ArticleNature microbiology2021
Interaction dynamics and virus-host range for estuarine actinophages captured by epicPCR.
Article in Nature microbiology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed, 69 citations in OpenAlex.
- Salinity-driven niche partitioning of aquatic viruses in one of Europe's largest estuaries.Applied and environmental microbiology · 2026Article
- Tools and approaches to study the human gut virome: from the bench to bioinformatics.mSystems · 2026Review
- Cross-order detection of bacteriophage transduction in microbial communities using RNA barcoding.Nature communications · 2026Article
- Diversity and ecological roles of hidden viral players in groundwater microbiomes.Nature communications · 2026Article
- Benchmarking with synthetic communities provides a baseline for virus-host inferences from Hi-C proximity linking.PLoS biology · 2025Article
- Synthetic community Hi-C benchmarking provides a baseline for virus-host inferences.bioRxiv : the preprint server for biology · 2025Article
- Global biogeography of airborne viruses in public transit systems and their host interactions.Microbiome · 2025Article
- Metagenomes and 1,313 metagenome-assembled genomes from a northern Gulf of Mexico coastal time series.Scientific data · 2025Article
- Current Perspectives on Functional Involvement of Micropeptides in Virus-Host Interactions.International journal of molecular sciences · 2025Review
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- Evaluating phage lytic activity: from plaque assays to single-cell technologies.Frontiers in microbiology · 2025Review
- Contrasting defense strategies of oligotrophs and copiotrophs revealed by single-cell-resolved virus-host pairing of freshwater bacteria.ISME communications · 2025Article
- Use of sequence barcodes for tracking horizontal gene transfer of antimicrobial resistance genes in a microbial community.ISME communications · 2025Article
- New isolates refine the ecophysiology of the Roseobacter CHAB-I-5 lineage.ISME communications · 2025Article
- Virus-host interactions predictor (VHIP): Machine learning approach to resolve microbial virus-host interaction networks.PLoS computational biology · 2024Article
- Article
- Establishing Host-Virus Link Through Host Metabolism: Viral DNA SIP Validation Using T4 Bacteriophage and E. coli.Current microbiology · 2024Article
- Biogeographic patterns and drivers of soil viromes.Nature ecology & evolution · 2024Article
Corrections and comments
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Viruses impact microbial diversity, gene flow and function through virus-host interactions. Although metagenomics surveys are rapidly cataloguing viral diversity, methods are needed to capture specific virus-host interactions in situ. Here, we leveraged metagenomics and repurposed emulsion paired isolation-concatenation PCR (epicPCR) to investigate viral diversity and virus-host interactions in situ over time in an estuarine environment. The method fuses a phage marker, the ribonucleotide reductase gene, with the host 16S rRNA gene of infected bacterial cells within emulsion droplets providing single-cell resolution for dozens of samples. EpicPCR captured in situ virus-host interactions for viral clades with no closely related database representatives. Abundant freshwater Actinobacteria lineages, in particular Rhodoluna sp., were the most common hosts for these poorly characterized viruses, with interactions correlated with environmental factors. Multiple methods used to identify virus-host interactions, including epicPCR, identified different and largely non-overlapping interactions within the vast virus-host interaction space. Tracking virus-host interaction dynamics also revealed that multi-host viruses had significantly longer periods with observed virus-host interactions, whereas single-host viruses were observed interacting with hosts at lower minimum abundances, suggesting more efficient interactions. Capturing in situ interactions with epicPCR revealed environmental and ecological factors shaping virus-host interactions, highlighting epicPCR as a valuable technique in viral ecology.
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