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Nat Commun. 2016 Feb 3;7:10613. doi: 10.1038/ncomms10613.

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

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Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, California 94720, USA.
Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA.
Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California 94720, USA.
Department of Environmental Science, Policy and Management, University of California, Berkeley, California 94720, USA.


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.

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