ArticleEnvironmental microbiology2013
Evaluation of methods to concentrate and purify ocean virus communities through comparative, replicated metagenomics.
Article in Environmental microbiology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 116 papers.
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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.
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Who cites it
116 citing papers in PubMed, 205 citations in OpenAlex.
- Microbiota Transfer Therapy alters gut ecosystem and improves gastrointestinal and autism symptoms: an open-label study.Microbiome · 2017Trial
- Systematic scale-up and enhanced purification of marine cyanophage P-SSP7.Frontiers in microbiology · 2026Article
- Virus-encoded metabolism may support environmental stress adaptation of microbial hosts in an estuarine hypoxic zone.Frontiers in microbiology · 2026Article
- Limited consensus of marine viral diversity observed across techniques.Environmental microbiome · 2025Article
- Seasonal enhancement of the viral shunt catalyzes a subsurface oxygen maximum in the Sargasso Sea.Nature communications · 2025Article
- Differences in prokaryotic and viral community between rumen and feces.Scientific reports · 2025Article
- Biogeography of Virioplankton Abundance and Subcluster Patterns in the Northwest Pacific: A Large-Scale Perspective.MicrobiologyOpen · 2025Article
- Evaluation of Enrichment Approaches for the Study of the Viromes in Mollusk Species.Food and environmental virology · 2025Article
- Review
- From microscale to microbial insights: validating high-throughput microvolume extraction (HiMEx) methods for marine microbial ecology.ISME communications · 2025Article
- Environmental gradients shape viral-host dynamics in the Pearl River estuary.ISME communications · 2025Article
- Cave Pools in Carlsbad Caverns National Park Contain Diverse Bacteriophage Communities and Novel Viral Sequences.Microbial ecology · 2024Article
- Sxt1, Isolated from a Therapeutic Phage Cocktail, Is a Broader Host Range Relative of the Phage T3.Viruses · 2024Article
- Seasonal dynamics and diversity of Antarctic marine viruses reveal a novel viral seascape.Nature communications · 2024Article
- Distributions, interactions, and dynamics of prokaryotes and phages in a hybrid biological wastewater treatment system.Microbiome · 2024Article
- Article
- Environmental viromes reveal the global distribution signatures of deep-sea DNA viruses.Journal of advanced research · 2024Article
- A rumen virosphere with implications of contribution to fermentation and methane production, and endemism in cattle breeds and individuals.Applied and environmental microbiology · 2024Article
- Freshwater Viral Metagenome Analyses Targeting dsDNA Viruses.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Exploring the Archaeal Virosphere by Metagenomics.Methods in molecular biology (Clifton, N.J.) · 2024Article
56 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
4 authors at 1 institution in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Viruses have global impact through mortality, nutrient cycling and horizontal gene transfer, yet their study is limited by complex methodologies with little validation. Here, we use triplicate metagenomes to compare common aquatic viral concentration and purification methods across four combinations as follows: (i) tangential flow filtration (TFF) and DNase + CsCl, (ii) FeCl3 precipitation and DNase, (iii) FeCl3 precipitation and DNase + CsCl and (iv) FeCl3 precipitation and DNase + sucrose. Taxonomic data (30% of reads) suggested that purification methods were statistically indistinguishable at any taxonomic level while concentration methods were significantly different at family and genus levels. Specifically, TFF-concentrated viral metagenomes had significantly fewer abundant viral types (Podoviridae and Phycodnaviridae) and more variability among Myoviridae than FeCl3 -precipitated viral metagenomes. More comprehensive analyses using protein clusters (66% of reads) and k-mers (100% of reads) showed 50-53% of these data were common to all four methods, and revealed trace bacterial DNA contamination in TFF-concentrated metagenomes and one of three replicates concentrated using FeCl3 and purified by DNase alone. Shared k-mer analyses also revealed that polymerases used in amplification impact the resulting metagenomes, with TaKaRa enriching for 'rare' reads relative to PfuTurbo. Together these results provide empirical data for making experimental design decisions in culture-independent viral ecology studies.
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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.