1887

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Volume 8, Issue 9

Single-cell genomics reveals population structures from evolutionary studies of Open Access

Abstract

Single-cell DNA sequencing has the potential to reveal detailed hierarchical structures in evolving populations of cells. Single cell approaches are increasingly used to study clonal evolution in human ageing and cancer but have not yet been deployed to study evolving clonal microbial populations. Here, we present an approach for single bacterial genomic analysis for evolution experiments using FACS isolation of individual bacteria followed by whole-genome amplification and sequencing. We apply this to the experimental evolution of a hypermutator strain of in response to antibiotic stress (ciprofloxacin). By analysing sequence polymorphisms in individual cells from populations we identified the presence and prevalence of sub-populations which have acquired polymorphisms in genes previously demonstrated to be associated with ciprofloxacin susceptibility. We were also able to identify that the population exposed to antibiotic stress was able to develop resistance whilst maintaining diversity. This population structure could not be resolved from bulk sequence data, and our results show how high-throughput single-cell sequencing can enhance experimental studies of bacterial evolution.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): evolution , genomics , salmonella and single-cell
Funding
This study was supported by the:
  • Biotechnology and Biological Sciences Research Council (Award BB/P022073/1)
    • Principle Award Recipient: MacaulayIain C.
  • Biotechnology and Biological Sciences Research Council (Award BB/CCG1720/1)
  • Biotechnology and Biological Sciences Research Council (Award BB/R012504/1)
  • Biotechnology and Biological Sciences Research Council (Award BB/R022526/1)
    • Principle Award Recipient: HallNeil
© 2022 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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2022-09-20
2024-04-25
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Single-cell genomics reveals population structures from in vitro evolutionary studies of Salmonella
M Gen 8, 000871 (2022); https://doi.org/10.1099/mgen.0.000871
/content/journal/mgen/10.1099/mgen.0.000871
/content/journal/mgen/10.1099/mgen.0.000871
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