ArticleISME communications2023
Extracellular vesicles are the main contributor to the non-viral protected extracellular sequence space.
Article in ISME communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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
15 citing papers in PubMed, 16 citations in OpenAlex.
- High throughput chromatographic ultra-purification of virus-like particles for downstream viromics.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
- Unveiling Marine Vesicle Uptake in Vibrio spp: Taxonomic and Environmental Insights.MicrobiologyOpen · 2026Article
- TrIdent - An R package to automate transductomics analysis of virus-like particle mediated DNA mobilization.bioRxiv : the preprint server for biology · 2026Article
- Extracellular vesicles drive stress-induced antibiotic resistance spread in soil.Environmental science and ecotechnology · 2026Article
- Large-scale capsid-mediated mobilisation of bacterial genomic DNA in the gut microbiome.Nature communications · 2026Article
- Bacterial extracellular vesicles exhibit distinct functional potential across biogeographic provinces of the South Pacific Ocean.The ISME journal · 2026Article
- Viromics approaches for the study of viral diversity and ecology in microbiomes.Nature reviews. Genetics · 2026Review
- A One Health perspective on bacterial extracellular vesicles as mediators of antimicrobial resistance spread.ISME communications · 2026Article
- Computational Microbial and Viral Ecology Analysis.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Central carbon metabolism switching in lytic versus temperate coral reef viral communities.bioRxiv : the preprint server for biology · 2025Article
- Distinct horizontal gene transfer potential of extracellular vesicles versus viral-like particles in marine habitats.Nature communications · 2025Article
- Identification and characterization ofMicrobiology spectrum · 2025Article
- Viromes vs. mixed community metagenomes: choice of method dictates interpretation of viral community ecology.Microbiome · 2024Article
- Viromes vs. mixed community metagenomes: choice of method dictates interpretation of viral community ecology.bioRxiv : the preprint server for biology · 2023Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Environmental virus metagenomes, commonly referred to as "viromes", are typically generated by physically separating virus-like particles (VLPs) from the microbial fraction based on their size and mass. However, most methods used to purify VLPs, enrich extracellular vesicles (EVs) and gene transfer agents (GTAs) simultaneously. Consequently, the sequence space traditionally referred to as a "virome" contains host-associated sequences, transported via EVs or GTAs. We therefore propose to call the genetic material isolated from size-fractionated (0.22 µm) and DNase-treated samples protected environmental DNA (peDNA). This sequence space contains viral genomes, DNA transduced by viruses and DNA transported in EVs and GTAs. Since there is no genetic signature for peDNA transported in EVs, GTAs and virus particles, we rely on the successful removal of contaminating remaining cellular and free DNA when analyzing peDNA. Using marine samples collected from the North Sea, we generated a thoroughly purified peDNA dataset and developed a bioinformatic pipeline to determine the potential origin of the purified DNA. This pipeline was applied to our dataset as well as existing global marine "viromes". Through this pipeline, we identified known GTA and EV producers, as well as organisms with actively transducing proviruses as the source of the peDNA, thus confirming the reliability of our approach. Additionally, we identified novel and widespread EV producers, and found quantitative evidence suggesting that EV-mediated gene transfer plays a significant role in driving horizontal gene transfer (HGT) in the world's oceans.
Identifiers
What OpenQuestion holds
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.