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

## TL;DR

This study shows that bacteriophages and gene transfer agents in the gut microbiome frequently package and transfer bacterial DNA, with specific activity in certain bacterial families.

## Contribution

The study introduces a novel method using nanopore sequencing to identify capsid-packaged DNA, revealing widespread bacterial DNA mobilization in the gut.

## Key findings

- Up to 5.4% of capsid-packaged DNA in the gut microbiome is derived from bacterial genomes.
- Generalized transduction and GTA activity are prominent in Oscillospiraceae and Ruminococcaceae.
- Lateral transduction was observed in Bacteroides, and prophage induction was detected in several gut taxa.

## Abstract

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.

Here, the authors show that packaging of bacterial DNA by phage-like particles is widespread in the gut microbiome, with activity of gene transfer agents being prominent in Oscillospiraceae and Ruminococcaceae; and identifying lateral transduction by a temperate phage in Bacteroides.