Phase variation is an important mechanism contributing to the virulence of numerous human pathogens including Streptococcus pneumoniae. The Type I restriction modification system SpnD39III acts as a defence mechanism against infection by the novel temperate bacteriophage SpSL1. We have previously demonstrated that SpnD39III is phase variable and switches between six alleles with different DNA binding specificities and virulence phenotypes. Therefore, only bacteriophages displaying the same methylation pattern as the host are able to infect and undergo the lytic cycle. We are investigating the effect of bacteriophage infection on the rate of switching between different alleles and hope to determine if certain allele types confer a selective advantage in their ability to restrict bacteriophages. RNAseq data also show distinct transcriptional responses by both bacteria and virus to infection with self and non-self bacteriophages. These studies should help us to further understand the role of the Type I system in S. pneumoniae and contribute to our understanding of the complex dynamics of the bacterial-virus interaction.