Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

Evolutionary dynamics of bacteria in the gut microbiome within and across hosts

Nandita R. Garud, Benjamin H. Good, Oskar Hallatschek, Katherine S. Pollard
doi: https://doi.org/10.1101/210955
Nandita R. Garud
1Gladstone Institutes, San Francisco, CA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Benjamin H. Good
2Department of Physics, University of California, Berkeley, CA
3Department of Bioengineering, University of California, Berkeley, CA
5Kavli Institute for Theoretical Physics, University of California, Santa Barbara, CA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Oskar Hallatschek
2Department of Physics, University of California, Berkeley, CA
4Department of Integrative Biology, University of California, Berkeley, CA
5Kavli Institute for Theoretical Physics, University of California, Santa Barbara, CA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Katherine S. Pollard
1Gladstone Institutes, San Francisco, CA
6Department of Epidemiology & Biostatistics, University of California, San Francisco, CA
7Institute for Human Genetics and Institute for Computational Health Sciences, University of California, San Francisco, CA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Preview PDF
Loading

Abstract

The structure and function of the gut microbiome are shaped by a combination of ecological and evolutionary forces. While the ecological dynamics of the community have been extensively studied, much less is known about how strains of gut bacteria evolve over time. Here we show that with a model-based analysis of existing shotgun metagenomic data, we can gain new insights into the evolutionary dynamics of gut bacteria within and across hosts. We find that long-term evolution across hosts is consistent with quasi-sexual evolution and purifying selection, with relatively weak geographic structure in many prevalent species. However, our quantitative approach also reveals new between-host genealogical signatures that cannot be explained by standard population genetic models. By comparing samples from the same host over ~6 month timescales, we find that within-host differences rarely arise from the invasion of strains as distantly related as those in other hosts. Instead, we more commonly observe a small number of evolutionary changes in resident strains, in which nucleotide variants or gene gains or losses rapidly sweep to high frequency within a host. By comparing the signatures of these mutations with the typical between-host differences, we find evidence that many sweeps are driven by introgression from existing species or strains, rather than by de novo mutations. These data suggest that bacteria in the microbiome can evolve on human relevant timescales, and highlight the feedback between these short-term changes and the longer-term evolution across hosts.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
Back to top
PreviousNext
Posted October 30, 2017.
Download PDF

Supplementary Material

Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
Evolutionary dynamics of bacteria in the gut microbiome within and across hosts
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Evolutionary dynamics of bacteria in the gut microbiome within and across hosts
Nandita R. Garud, Benjamin H. Good, Oskar Hallatschek, Katherine S. Pollard
bioRxiv 210955; doi: https://doi.org/10.1101/210955
Digg logo Reddit logo Twitter logo Facebook logo Google logo LinkedIn logo Mendeley logo
Citation Tools
Evolutionary dynamics of bacteria in the gut microbiome within and across hosts
Nandita R. Garud, Benjamin H. Good, Oskar Hallatschek, Katherine S. Pollard
bioRxiv 210955; doi: https://doi.org/10.1101/210955

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Evolutionary Biology
Subject Areas
All Articles
  • Animal Behavior and Cognition (3686)
  • Biochemistry (7780)
  • Bioengineering (5671)
  • Bioinformatics (21250)
  • Biophysics (10565)
  • Cancer Biology (8164)
  • Cell Biology (11915)
  • Clinical Trials (138)
  • Developmental Biology (6740)
  • Ecology (10388)
  • Epidemiology (2065)
  • Evolutionary Biology (13845)
  • Genetics (9695)
  • Genomics (13058)
  • Immunology (8129)
  • Microbiology (19970)
  • Molecular Biology (7839)
  • Neuroscience (42991)
  • Paleontology (318)
  • Pathology (1276)
  • Pharmacology and Toxicology (2257)
  • Physiology (3350)
  • Plant Biology (7208)
  • Scientific Communication and Education (1309)
  • Synthetic Biology (2000)
  • Systems Biology (5529)
  • Zoology (1126)