PRISM: A platform for illuminating viral dark matter

The exploration of bacteriophage diversity remains constrained by reliance on conventional plaque assays, which bias discovery toward phages that form visible plaques and propagate efficiently. The discovery process, as well as measuring correct phage concentrations and phage resistance frequencies, are also time-consuming and labor intensive. Here, we present PRISM (Phage Recovery and Investigation in Single-droplet Microenvironments), a droplet microfluidics-based, plating-independent platform for the high-throughput isolation, quantification, and characterization of bacteriophages. By encapsulating phage–host interactions in water-in-oil microdroplets at single-phase resolution, and then coupling them with fluorescence-based detection and sorting at million-droplet scale, PRISM enables rapid identification of novel phages, including those that evade detection in conventional assays. We demonstrate PRISM’s capabilities across several key applications: (i) recovery of both novel “plaquing” and “non-plaquing” Salmonella phages from a concentrated environmental sample, where PRISM recovered multiple representatives of a non-plaquing genus completely missed by conventional plating-based approaches; (ii) accurate titering of poor-plaquing phages such as Rhodococcus phage ReqiDocB7, for which PRISM reported a 2-fold higher titer than conventional plaque assays; and (iii) plating-free determination of phage resistance frequency, with PRISM yielding resistance and lysogeny frequencies (e.g., 1 in 4.4 × 10 5 cells for T7 Escherichia phage resistance and 1 in 21 cells for Escherichia Lambda phage lysogeny) that closely match conventional estimates. These data highlight PRISM’s enhanced resolution and accuracy, as well as its ability to detect rare, non-plaquing, or slow-replicating phages, in a high speed and automated fashion, thereby underscoring the platform’s power to access viral “dark matter” traditionally overlooked using conventional methods.