  [2];  [4];  [5];  [2];  [5];  [2]
  1. Iowa State Univ., Ames, IA (United States); Argonne National Lab. (ANL), Argonne, IL (United States)
  2. Univ. of Chicago, Chicago, IL (United States)
  3. Iowa State Univ., Ames, IA (United States)
  4. Argonne National Lab. (ANL), Argonne, IL (United States)
  5. Argonne National Lab. (ANL), Argonne, IL (United States); Univ. of Chicago, Chicago, IL (United States)
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States)
Sponsoring Org.:
USDOE; National Institutes of Health (NIH)
OSTI Identifier:
1315658
Grant/Contract Number:  
AC02-06CH11357
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
The ISME Journal
Additional Journal Information:
Journal Volume: 10; Journal Issue: 5; Journal ID: ISSN 1751-7362
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Howe, Adina, Ringus, Daina L., Williams, Ryan J., Choo, Zi -Ning, Greenwald, Stephanie M., Owens, Sarah M., Coleman, Maureen L., Meyer, Folker, and Chang, Eugene B. Divergent responses of viral and bacterial communities in the gut microbiome to dietary disturbances in mice. United States: N. p., 2015. Web. doi:10.1038/ismej.2015.183.
Howe, Adina, Ringus, Daina L., Williams, Ryan J., Choo, Zi -Ning, Greenwald, Stephanie M., Owens, Sarah M., Coleman, Maureen L., Meyer, Folker, & Chang, Eugene B. Divergent responses of viral and bacterial communities in the gut microbiome to dietary disturbances in mice. United States. doi:10.1038/ismej.2015.183.
Howe, Adina, Ringus, Daina L., Williams, Ryan J., Choo, Zi -Ning, Greenwald, Stephanie M., Owens, Sarah M., Coleman, Maureen L., Meyer, Folker, and Chang, Eugene B. Fri . "Divergent responses of viral and bacterial communities in the gut microbiome to dietary disturbances in mice". United States. doi:10.1038/ismej.2015.183. https://www.osti.gov/servlets/purl/1315658.
@article{osti_1315658,
title = {Divergent responses of viral and bacterial communities in the gut microbiome to dietary disturbances in mice},
author = {Howe, Adina and Ringus, Daina L. and Williams, Ryan J. and Choo, Zi -Ning and Greenwald, Stephanie M. and Owens, Sarah M. and Coleman, Maureen L. and Meyer, Folker and Chang, Eugene B.},
abstractNote = {To improve our understanding of the stability of mammalian intestinal communities, we characterized the responses of both bacterial and viral communities in murine fecal samples to dietary changes between high- and low-fat (LF) diets. Targeted DNA extraction methods for bacteria, virus-like particles and induced prophages were used to generate bacterial and viral metagenomes as well as 16S ribosomal RNA amplicons. Gut microbiome communities from two cohorts of C57BL/6 mice were characterized in a 6-week diet perturbation study in response to high fiber, LF and high-refined sugar, milkfat (MF) diets. The resulting metagenomes from induced bacterial prophages and extracellular viruses showed significant overlap, supporting a largely temperate viral lifestyle within these gut microbiomes. The resistance of baseline communities to dietary disturbances was evaluated, and we observed contrasting responses of baseline LF and MF bacterial and viral communities. In contrast to baseline LF viral communities and bacterial communities in both diet treatments, baseline MF viral communities were sensitive to dietary disturbances as reflected in their non-recovery during the washout period. Finally, the contrasting responses of bacterial and viral communities suggest that these communities can respond to perturbations independently of each other and highlight the potentially unique role of viruses in gut health.},
doi = {10.1038/ismej.2015.183},
journal = {The ISME Journal},
issn = {1751-7362},
number = 5,
volume = 10,
place = {United States},
year = {2015},
month = {10}
}

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Cited by: 10 works
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