ArticleNature communications2026
Large-scale capsid-mediated mobilisation of bacterial genomic DNA in the gut microbiome.
Article in Nature communications, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
What it found
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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
11 citing papers in PubMed.
- Firewalled synthetic commensal blocks horizontal gene transfer in the gut.bioRxiv : the preprint server for biology · 2026Article
- Perturbations shift the composition of bacterial DNA carried by virus-like particles in the murine gut microbiome.bioRxiv : the preprint server for biology · 2026Article
- High throughput chromatographic ultra-purification of virus-like particles for downstream viromics.bioRxiv : the preprint server for biology · 2026Article
- TrIdent - An R package to automate transductomics analysis of virus-like particle mediated DNA mobilization.bioRxiv : the preprint server for biology · 2026Article
- Dynamics of gut bacteriophage in diversity outbred mice studied over lifespan and during extreme caloric restriction.Microbiome · 2026Article
- Bacteriophages mobilize bacterial defense systems via lateral transduction.Science advances · 2026Article
- Gut phages are linked to off-target antimicrobial resistance genes in orthopedic patients receiving peri-surgical antibiotics.Frontiers in microbiology · 2026Article
- We need to talk about the virome.Microbiome research reports · 2026Article
- Article
- Effects of bacteriophages on gut microbiome functionality.Gut microbes · 2025Review
- Discovering Broader Host Ranges and an IS-bound Prophage Class Through Long-Read Metagenomics.bioRxiv : the preprint server for biology · 2025Article
Corrections and comments
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Authors and funding
12 authors.
Funding
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.