Major bacterial lineages are essentially devoid of CRISPR-Cas viral defence systems

David Burstein, Christine L. Sun, Christopher T. Brown, Itai Sharon, Karthik Anantharaman, Alexander J. Probst, Brian C. Thomas, Jillian F. Banfield*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

152 Scopus citations


Current understanding of microorganism-virus interactions, which shape the evolution and functioning of Earth's ecosystems, is based primarily on cultivated organisms. Here we investigate thousands of viral and microbial genomes recovered using a cultivation-independent approach to study the frequency, variety and taxonomic distribution of viral defence mechanisms. CRISPR-Cas systems that confer microorganisms with immunity to viruses are present in only 10% of 1,724 sampled microorganisms, compared with previous reports of 40% occurrence in bacteria and 81% in archaea. We attribute this large difference to the lack of CRISPR-Cas systems across major bacterial lineages that have no cultivated representatives. We correlate absence of CRISPR-Cas with lack of nucleotide biosynthesis capacity and a symbiotic lifestyle. Restriction systems are well represented in these lineages and might provide both non-specific viral defence and access to nucleotides.

Original languageEnglish
Article number10613
JournalNature Communications
StatePublished - 3 Feb 2016
Externally publishedYes


FundersFunder number
U.S. Department of Energy
European Molecular Biology Organization
University of CaliforniaDE-SC0004918
University of California
Office of Science
Biological and Environmental ResearchDE-AC02–05CH11231
Biological and Environmental Research
Joint Genome Institute


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