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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.

Author information

1
Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, California 94720, USA.
2
Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA.
3
Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California 94720, USA.
4
Department of Environmental Science, Policy and Management, University of California, Berkeley, California 94720, USA.

Abstract

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.

PMID:
26837824
PMCID:
PMC4742961
DOI:
10.1038/ncomms10613
[Indexed for MEDLINE]
Free PMC Article

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