The bacterial immune system: identifying evolved defense adaptations

Ellinor Alseth , Sam P Brown

The last few years have witnessed a rapid expansion of reported bacterial defense mechanisms. Alongside established mechanisms of defense against molecular parasites (e.g. CRISPR-Cas, restriction-modification), hundreds of novel defenses are being described each year, 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 they can also be read as implying an evolutionary adaptation with a specific anti-infection function. Despite the field’s rapid progress, there is currently no widely agreed framework for identifying bacterial defense adaptations. The question then emerges: when is a defense mechanism an evolved adaptation? Here, we leverage prior debates in evolutionary biology over adaptation to propose four main ‘evidence’ criteria, spanning bioinformatic comparative tests, experimental fitness assays, evolutionary theory, and their integration. Together, these criteria can strengthen the case that a defense mechanism is an evolved defensive adaptation. We highlight how these criteria are met for the most established model systems such as CRISPR-Cas, and how they also provide a clear research agenda for other newly identified defense mechanisms. Beyond bacterial immunity, these criteria offer a research roadmap to address functional controversies across microbiology.