Phage lambda has a spontaneous excision rate of 106 per cell division under non-stressful conditions, which can increase by orders of magnitude under stressful conditions. Thus, it is predicted that functional prophages will not persist in the bacterial chromosome for an extended time period. In a recent study, we could confirm these predictions by demonstrating that, driven by environment-specific sequences of selective sweeps, prophages can rapidly disappear from a lysogen population, if prophage-associated costs outweigh their benefits (Bailey at al. 2024). While our study highlights the complexity of selection pressures that act on functional prophages in vitro, we know little about the long-term maintenance of functional prophages in natural populations. This project explores the persistence and evolution of prophages in natural bacterial communities. To do so, we are conducting a prospective cohort study during which we are repeatedly sampling resident E. coli from human gut microbiomes. By combining the cohort study with in vitro gut mesocosms experiments and advanced bioinformatic analyses we address fundamental questions in prophage ecology and evolution: are prophages persistent or transient? Which ecological and evolutionary factors promote or constrain prophage persistence in natural communities over time?

https://spp2330.de/project-wendling/