Systems Analysis of The Physiological Determinants of Phage Infection Dynamics

Bacteriophages (phages) are viruses that infect and kill bacteria, playing a crucial role in shaping microbial communities. They are also emerging as precision tools for combating antibiotic-resistant bacteria, targeted biocontrol, and microbiome modulation.As obligate parasites, phages rely on the physiological state of their bacterial hosts to progress through infection stages. However, the mechanisms by which host physiology affects the success of phage infection within cells and how host variability impacts phage effectiveness in eradicating bacterial populations remain poorly understood. This knowledge gap limits our ability to predict phage performance across environments and engineer them for reliable use.Progress has been hindered by the lack of tools to link host cell physiology to phage infection dynamics and to connect single-cell variability to population-level outcomes. To address this, we have developed innovative methodologies, including a high-throughput imaging system for real-time tracking of phage infection progression within individual infected cells and the microCOSM platform, which integrates single-cell responses with population-level dynamics. Using these systems, combined with data-driven models and model-guided experiments, we will address three key questions:How do host physiological factors, such as metabolism and stress responses, govern phage infection success and progression at the single-cell level?How does variability in host cell physiology shape phage efficacy at the population level, and when do phage-tolerant subpopulations emerge?How do changes in the physical and biochemical nature of the host’s environment affect phage efficacy and how can we leverage physiological perturbations to steer infection outcome?This study will uncover the physiological determinants of phage efficacy and phage tolerance, enabling the design of phages as precise, reliable tools for combating antibiotic resistance and modulating microbiomes.