Streptococcus thermophilus with Phage Challenge Genome Sequencing

CRISPR-Cas systems provide adaptive immunity against phage via spacer-encoded CRISPR RNAs that are complementary to invasive nucleic acids. We challenged Streptococcus thermophilus with a bacteriophage, and used PCR-based metagenomics to monitor phage-derived spacers daily for fifteen days in two experiments. Spacers that target the host chromosome were infrequent and strongly selected against, suggesting auto-immunity is lethal. In experiments that recovered over half a million spacers, we observed early dominance by a few spacer subpopulations and rapid oscillations in subpopulation abundances. In two CRISPR systems and in replicate experiments, a few spacers account for the majority of spacer sequences. Nearly all phage locations targeted by the acquired spacers have a proto-spacer adjacent motif (PAM), indicating PAMs are involved in spacer acquisition. We detect a strong and reproducible bias in the phage genome locations from which spacers derive. This may reflect selection for specific spacers based on location and effectiveness.