The emergence of antibiotic-resistant bacterial “superbugs” is a looming crisis. Bacteriophages are viruses that have co-evolved a variety of strategies to kill bacteria over billions of years, and bacteriophage therapy is an alluring alternative to antibiotics.

However, the complex relationships between phages and their bacterial hosts make this a challenging endeavor, and existing bacteriophage therapies have largely been discovered by trial and error. To enable rational design of phage therapy, we have built an integrated computational and experimental framework to systematically characterize phage-encoded immune activators and inhibitors in clinically relevant bacteria.