Open Access Research article

Conservation of streptococcal CRISPRs on human skin and saliva

Refugio Robles-Sikisaka1, Mayuri Naidu1, Melissa Ly1, Julia Salzman2, Shira R Abeles3, Tobias K Boehm4 and David T Pride13*

Author Affiliations

1 Department of Pathology, University of California, San Diego, 9500 Gilman Drive, MC 0612, La Jolla, CA 92093-0612, USA

2 Department of Biochemistry, Stanford University School of Medicine, 279 Campus Drive, Stanford, CA 94305-5329, USA

3 Department of Medicine, University of California, San Diego, 9500 Gilman Drive, MC 0612, La Jolla, CA 92093-0612, USA

4 College of Dental Medicine, Western University of Health Sciences, 309 E Second Street, Pomona, CA 91766, USA

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BMC Microbiology 2014, 14:146  doi:10.1186/1471-2180-14-146

Published: 6 June 2014



Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) are utilized by bacteria to resist encounters with their viruses. Human body surfaces have numerous bacteria that harbor CRISPRs, and their content can provide clues as to the types and features of viruses they may have encountered.


We investigated the conservation of CRISPR content from streptococci on skin and saliva of human subjects over 8-weeks to determine whether similarities existed in the CRISPR spacer profiles and whether CRISPR spacers were a stable component of each biogeographic site. Most of the CRISPR sequences identified were unique, but a small proportion of spacers from the skin and saliva of each subject matched spacers derived from previously sequenced loci of S. thermophilus and other streptococci. There were significant proportions of CRISPR spacers conserved over the entire 8-week study period for all subjects, and salivary CRISPR spacers sampled in the mornings showed significantly higher levels of conservation than any other time of day. We also found substantial similarities in the spacer repertoires of the skin and saliva of each subject. Many skin-derived spacers matched salivary viruses, supporting that bacteria of the skin may encounter viruses with similar sequences to those found in the mouth. Despite the similarities between skin and salivary spacer repertoires, the variation present was distinct based on each subject and body site.


The conservation of CRISPR spacers in the saliva and the skin of human subjects over the time period studied suggests a relative conservation of the bacteria harboring them.

CRISPR; Skin microbiome; Saliva microbiome; Virome; Virus