Restriction-modification systems and prophages drive genomic diversification in Priestia megaterium

Bacteria are frequently stressed by bacteriophages. Priestia megaterium is a bacterium of both agricultural and biotechnological importance, yet it has been unclear how the interplay between phage-imposed stress and bacterial immunity shapes the genome evolution and stability in P. megaterium. Through comparative genomics and methylome profiling, herein we show that restriction-modification (RM) systems are the dominant and ubiquitous barrier to lysogeny in P. megaterium. Intact prophages disproportionately carry anti-restriction genes, including multiple DNA methyltransferases and anti-restriction proteins, revealing the molecular strategies required to overcome the strong RM-mediated selective pressure inherent to this species. Prophage-derived genes are significantly enriched within the unique pangenome fraction and include auxiliary metabolic genes absent in host genomes. Moreover, prophage content strongly predicts phylogenetic structure in P. megaterium. Together, our findings demonstrate how defensive constraints, phage counter-adaptations, and horizontal acquisition jointly drive genomic diversification of P. megaterium.