ArticlePeerJ2016
Towards quantitative viromics for both double-stranded and single-stranded DNA viruses.
Article in PeerJ, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 119 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
119 citing papers in PubMed, 229 citations in OpenAlex.
- Distinct Evolutionary Selection Patterns in Temperate and Filamentous Phages of Phocaeicola vulgatus in Health and IBD.Research square · 2026Article
- Hawaiian geothermal fumaroles contain diverse and novel viruses.Microbiology spectrum · 2026Article
- Viruses help shape microbiome response to polyphenol rewiring of methane-suppressed peat microcosms.PLoS biology · 2026Article
- Evolving strategies for virus discovery.Microbial genomics · 2026Review
- Optimizing methods for virome analysis based on studies of a synthetic viral community.mSystems · 2026Article
- Hawaiian Geothermal Fumaroles Contain Diverse and Novel Viruses.bioRxiv : the preprint server for biology · 2026Article
- Article
- Tools and approaches to study the human gut virome: from the bench to bioinformatics.mSystems · 2026Review
- DNA Viral Size Fraction Metagenomics for Human Stool Samples.Journal of visualized experiments : JoVE · 2026Article
- Interkingdom microbiome physiology in colorectal cancer: barrier dysfunction, immune-metabolic signaling, and therapeutic resistance.Frontiers in physiology · 2026Review
- A comparison of methods for the optimal recovery of the human fecal virome.ISME communications · 2026Article
- Limited consensus of marine viral diversity observed across techniques.Environmental microbiome · 2025Article
- Population ecology and biogeochemical implications of ssDNA and dsDNA viruses along a permafrost thaw gradient.Nature communications · 2025Article
- The influence of early life exposures on the infant gut virome.Gut microbes · 2025Article
- DNA extraction and virome processing methods strongly influence recovered human gut viral community characteristics.bioRxiv : the preprint server for biology · 2025Article
- Evolutionary interplay between viruses and R-loops.FEBS letters · 2025Review
- Optimizing methods for virome analysis based on studies of a synthetic viral community.bioRxiv : the preprint server for biology · 2025Article
- Biases and complementarity in gut viromes obtained from bulk and virus-like particle-enriched metagenomic sequencing.Microbiology spectrum · 2025Article
- Marine Bacteriophages as Next-Generation Therapeutics: Insights into Antimicrobial Potential and Application.Viruses · 2025Review
- Taxonomically distinct diatom viruses differentially impact microbial processing of organic matter.Science advances · 2025Article
59 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors at 5 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundViruses strongly influence microbial population dynamics and ecosystem functions. However, our ability to quantitatively evaluate those viral impacts is limited to the few cultivated viruses and double-stranded DNA (dsDNA) viral genomes captured in quantitative viral metagenomes (viromes). This leaves the ecology of non-dsDNA viruses nearly unknown, including single-stranded DNA (ssDNA) viruses that have been frequently observed in viromes, but not quantified due to amplification biases in sequencing library preparations (Multiple Displacement Amplification, Linker Amplification or Tagmentation).
methodsHere we designed mock viral communities including both ssDNA and dsDNA viruses to evaluate the capability of a sequencing library preparation approach including an Adaptase step prior to Linker Amplification for quantitative amplification of both dsDNA and ssDNA templates. We then surveyed aquatic samples to provide first estimates of the abundance of ssDNA viruses.
resultsMock community experiments confirmed the biased nature of existing library preparation methods for ssDNA templates (either largely enriched or selected against) and showed that the protocol using Adaptase plus Linker Amplification yielded viromes that were ±1.8-fold quantitative for ssDNA and dsDNA viruses. Application of this protocol to community virus DNA from three freshwater and three marine samples revealed that ssDNA viruses as a whole represent only a minor fraction (<5%) of DNA virus communities, though individual ssDNA genomes, both eukaryote-infecting Circular Rep-Encoding Single-Stranded DNA (CRESS-DNA) viruses and bacteriophages from the DISCUSSION: Together these findings provide empirical data for a new virome library preparation protocol, and a first estimate of ssDNA virus abundance in aquatic systems.
Indexed as
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.