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Front Microbiol. 2014 Dec 23;5:724. doi: 10.3389/fmicb.2014.00724. eCollection 2014.

Emerging methods to study bacteriophage infection at the single-cell level.

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Department of Ecology and Evolutionary Biology, University of Arizona Tucson, AZ, USA.
Department of Ecology and Evolutionary Biology, University of Arizona Tucson, AZ, USA ; Department of Molecular and Cellular Biology, University of Arizona Tucson, AZ, USA.


Bacteria and their viruses (phages) are abundant across diverse ecosystems and their interactions influence global biogeochemical cycles and incidence of disease. Problematically, both classical and metagenomic methods insufficiently assess the host specificity of phages and phage-host infection dynamics in nature. Here we review emerging methods to study phage-host interaction and infection dynamics with a focus on those that offer resolution at the single-cell level. These methods leverage ever-increasing sequence data to identify virus signals from single-cell amplified genome datasets or to produce primers/probes to target particular phage-bacteria pairs (digital PCR and phageFISH), even in complex communities. All three methods enable study of phage infection of uncultured bacteria from environmental samples, while the latter also discriminates between phage-host interaction outcomes (e.g., lytic, chronic, lysogenic) in model systems. Together these techniques enable quantitative, spatiotemporal studies of phage-bacteria interactions from environmental samples of any ecosystem, which will help elucidate and predict the ecological and evolutionary impacts of specific phage-host pairings in nature.


digital PCR; infection strategy; phageFISH; phage–bacteria interaction; single-cell amplified genome

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