Sedentary chromosomal integrons as biobanks of bacterial anti-phage defence systems

Integrons are genetic systems that drive bacterial adaptation by acquiring, expressing and shuffling gene cassettes. While mobile integrons are well-known for spreading antibiotic resistance genes, the functions of the hundreds of cassettes carried by sedentary integrons remain largely unexplored. We show that many of these cassettes encode streamlined variants of known anti-phage systems that facilitate their inclusion in the integron. We also demonstrate that nearly 10% of the integron cassettes in the pandemic Vibrio cholerae strain encode novel anti-phage functions. Most of them have little or no similarity to previously known ones, with several providing defence through cell lysis or growth arrest. Our work highlights the stabilization and prevalence of streamlined anti-phage systems within integrons, making them an untapped treasure trove of defence mechanisms.