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, California, United States of America
  • 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, California, United States of America
3Department of Bioengineering, University of California, Berkeley, California, United States of America
5Kavli Institute for Theoretical Physics, University of California, Santa Barbara, California, United States of America
  • 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, California, United States of America
4Department of Integrative Biology, University of California, Berkeley, California, United States of America
5Kavli Institute for Theoretical Physics, University of California, Santa Barbara, California, United States of America
  • 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, California, United States of America
6Department of Epidemiology & Biostatistics, Institute for Human Genetics, Quantitative Biology Institute, and Institute for Computational Health Sciences, University of California, San Francisco, California, United States of America
7Chan-Zuckerberg Biohub, San Francisco, California, United States of America
  • 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

Gut microbiota are shaped by a combination of ecological and evolutionary forces. While the ecological dynamics have been extensively studied, much less is known about how species of gut bacteria evolve over time. Here we introduce a model-based framework for quantifying evolutionary dynamics within and across hosts using a panel of metagenomic samples. We use this approach to study evolution in ∼30 prevalent species in the human gut. Although the patterns of between-host diversity are consistent with quasi-sexual evolution and purifying selection on long timescales, we identify new genealogical signatures that challenge standard population genetic models of these processes. Within hosts, we find that genetic differences that accumulate over ∼6 month timescales are only rarely attributable to replacement by distantly related strains. Instead, the resident strains more commonly acquire a smaller number of putative evolutionary changes, in which nucleotide variants or gene gains or losses rapidly sweep to high frequency. By comparing these mutations with the typical between-host differences, we find evidence that some sweeps are seeded by recombination, in addition to new mutations. However, comparisons of adult twins suggest that replacement eventually overwhelms evolution over multi-decade timescales, hinting at fundamental limits to the extent of local adaptation. Together, our results suggest that gut bacteria can evolve on human-relevant timescales, and they highlight the connections between these short-term evolutionary dynamics and 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 September 14, 2018.
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 (3701)
  • Biochemistry (7820)
  • Bioengineering (5695)
  • Bioinformatics (21343)
  • Biophysics (10603)
  • Cancer Biology (8206)
  • Cell Biology (11974)
  • Clinical Trials (138)
  • Developmental Biology (6786)
  • Ecology (10425)
  • Epidemiology (2065)
  • Evolutionary Biology (13908)
  • Genetics (9731)
  • Genomics (13109)
  • Immunology (8171)
  • Microbiology (20064)
  • Molecular Biology (7875)
  • Neuroscience (43171)
  • Paleontology (321)
  • Pathology (1282)
  • Pharmacology and Toxicology (2267)
  • Physiology (3363)
  • Plant Biology (7254)
  • Scientific Communication and Education (1316)
  • Synthetic Biology (2012)
  • Systems Biology (5550)
  • Zoology (1133)