Year: 2026
Type: article
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.
Source: Nature Communications
Language: English
Subfield: Ecology
Field: Environmental Science
Domain: Physical Sciences
Open Access status: gold
Estimated APC paid: $6,990
Awards: Field Operational Tests of Aftermarket and Nomadic Devices in Vehicles, G1495066884, Technologies for the Future, Harnessing the potential of atypical gDNA processing by domesticated viruses, G3271259483, G347064151, G434337789, G4713448759, Structural basis of high-frequency horizontal gene transfer mediated by bacteriophage-like particles, G4921913450, G5261025856, Core Capability - University of York, crAssphages - the most abundant viruses of the human gut, G9000201684
OpenAlex ID: W7125696056