ArticleEnvironmental microbiology2013
Single-cell and population level viral infection dynamics revealed by phageFISH, a method to visualize intracellular and free viruses.
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 67 papers.
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Who cites it
67 citing papers in PubMed, 139 citations in OpenAlex.
- 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
- Stable co-existence ofmBio · 2026Article
- A single-cell perspective on host-virus dynamics in the ocean.Trends in microbiology · 2025Review
- Bacteriophage-driven microbial phenotypic heterogeneity: ecological and biogeochemical importance.NPJ biofilms and microbiomes · 2025Review
- Molecular piracy in deep-sea hydrothermal vent: phage-plasmid interactions revealed by phage-FISH inApplied and environmental microbiology · 2025Article
- Review
- Evaluating phage lytic activity: from plaque assays to single-cell technologies.Frontiers in microbiology · 2025Review
- CleanBar: a versatile demultiplexing tool for split-and-pool barcoding in single-cell omics.ISME communications · 2025Article
- Contrasting defense strategies of oligotrophs and copiotrophs revealed by single-cell-resolved virus-host pairing of freshwater bacteria.ISME communications · 2025Article
- Spatial mapping of mobile genetic elements and their bacterial hosts in complex microbiomes.Nature microbiology · 2024Article
- An electrochemical biosensor for sensitive detection of live Salmonella in food via MXene amplified methylene blue signals and electrostatic immobilization of bacteriophages.Mikrochimica acta · 2024Article
- MinisculeSustainable microbiology · 2024Review
- Spatial Mapping of Mobile Genetic Elements and their Cognate Hosts in Complex Microbiomes.bioRxiv : the preprint server for biology · 2023Article
- Visualization of RNA virus infection in a marine protist with a universal biomarker.Scientific reports · 2023Article
- Detection of specific uncultured bacteriophages by fluorescence in situ hybridisation in pig microbiome.PloS one · 2023Article
- Diversity of novel archaeal viruses infecting methanogens discovered through coupling of stable isotope probing and metagenomics.Environmental microbiology · 2022Article
- Aminoglycoside Antibiotics Inhibit Phage Infection by Blocking an Early Step of the Infection Cycle.mBio · 2022Article
- Article
- NewVirus evolution · 2022Article
7 more citing papers are in PubMed but not listed here.
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Authors and funding
8 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Microbes drive the biogeochemical cycles that fuel planet Earth, and their viruses (phages) alter microbial population structure, genome repertoire, and metabolic capacity. However, our ability to understand and quantify phage-host interactions is technique-limited. Here, we introduce phageFISH - a markedly improved geneFISH protocol that increases gene detection efficiency from 40% to > 92% and is optimized for detection and visualization of intra- and extracellular phage DNA. The application of phageFISH to characterize infection dynamics in a marine podovirus-gammaproteobacterial host model system corroborated classical metrics (qPCR, plaque assay, FVIC, DAPI) and outperformed most of them to reveal new biology. PhageFISH detected both replicating and encapsidated (intracellular and extracellular) phage DNA, while simultaneously identifying and quantifying host cells during all stages of infection. Additionally, phageFISH allowed per-cell relative measurements of phage DNA, enabling single-cell documentation of infection status (e.g. early vs late stage infections). Further, it discriminated between two waves of infection, which no other measurement could due to population-averaged signals. Together, these findings richly characterize the infection dynamics of a novel model phage-host system, and debut phageFISH as a much-needed tool for studying phage-host interactions in the laboratory, with great promise for environmental surveys and lineage-specific population ecology of free phages.
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