Digital Phage Biology in Droplets

Abstract

Since their discovery, bacteriophages - viruses that infect bacteria - have been an invaluable source of insight for molecular biology and have provided a plethora of molecular components for biotechnology. Driven by the imminent global antibiotic crisis, interest in using bacteriophages as antimicrobial agents has strongly increased in the past few years. While standard quantification of phage counts and infectivity by 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 introduce a novel high-throughput method using droplet microfluidics to quantify individual phage infection events, enhancing the understanding of phage-host dynamics at the single-event level. By co-encapsulating individual phages and bacteria in microfluidic droplets, we can control key experimental parameters such as exposure time and the ratio of phages to bacteria. Our system allows for precise quantification of lysis events and the direct observation of lysis kinetics unaffected by the continuous release of progeny phages that is typical in bulk cultures. Moreover, our method is potentially applicable to any phage-host pair. Our findings suggest that droplet microfluidics can provide a more accurate and dynamic understanding of phage biology. This approach could be particularly valuable in the development of phage-based antimicrobial strategies in the face of rising antibiotic resistance.