CRISPR‐Cas, Horizontal Gene Transfer, and the Flexible (Pan) Genome

Most known CRISPR-Cas systems primarily provide acquired, heritable immunity to bacteria and archaea against invasion by selfish DNA elements. Consequently, the main activity of these systems is to destroy incoming DNA that matches their immune memory–spacers within the CRISPR array. This chapter discusses, the evidence for and against such a trade off between CRISPR-Cas and the ability to maintain high genomic diversity (and the benefits that come with it) via horizontal gene transfer. Most viruses that infect bacteria and archaea and are capable of a temperate (nonlytic) lifestyle can integrate into the genomes of their hosts. Integrated proviruses represent an important part of microbial pangenomes, can provide a benefit to the host under a variety of stresses and environmental conditions and can contribute to bacterial virulence.