ArticleeLife2015
Viral dark matter and virus-host interactions resolved from publicly available microbial genomes.
Article in eLife, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 298 papers, 1 of them a synthesis that pooled it.
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.
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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
298 citing papers in PubMed, 1 synthesis or guideline pooled it.
- The virome in early life and childhood and development of islet autoimmunity and type 1 diabetes: A systematic review and meta-analysis of observational studies.Reviews in medical virology · 2021Pooled it
- Deciphering pervasive domestication and active "dark matter" of proviruses in prokaryotes via precision border mapping.Science advances · 2026Article
- Revisiting the life cycle of temperate phages.Nature reviews. Microbiology · 2026Review
- Smaller Genomes and Shorter Prophage Sequences Differentiate Clinical from Environmental Isolates ofbioRxiv : the preprint server for biology · 2026Article
- Two coinfecting archaeal viruses provide insights into virus-virus interactions.Communications biology · 2026Article
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- Evolving strategies for virus discovery.Microbial genomics · 2026Review
- Mining viruses in public databases unveils the diversity within the Deltaflexiviridae family.Archives of virology · 2026Article
- Optimizing methods for virome analysis based on studies of a synthetic viral community.mSystems · 2026Article
- Article
- Review
- Uncovering novel virophages and giant viruses in high-altitude Lake Namtso: diversity and evolution of host-virus-virophage tripartite interaction systems.Archives of microbiology · 2026Article
- Differences in metaviromes between Aedes aegypti and Aedes albopictus from sympatric areas on Hainan Island and the Leizhou Peninsula, China.Parasites & vectors · 2026Article
- Prophage: agent provocateur?Archives of microbiology · 2026Review
- Bacteriophages in gut metagenomes: from analysis to application.Virology journal · 2026Review
- Prophage-encoded RexAB-type phage defense system in Pseudomonas putida.Scientific reports · 2026Article
- Differences in metavirome among Aedes albopictus, Culex tritaeniorhynchus, and Anopheles sinensis in Jiangxi Province, China.Parasites & vectors · 2026Article
- High-throughput sequencing reveals the virome characteristics of wastewater in Gansu Province, China from 2024 to 2026.Frontiers in microbiology · 2026Article
- CRISPR spacer profiling and prophage mining reveal diverse bacteriophages associated withJournal of oral microbiology · 2026Article
- Illuminating the newly produced viruses within the virosphere with bioorthogonal noncanonical amino acid tagging and single-virus genomic sequencing technologies.ISME communications · 2026Article
238 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The ecological importance of viruses is now widely recognized, yet our limited knowledge of viral sequence space and virus-host interactions precludes accurate prediction of their roles and impacts. In this study, we mined publicly available bacterial and archaeal genomic data sets to identify 12,498 high-confidence viral genomes linked to their microbial hosts. These data augment public data sets 10-fold, provide first viral sequences for 13 new bacterial phyla including ecologically abundant phyla, and help taxonomically identify 7-38% of 'unknown' sequence space in viromes. Genome- and network-based classification was largely consistent with accepted viral taxonomy and suggested that (i) 264 new viral genera were identified (doubling known genera) and (ii) cross-taxon genomic recombination is limited. Further analyses provided empirical data on extrachromosomal prophages and coinfection prevalences, as well as evaluation of in silico virus-host linkage predictions. Together these findings illustrate the value of mining viral signal from microbial genomes.
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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.