We study how pathogens evolve in response to abiotic and biotic environmental interactions with a specific focus on one of the most important players that influence a bacterium’s pathogenicity: mobile genetic elements (MGEs), including plasmids and phages, which can provide their bacterial hosts with virulence and/ or antibiotic resistance genes. Taking an evolutionary approach, we investigate the intricate dynamics of prophages, their role in the emergence of gastrointestinal infections and in the evolution and spread of antibiotic resistance. Furthermore, we explore the potential of prophages in phage therapy, aiming to develop novel treatments for drug-resistant bacterial infections.