Analysis of streptococcal CRISPRs from human saliva reveals substantial sequence diversity within and between subjects over time
- David T. Pride1,9,
- Christine L. Sun2,
- Julia Salzman3,
- Nitya Rao4,
- Peter Loomer5,
- Gary C. Armitage5,
- Jillian F. Banfield6 and
- David A. Relman4,7,8
- 1Department of Pathology, University of California, San Diego, La Jolla, California 92093, USA;
- 2Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA;
- 3Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, USA;
- 4Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, California 94305, USA;
- 5Division of Periodontology, School of Dentistry, University of California, San Francisco, California 94143, USA;
- 6Department of Environmental Science, Policy, and Management, University of California, Berkeley, California 94720, USA;
- 7Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, California 94305, USA;
- 8Veterans Affairs Palo Alto Health Care System, Palo Alto, California 94304, USA
Abstract
Viruses may play an important role in the evolution of human microbial communities. Clustered regularly interspaced short palindromic repeats (CRISPRs) provide bacteria and archaea with adaptive immunity to previously encountered viruses. Little is known about CRISPR composition in members of human microbial communities, the relative rate of CRISPR locus change, or how CRISPR loci differ between the microbiota of different individuals. We collected saliva from four periodontally healthy human subjects over an 11- to 17-mo time period and analyzed CRISPR sequences with corresponding streptococcal repeats in order to improve our understanding of the predominant features of oral streptococcal adaptive immune repertoires. We analyzed a total of 6859 CRISPR bearing reads and 427,917 bacterial 16S rRNA gene sequences. We found a core (ranging from 7% to 22%) of shared CRISPR spacers that remained stable over time within each subject, but nearly a third of CRISPR spacers varied between time points. We document high spacer diversity within each subject, suggesting constant addition of new CRISPR spacers. No greater than 2% of CRISPR spacers were shared between subjects, suggesting that each individual was exposed to different virus populations. We detect changes in CRISPR spacer sequence diversity over time that may be attributable to locus diversification or to changes in streptococcal population structure, yet the composition of the populations within subjects remained relatively stable. The individual-specific and traceable character of CRISPR spacer complements could potentially open the way for expansion of the domain of personalized medicine to the oral microbiome, where lineages may be tracked as a function of health and other factors.
Footnotes
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↵9 Corresponding author.
E-mail dpride{at}ucsd.edu; fax (858) 534-5724.
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[Supplemental material is available for this article. The sequence data from this study have been submitted to the NCBI Sequence Read Archive (http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi) under accession no. SRA024393.1.]
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Article published online before print. Article, Supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.111732.110.
- Received June 14, 2010.
- Accepted October 28, 2010.
- Copyright © 2011 by Cold Spring Harbor Laboratory Press
