The bacterial immune system: identifying evolved defense adaptations

Recent years have witnessed a rapid expansion in bacterial defense mechanisms. Alongside established defenses against molecular parasites, hundreds of novel mechanisms are being described annually, contributing to an ever-expanding 'bacterial immune system'. Terms like 'defense' and 'immune' are often used as shorthand for an observed anti-infection phenotype, but can also imply an evolutionary adaptation with a specific anti-infection function. Despite the field's growth, no agreed-upon framework exists for identifying defense adaptations. When is a defense mechanism an evolved adaptation? Here, we review prior debates in evolutionary biology and propose a four-part framework to evaluate the case for a defense mechanism being an evolved adaptation. Beyond bacterial immunity, these criteria offer a research roadmap to address functional controversies across microbiology.