Extensive horizontal gene transfer in cheese-associated bacteria

Abstract
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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

(2016) Datasets associated with Bonham et al.
Publicly available at the Zenodo data repository.

https://doi.org/10.5281/zenodo.163212
(2017) Datasets associated with Bonham et al.
PRJNA387187.

http://www.ncbi.nlm.nih.gov/bioproject/387187

The following previously published data sets were used

(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.

https://cdn.elifesciences.org/articles/22144/metagenomics.anl.gov

Article and author information

Author details

Kevin S Bonham

Molecular Biology, University of California, San Diego, La Jolla, United States

Competing interests
The authors declare that no competing interests exist.
Benjamin E Wolfe

Biology, Tufts University, Medford, United States

Competing interests
The authors declare that no competing interests exist.
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.

"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.

Copyright

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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Kevin S Bonham
Benjamin E Wolfe
Rachel J Dutton

(2017)

Extensive horizontal gene transfer in cheese-associated bacteria

eLife 6:e22144.

https://doi.org/10.7554/eLife.22144

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