Large-scale network analysis captures biological features of bacterial plasmids

Mislav Acman (), Lucy van Dorp, Joanne M. Santini and Francois Balloux ()
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Mislav Acman: University College London
Lucy van Dorp: University College London
Joanne M. Santini: University College London
Francois Balloux: University College London

Nature Communications, 2020, vol. 11, issue 1, 1-11

Abstract: Abstract Many bacteria can exchange genetic material through horizontal gene transfer (HGT) mediated by plasmids and plasmid-borne transposable elements. Here, we study the population structure and dynamics of over 10,000 bacterial plasmids, by quantifying their genetic similarities and reconstructing a network based on their shared k-mer content. We use a community detection algorithm to assign plasmids into cliques, which correlate with plasmid gene content, bacterial host range, GC content, and existing classifications based on replicon and mobility (MOB) types. Further analysis of plasmid population structure allows us to uncover candidates for yet undescribed replicon genes, and to identify transposable elements as the main drivers of HGT at broad phylogenetic scales. Our work illustrates the potential of network-based analyses of the bacterial ‘mobilome’ and opens up the prospect of a natural, exhaustive classification framework for bacterial plasmids.

Date: 2020
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DOI: 10.1038/s41467-020-16282-w

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