CRISPR-Cas systems to probe ecological diversity and host-viral interactions

Nicole L. Held, Lauren M. Childs, Michelle Davison, Joshua S. Weitz, Rachel J. Whitaker, Devaki Bhaya

Research output: Chapter in Book/Report/Conference proceedingChapter


A key feature of the CRISPR-Cas defense system is the ability of the host to rapidly acquire novel spacers from invasive foreign genetic elements such as plasmids, viruses, or transposons. Consequently, host CRISPR loci have the potential to provide time-resolved information about exposure to foreign genetic elements as well as fine-scale ecological diversity. Furthermore, viral genomes can mutate rapidly, allowing viruses to circumvent the host CRISPR-encoded immunity system, which relies on close matches between spacers and incoming nucleic acids. Thus, CRISPR-Cas systems may drive complex, coevolving relationships between bacteria or archaea and viruses. We discuss how ecologically based approaches, in both natural and experimental systems, provide unique insights into host and viral diversity and horizontal gene transfer of CRISPR loci. We critically review recent attempts to model host-viral coevolutionary dynamics in the context of CRISPR loci. Finally, we highlight the future directions in which experimental analyses of host-viral coevolution can be fruitfully combined with theoretical approaches.

Original languageEnglish (US)
Title of host publicationCRISPR-Cas Systems
Subtitle of host publicationRNA-Mediated Adaptive Immunity in Bacteria and Archaea
EditorsRodolphe Barrangou, John van der Oost
Number of pages30
ISBN (Electronic)9783642346576
ISBN (Print)9783642346569
StatePublished - Jan 1 2013


  • strain-specific spacers

ASJC Scopus subject areas

  • General Immunology and Microbiology


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