Global transcription of CRISPR loci in the human oral cavity

BMC Genomics

David T Pride²  Tobias K Boehm³  Mayuri Naidu¹  Tasha M Santiago-Rodriguez¹  Melissa Ly¹  Andrew G Lum¹ 

[1] Department of Pathology, University of California, San Diego, 9500 Gilman Drive, MC 0612, La Jolla 92093-0612, CA, USA;Department of Medicine, University of California, San Diego, 9500 Gilman Drive, MC 0612, La Jolla 92093-0612, CA, USA;College of Dental Medicine, Western University of Health Sciences, 309 E Second Street, Pomona 91766, CA, USA

关键词: Virus;    Virome;    Oral microbiome;    Microbiome;    CRISPR;   

Others  :  1203906
DOI  :  10.1186/s12864-015-1615-0

 received in 2014-07-07, accepted in 2015-05-05,  发布年份 2015

【 摘 要 】

Background

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) are active in acquired resistance against bacteriophage and plasmids in a number of environments. In the human mouth, CRISPR loci evolve to counteract oral phage, but the expression of these CRISPR loci has not previously been investigated. We sequenced cDNA from CRISPR loci found in numerous different oral bacteria and compared with oral phage communities to determine whether the transcription of CRISPR loci is specifically targeted towards highly abundant phage present in the oral environment.

Results

We found that of the 529,027 CRISPR spacer groups studied, 88 % could be identified in transcripts, indicating that the vast majority of CRISPR loci in the oral cavity were transcribed. There were no strong associations between CRISPR spacer repertoires and oral health status or nucleic acid type. We also compared CRISPR repertoires with oral bacteriophage communities, and found that there was no significant association between CRISPR transcripts and oral phage, regardless of the CRISPR type being evaluated. We characterized highly expressed CRISPR spacers and found that they were no more likely than other spacers to match oral phage. By reassembling the CRISPR-bearing reads into longer CRISPR loci, we found that the majority of the loci did not have spacers matching viruses found in the oral cavities of the subjects studied. For some CRISPR types, loci containing spacers matching oral phage were significantly more likely to have multiple spacers rather than a single spacer matching oral phage.

Conclusions

These data suggest that the transcription of oral CRISPR loci is relatively ubiquitous and that highly expressed CRISPR spacers do not necessarily target the most abundant oral phage.

【 授权许可】

   
2015 Lum et al.; licensee BioMed Central.

【 图 表 】

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