1. Genetics and Genomics
  2. Microbiology and Infectious Disease
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Extensive horizontal gene transfer in cheese-associated bacteria

  1. Kevin S Bonham
  2. Benjamin E Wolfe
  3. Rachel J Dutton  Is a corresponding author
  1. University of California, San Diego, United States
  2. Tufts University, United States
  3. UC San Diego, United States
Research Article
  • Cited 42
  • Views 7,119
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Cite this article as: eLife 2017;6:e22144 doi: 10.7554/eLife.22144

Abstract

Acquisition of genes through horizontal gene transfer (HGT) allows microbes to rapidly gain new capabilities and adapt to new or changing environments. Identifying widespread HGT regions within multispecies microbiomes can pinpoint the molecular mechanisms that play key roles in microbiome assembly. We sought to identify horizontally transferred genes within a model microbiome, the cheese rind. Comparing 31 newly-sequenced and 134 previously sequenced bacterial isolates from cheese rinds, we identified over 200 putative horizontally transferred genomic regions containing 4,844 protein coding genes. The largest of these regions are enriched for genes involved in siderophore acquisition, and are widely distributed in cheese rinds in both Europe and the US. These results suggest that horizontal gene transfer (HGT) is prevalent in cheese rind microbiomes, and the identification of genes that are frequently transferred in a particular environment may provide insight into the selective forces shaping microbial communities.

Data availability

The following data sets were generated
The following previously published data sets were used
    1. Wolfe BE
    2. Button JE
    3. Santarelli M
    4. Dutton RJ
    (2014) shotgun metagenomic data from cheese rinds used in Figure 4
    4524487.3, 4524500.3, 4524498.3, 4524496.3, 4524502.3, 4524495.3, 4524488.3, 4524490.3, 4524499.3, 4524497.3, 4524491.3, 4524493.3, 4524501.3, 4524482.3, 4524489.3, 4524483.3, 4524505.3, 4524494.3, 4524486.3, 4524504.3, 4524485.3, and 4524484.3.

Article and author information

Author details

  1. Kevin S Bonham

    Molecular Biology, University of California, San Diego, La Jolla, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. Benjamin E Wolfe

    Biology, Tufts University, Medford, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Rachel J Dutton

    Molecular Biology, UC San Diego, La Jolla, United States
    For correspondence
    rjdutton@ucsd.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-2944-2182

Funding

National Institutes of Health (P50 GM068763)

  • Kevin S Bonham
  • Benjamin E Wolfe
  • Rachel J Dutton

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Kim Handley, The University of Auckland, New Zealand

Publication history

  1. Received: October 6, 2016
  2. Accepted: June 20, 2017
  3. Accepted Manuscript published: June 23, 2017 (version 1)
  4. Version of Record published: July 25, 2017 (version 2)

Copyright

© 2017, Bonham et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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