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Clustered regularly interspaced short palindromic repeats (CRISPR), which are widely present in prokaryotic genomes (Grissa et al., 2007), belong to a family of DNA sequences characterized as short direct repeats (DR) separated by spacers (Jansen et al., 2002). CRISPR and CRISPR-associated (cas) genes are involved in resistance against exogenous sequences, and recognition of infected bacteriophages depends on the sequence similarity between spacers and targeted phage DNA segments (Barrangou et al., 2007). CRISPRs exhibited diversity in different microbial communities, and that may be the response to different phage infections (Tyson and Banfield, 2008). Dynamic change of spacers in CRIPSR reflects altered resistance to viruses (Andersson and Banfield, 2008), which may play important roles in shaping the structure and driving the evolution of microbial communities. Consequently, in addition to a tool designed for genome editing (Ghorbal et al., 2014), CRISPRs are widely used to demonstrate the dynamic changes of bacteria and phage communities. In human microbial communities, a study involving more than 700 datasets of metagenomic sequencing reported that only a few spacers were shared among different body sites or individuals although known CRISPRs can be found in most human oral microbiome (Rho et al., 2012). A study on oral microbiome also found that less than 2% spacers were shared between healthy people as a result of different people may encounter different virus population (Pride et al., 2011). Comparison between oral CRISPR sequences and virome further indicated that viruses and CRISPR diverged significantly among individuals and a large proportion of spacers were specific to each individual and time point (Pride et al., 2012). Another study on CRISPR suggested that spacers from oral bacteria were associated with oral viral ecology (Robles-Sikisaka et al., 2013). These results reveal that CRISPRs were under pressure of dynamic change of viruses in oral environment. Despite the potential effect on oral microbial ecology, little attention was paid to the comparison between CRISPRs under disease and health status until now. As oral cavity is a very complicated environment with diverse bacterial communities and periodontitis is a common disease closely related to microbial flora disorders (Belda-Ferre et al., 2012), we focused on the comparison of CRISPRs of bacterial communities under different periodontal status (in periodontal health and in periodontitis) in this study. To characterize the CRISPR compositions under different periodontal status and the relationship between healthy and periodontitis patients, we recruited 9 human subjects suffered from periodontitis and 9 health controls. They were selected from mature non-smoking females among 30∼60 years old without any other systemic disease. Periodontal status of these volunteers was clinical monitored at six sites per tooth by a periodontist. Probing depth and attachment loss were taken as the main classification criteria. Chronic periodontitis was selected whose periodontal pockets ≥4 mm and attachment loss ≥6 mm at more than 4 tooth sites. Periodontal health had no probing depth >2 mm or attachment loss >2 mm at any site. Dental plaques were individually collected at least 2 h after eating and 6 h after tooth brushing, and DNA was extracted and then was disrupted into fragments with ∼180 bp in length. To assess the composition of the microbial communities, they were sequenced to 2× 100 bp paired-end (PE) reads by an Illumina HiSeq 2000 sequencing instrument. In total, we got 176,931,096 reads for 18 samples (Table S1). Previous studies always assemble the reads to contigs to identify CRIPSR arrays, but part of the reads will be omitted in the assembly. To fulfill all the information of the reads, we identified DRs and spacers directly from raw reads by Crass 0.3.12 (Skennerton et al., 2013) which is on the basis of the distinctive structure of CRISPR. By this step we got 844 DR and 24,841 spacer sequences. The length of DRs and spacers mostly distributed from 30 bp to 40 bp (Fig. 1A). To classify these CRISPR elements, DRs and spacers were respectively aligned to bacteria and phage genomes in NCBI non-redundant (NR) database. Accordingly, DRs were assigned to 68 bacterial genera (Table S2), with 48 in periodontal health (PH) and 59 in periodontal disease (PD). Spacers were assigned to 444 phage species (444 in PH and 411 in PD, Table S3). Though

CRISPRs provide broad and robust protection to oral microbial flora of gingival health against bacteriophage challenge