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Bacteria and archaea have evolved an adaptive, heritable immune system thatrecognizes and protects against viruses or plasmids. This system, known as theCRISPR-Cas system, allows the host to recognize and incorporate short foreignDNA or RNA sequences, called `spacers' into its CRISPR system. Spacers in theCRISPR system provide a record of the history of bacteria and phagecoevolution. We use a physical model to study the dynamics of this coevolutionas it evolves stochastically over time. We focus on the impact of mutation andrecombination on bacteria and phage evolution and evasion. We discuss theeffect of different spacer deletion mechanisms on the coevolutionary dynamics.We make predictions about bacteria and phage population growth, spacerdiversity within the CRISPR locus, and spacer protection against the phagepopulation.

Physical Model of the Immune Response of Bacteria Against Bacteriophage Through the Adaptive CRISPR-Cas Immune System