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 4733 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 HGT is prevalent in cheese rind microbiomes, and that identification of genes that are frequently transferred in a particular environment may provide insight into the selective forces shaping microbial communities.
Highlights
Great strides have been made in characterizing the composition of microbiomes, and in understanding their importance in the ecology of natural systems, in agriculture and in human health
We included genomes from the NCBI reference sequence (RefSeq) database that are associated with cheese, for a total of 165 bacterial genomes
We developed a computational pipeline for the identification of putative horizontally transferred genes adapted from work on the human microbiome [10]
Summary
Great strides have been made in characterizing the composition of microbiomes, and in understanding their importance in the ecology of natural systems, in agriculture and in human health Despite these advances, the forces that shape the diversity, structure, and function of microbiomes remain poorly understood [1]. Replicating microbial communities in vitro is an enormous challenge, due to high levels of diversity and the difficulties in establishing pure cultures of most bacterial species These obstacles significantly hamper our ability to move from observations of microbial diversity to the molecular mechanisms shaping key processes such as species interactions and microbial evolution. The copyright holder for this preprint It is made available under
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