Revisiting the life cycle of temperate phages

Temperate bacteriophages (phages) are ubiquitous viruses that co-evolve with their bacterial hosts. They are defined by their ability to undergo two distinct life cycles: the lytic cycle, in which the phage produces more viral copies and kills the host, and the lysogenic cycle, in which the temperate phage exists as a prophage in the host. Temperate phages have long served as fundamental models in microbiology, genetics and evolutionary biology research, and their life cycles are among the most thoroughly characterized in virology. Historically, the phage life cycle was viewed primarily through the lens of how excision, replication and packaging drive the formation of infective particles. Although it captures the central processes of the phage life cycle, this narrow perspective overlooks the full range of interactions with the host and with other mobile genetic elements. In this Review, we re-examine the temperate phage life cycle in light of emerging insights that expand on this framework with unanticipated complexities. We argue that many properties of (pro)phages should be viewed as integral parts of their life cycle instead of being discussed separately. This holistic view is important to fully appreciate the intricacies of the temperate phage life cycle and the key roles of these viruses in microbiology and biotechnological applications.