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.
Datasets associated with Bonham et al.Publicly available at the Zenodo data repository.
Datasets associated with Bonham et al.PRJNA387187.
shotgun metagenomic data from cheese rinds used in Figure 44524487.3, 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.
- 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.
- Kim Handley, The University of Auckland, New Zealand
© 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.