IV Jornadas Latinoamericanas de Bacteriófagos

Bacteria and bacteriophages (phages) undergo continuous coevolution, driving phage genetic diversification. This coevolution allows in vitro phage training approaches aimed at selecting therapeutically relevant phages with expanded host ranges. Although interactions between lytic phages and their bacterial hosts during phage training have been described in several studies, the participation of viral elements integrated into bacterial genomes (prophages) in shaping phage-bacteria dynamics is comparatively understudied. In this study, we investigated the population dynamics of prophages excised from clinical bacterial strains during an Appelmans coevolution experiment, and compared their resulting genome sequences with those of related, publicly available phages. Initial conditions for this experiment were ten Pseudomonas aeruginosa strains and a three-phage cocktail. Six samples were collected over a 30-day period. DNA was extracted and sequenced. In addition, two phage genomes (ph_IMP16E and ph_1136E) isolated at the end of the experiment were also sequenced. Our results revealed the persistent dominance of a complete prophage genome identified as Iggyvirus sp., which was detected at high abundance in all samples. A second genome corresponding to the excised prophage ph_IMP16E, classified as Hollowayvirus sp., was abundant mainly during the early rounds of the experiment. In contrast, phage ph_1136E, classified as Pbunavirus sp., emerged as a highly abundant population exclusively on day 30, suggesting late emergence. The three lytic phages included in the initial cocktail were detected only at low abundance and primarily during the early stages of the experiment. Together, these findings demonstrate that prophages can actively excise, proliferate, and dominate phage populations during coevolution experiments. This highlights an overlooked role of prophages in phage-bacteria coevolution, with important implications for experimental evolution studies and phage therapy strategies.