ArticleNature biotechnology2019
Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks.
Article in Nature biotechnology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 535 papers, 2 of them syntheses that pooled it.
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Who cites it
535 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Bioinformatics Tools and Approaches for Virus Discovery in Genomic Data: A Systematic Review.Viruses · 2025Pooled it
- Engrafting gut bacteriophages have potential to modulate microbial metabolism in fecal microbiota transplantation.Microbiome · 2025Pooled it
- Long-term health outcomes in adolescents with obesity treated with faecal microbiota transplantation: 4-year follow-up.Nature communications · 2025Trial
- The phageome of patients with ulcerative colitis treated with donor fecal microbiota reveals markers associated with disease remission.Nature communications · 2024Trial
- CRISPR-Cas immune repertoires as an ecological record of bacterial interactions with mobile genetic elements in the human gut.Gut microbes · 2026Article
- Isolation and genomic characterization of a Teetrevirus phage infecting Klebsiella quasipneumoniae with a putative SAMase gene.Archives of virology · 2026Article
- Jestvirus, a Novel Genus in the Family Autotranscriptaviridae Infecting Aeromonas.Current microbiology · 2026Article
- Deciphering pervasive domestication and active "dark matter" of proviruses in prokaryotes via precision border mapping.Science advances · 2026Article
- Spatial heterogeneity of viral communities across the gastrointestinal tracts of ruminants.Journal of advanced research · 2026Article
- Two coinfecting archaeal viruses provide insights into virus-virus interactions.Communications biology · 2026Article
- A phage DUF669 protein mediates post-cleavage DNA repair against host CRISPR immunity.Nature communications · 2026Article
- Distinct Evolutionary Selection Patterns in Temperate and Filamentous Phages of Phocaeicola vulgatus in Health and IBD.Research square · 2026Article
- LAMBDA: a prophage detection benchmark for genomic language models.NAR genomics and bioinformatics · 2026Article
- Maternal contact and age-dependent succession influence the assembly of the calf rumen microbiome and virome.Microbiology spectrum · 2026Article
- Phage bioinformatics tools: a review of computational approaches for bacteriophage research.Briefings in bioinformatics · 2026Review
- Decadal Resampling Reveals Widespread Increases in Soil Microbial Diversity Associated With Nitrogen Deposition.Global change biology · 2026Article
- Genomic analysis of prophage prevalence and diversity in the bovine mastitis pathogenMicrobial genomics · 2026Article
- Exploring the ecological drivers of bacteriophage diversity and functional viral potential in the skin of the axolotl Ambystoma altamirani.FEMS microbiology ecology · 2026Article
- Elevation-structured viral ecological strategies along glacier-fed rivers on the Qinghai-Tibet Plateau.Nature communications · 2026Article
- A generative model for bipartite gene-sharing networks.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
475 more citing papers are in PubMed but not listed here.
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Authors and funding
12 authors.
Funding
Abstract
Microbiomes from every environment contain a myriad of uncultivated archaeal and bacterial viruses, but studying these viruses is hampered by the lack of a universal, scalable taxonomic framework. We present vConTACT v.2.0, a network-based application utilizing whole genome gene-sharing profiles for virus taxonomy that integrates distance-based hierarchical clustering and confidence scores for all taxonomic predictions. We report near-identical (96%) replication of existing genus-level viral taxonomy assignments from the International Committee on Taxonomy of Viruses for National Center for Biotechnology Information virus RefSeq. Application of vConTACT v.2.0 to 1,364 previously unclassified viruses deposited in virus RefSeq as reference genomes produced automatic, high-confidence genus assignments for 820 of the 1,364. We applied vConTACT v.2.0 to analyze 15,280 Global Ocean Virome genome fragments and were able to provide taxonomic assignments for 31% of these data, which shows that our algorithm is scalable to very large metagenomic datasets. Our taxonomy tool can be automated and applied to metagenomes from any environment for virus classification.
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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.