Anti-phage defense systems in bacteria: molecular mechanisms and their role in shaping phage therapy strategies

Bacteria and phages are engaged in a persistent evolutionary struggle. To survive constant phage predation, bacteria have evolved a highly diverse and multi-layered immune arsenal that determines the success of therapeutic phage infection. Bacterial defenses include receptor blockade, DNA restriction systems, CRISPR-Cas adaptive immunity, and secondary messenger signaling systems that induce effector-mediated cell death. Recent mechanistic advances have elucidated systems such as Thoeris (gcADPR-activated SIR2 effectors depleting NAD⁺), CBASS (cyclic nucleotide-activated effectors disrupting cell integrity), and toxin-antitoxin systems (e.g., ShosTA disrupting purine metabolism). These defenses directly impact phage therapy outcomes. However, phages have evolved sophisticated countermeasures, including RNA-based anti-CRISPRs and enolase hijacking, while engineered phages carrying synthetic anti-defense proteins are being developed to overcome bacterial immunity. The present review integrates defense system classification, phage counter-defense evolution, and their associations with phage therapy outcomes within a unified framework for phage selection and engineering. This review provides a scientific basis for defense-informed phage selection, rational phage engineering, and the design of future clinical trials against multidrug-resistant infections.