Quantifying phage-host dynamics using droplet microfluidics

Abstract Since their discovery, bacteriophages—viruses that infect bacteria—have been invaluable to molecular biology and biotechnology. Renewed interest in phage-based antimicrobials, driven by the global antibiotic resistance crisis, highlights the need for improved quantitative tools. While conventional double-layer plaque assays (DLA) have provided foundational insights, they are limited by their inability to monitor infection dynamics over time and the inflexibility in experimental setups. Here, we present a high-throughput droplet microfluidics platform to quantify individual phage infection events. By co-encapsulating individual phages and bacteria in microfluidic droplets, we precisely control key experimental parameters such as exposure time and the ratio of phages to bacteria. This approach enables direct quantification of lysis events and measurement of lysis kinetics without interference from further progeny-driven infection processes inherent to bulk cultures. Applicable to diverse phage-host systems, this method offers a dynamic and accurate framework for studying phage biology and supports the development of phage-based antimicrobial strategies.