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Large-scale network analysis captures biological features of bacterial plasmids

Author

Listed:
  • Mislav Acman

    (University College London)

  • Lucy van Dorp

    (University College London)

  • Joanne M. Santini

    (University College London)

  • Francois Balloux

    (University College London)

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.

Suggested Citation

  • Mislav Acman & Lucy van Dorp & Joanne M. Santini & Francois Balloux, 2020. "Large-scale network analysis captures biological features of bacterial plasmids," Nature Communications, Nature, vol. 11(1), pages 1-11, December.
    • Handle: RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-16282-w
    DOI: 10.1038/s41467-020-16282-w
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    Cited by:

    1. Wang, Benyu & Gu, Yijun & Zheng, Diwen, 2022. "Community detection in error-prone environments based on particle cooperation and competition with distance dynamics," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 607(C).
    2. Samuel Lipworth & William Matlock & Liam Shaw & Karina-Doris Vihta & Gillian Rodger & Kevin Chau & Leanne Barker & Sophie George & James Kavanagh & Timothy Davies & Alison Vaughan & Monique Andersson , 2024. "The plasmidome associated with Gram-negative bloodstream infections: A large-scale observational study using complete plasmid assemblies," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    3. Alice Risely & Arthur Newbury & Thibault Stalder & Benno I. Simmons & Eva M. Top & Angus Buckling & Dirk Sanders, 2024. "Host- plasmid network structure in wastewater is linked to antimicrobial resistance genes," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
    4. Alvah Zorea & David Pellow & Liron Levin & Shai Pilosof & Jonathan Friedman & Ron Shamir & Itzhak Mizrahi, 2024. "Plasmids in the human gut reveal neutral dispersal and recombination that is overpowered by inflammatory diseases," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    5. Wanli He & Jakob Russel & Franziska Klincke & Joseph Nesme & Søren Johannes Sørensen, 2024. "Insights into the ecology of the infant gut plasmidome," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    6. Mislav Acman & Ruobing Wang & Lucy Dorp & Liam P. Shaw & Qi Wang & Nina Luhmann & Yuyao Yin & Shijun Sun & Hongbin Chen & Hui Wang & Francois Balloux, 2022. "Role of mobile genetic elements in the global dissemination of the carbapenem resistance gene blaNDM," Nature Communications, Nature, vol. 13(1), pages 1-13, December.

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