S. thermophilus satellite phages are induced by virulent phages

A satellite phage (SP) typically resides within repeat regions (attL and attR sites) of a bacterial genome. Its genome ranges from 7 to 20-kb and includes genes encoding for an integrase along with regulatory and DNA replication functions. However, it lacks genes associated with viral structural proteins. Streptococcus thermophilus (S.t.) is extensively utilized in the production of yogurt and specialty cheeses. Intriguingly, the majority of S.t. strains harbor a SP while only a few possess a complete prophage. This observation suggests that SPs may offer advantages to their hosts. In this study, we demonstrated that SPs of S.t. can excise from the bacterial chromosome after an overnight incubation. Furthermore, we also found that they can also be induced by virulent phages. By leveraging CRISPR-Cas9, we successfully selected S.t. cells devoid of any SPs. Additionally, we successfully mobilized a SP to a delta-SP strain, using only natural competence, bypassing the need for a helper phage. The resulting strain exhibited increased resistance to virulent phages. Through the isolation of phage mutants escaping the resistance phenotype, we pinpointed a specific phage protein responsible for the induction of SP. Our study introduces a novel natural approach to develop phage-resistant strains.