Serine recombinases are conserved genetic markers of antiphage defense systems.

Antiphage defense systems confer bacteriophage (phage) resistance in bacteria. Renewed interest in phage therapy indicates a need to understand the breadth and molecular mechanisms of antiphage defenses. Traditionally, strategies to identify antiphage defenses lack throughput or are biased toward model bacteria. Herein, we developed a bioinformatic pipeline that uses a serine recombinase to identify known and unknown antiphage defense systems. Using this approach to query reference genomes and metagenomes, we show that serine recombinase genes are genetically linked to antiphage defense systems and serve as bait for finding these systems across diverse bacterial phyla. Using co-transcription predictions and statistical analysis of protein domain abundances, we experimentally validated our informatic approach by discovering that KAP P-loop NTPases are fused to putative antiphage effector domains and prokaryotic Schlafen proteins support phage defense. Our work shows that serine recombinases are a reliable genetic marker for the discovery of antiphage defenses across diverse bacterial phyla.