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<p>Transducing bacteriophage and gene transfer agents (GTAs) are constrained by the structural limits of their capsids, which determine the maximum length of host DNA they can package. Here, we utilise nanopore sequencing of intact, capsid-packaged DNA molecules to recover full-length reads, thereby enabling the precise identification of encapsidated DNA and its bacterial origin. This approach was validated using well-characterised transducing systems and subsequently applied to faecal viromes from three healthy donors. Our analysis reveals that bacterial DNA encapsidation is widespread in the gut microbiome, with up to 5.4% of capsid-packaged DNA derived from bacterial genomes. Generalised transduction and GTA activity were especially prominent in <i>Oscillospiraceae</i> and <i>Ruminococcaceae</i> (e.g. <i>Faecalibacterium</i> spp.), while lateral transduction was observed in <i>Bacteroides</i>. Additionally, we detected induction of prophages in several highly prevalent gut bacterial taxa. These findings reveal the prevalence of bacterial DNA packaging via virus or virus-like capsids in the human gut, shedding light on the diverse mechanisms that drive this process.</p>

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Large-scale capsid-mediated mobilisation of bacterial genomic DNA in the gut microbiome

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年1月27日

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  • Tatiana Borodovich,
  • Colin Buttimer,
  • Jason S. Wilson,
  • Pavol Bardy,
  • Muireann Smith,
  • Conor Hill,
  • Ekaterina V. Khokhlova,
  • Matthew Harte,
  • Bianca Govi,
  • Paul C. M. Fogg,
  • Colin Hill,
  • Andrey N. Shkoporov

摘要

Transducing bacteriophage and gene transfer agents (GTAs) are constrained by the structural limits of their capsids, which determine the maximum length of host DNA they can package. Here, we utilise nanopore sequencing of intact, capsid-packaged DNA molecules to recover full-length reads, thereby enabling the precise identification of encapsidated DNA and its bacterial origin. This approach was validated using well-characterised transducing systems and subsequently applied to faecal viromes from three healthy donors. Our analysis reveals that bacterial DNA encapsidation is widespread in the gut microbiome, with up to 5.4% of capsid-packaged DNA derived from bacterial genomes. Generalised transduction and GTA activity were especially prominent in Oscillospiraceae and Ruminococcaceae (e.g. Faecalibacterium spp.), while lateral transduction was observed in Bacteroides. Additionally, we detected induction of prophages in several highly prevalent gut bacterial taxa. These findings reveal the prevalence of bacterial DNA packaging via virus or virus-like capsids in the human gut, shedding light on the diverse mechanisms that drive this process.