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

Zhou H, Zhao H, Zheng J, Gao Y, Zhang Y, Zhao F, Wang J - Protein Cell (2015)

View Article: PubMed Central - PubMed

Affiliation: Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China.

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Clustered regularly interspaced short palindromic repeats (CRISPR), which are widely present in prokaryotic genomes (Grissa et al., ), belong to a family of DNA sequences characterized as short direct repeats (DR) separated by spacers (Jansen et al., )... 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., )... 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... To classify these CRISPR elements, DRs and spacers were respectively aligned to bacteria and phage genomes in NCBI non-redundant (NR) database... When the oral microbial flora of patients suffered from chronic periodontitis encountered bacteriophages corresponding to the distinctive spacers hold only by healthy people, it is easier to be attacked and might not maintain a stable bacterial community, and microbiota disequilibrium was exactly the reason causing or increasing the susceptibility of periodontal diseases (Curtis et al., )... However, Streptococcus and Prevotella, which usually account for the dominant of oral microbiota, are not the leading contributors of DRs... This result suggests the abundance of CRISPRs of microbial community in human oral cavities is not only determined by the amount of bacteria, but also closely related with species composition... Porphyromonas gingivalis, Tannerella forsythia and Treponema denticola were also widely known as ‘the red complex’ to be involved in the periodontal diseases (Darveau, )... Although we found that the DR abundance of several genera (e.g., Prevotella, Selenomonas, Treponema and Tannerella) in PD samples was a little higher than that in PH samples, we did not observe any of them with significant difference by Mann-Whitney U test... In conclusion, by systematical analysis of CRISPR using whole genome sequencing data for oral microbiome, we found the composition of DRs and spacers are significantly different between PD and PH... Discrete dots indicated the bacteriophages that can better separate the samples (PSD 603 KB) The most variegated DRs (classified to bacterial genera by BLASTX) between the PD and PH samples... Red color represented PD (n = 9) and blue color represented PH (n = 9) samples... Scales on x-axis represent relative abundance (PSD 529 KB)

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The composition of the CRISPRs in samples collected from patients with chronic periodontitis (PD) and people with healthy gingiva (PH). (A) The distribution of the length of DRs (left panel) and spacers (right panel) identified from metagenomic sequencing data. (B) Numbers of DRs (left panel) and spacers (right panel) in PD (red circle) and PH (blue circle). (C) Shannon-Wiener diversities of the DRs in PD (red box), PH (blue box) and all (white box). (D) Shannon-Wiener diversities of the spacers. (E) Bray-Curtis diversities of the DRs. (F) Bray-Curtis diversities of the spacers. The boxes represent the interquartile range between the first and third quartiles. The whiskers denote the lowest and highest values within the interquartile ranges of the first and third quartiles. The thick lines inside the boxes represent the medians.
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Fig1: The composition of the CRISPRs in samples collected from patients with chronic periodontitis (PD) and people with healthy gingiva (PH). (A) The distribution of the length of DRs (left panel) and spacers (right panel) identified from metagenomic sequencing data. (B) Numbers of DRs (left panel) and spacers (right panel) in PD (red circle) and PH (blue circle). (C) Shannon-Wiener diversities of the DRs in PD (red box), PH (blue box) and all (white box). (D) Shannon-Wiener diversities of the spacers. (E) Bray-Curtis diversities of the DRs. (F) Bray-Curtis diversities of the spacers. The boxes represent the interquartile range between the first and third quartiles. The whiskers denote the lowest and highest values within the interquartile ranges of the first and third quartiles. The thick lines inside the boxes represent the medians.

Mentions: 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.Figure 1


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

Zhou H, Zhao H, Zheng J, Gao Y, Zhang Y, Zhao F, Wang J - Protein Cell (2015)

The composition of the CRISPRs in samples collected from patients with chronic periodontitis (PD) and people with healthy gingiva (PH). (A) The distribution of the length of DRs (left panel) and spacers (right panel) identified from metagenomic sequencing data. (B) Numbers of DRs (left panel) and spacers (right panel) in PD (red circle) and PH (blue circle). (C) Shannon-Wiener diversities of the DRs in PD (red box), PH (blue box) and all (white box). (D) Shannon-Wiener diversities of the spacers. (E) Bray-Curtis diversities of the DRs. (F) Bray-Curtis diversities of the spacers. The boxes represent the interquartile range between the first and third quartiles. The whiskers denote the lowest and highest values within the interquartile ranges of the first and third quartiles. The thick lines inside the boxes represent the medians.
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4491054&req=5

Fig1: The composition of the CRISPRs in samples collected from patients with chronic periodontitis (PD) and people with healthy gingiva (PH). (A) The distribution of the length of DRs (left panel) and spacers (right panel) identified from metagenomic sequencing data. (B) Numbers of DRs (left panel) and spacers (right panel) in PD (red circle) and PH (blue circle). (C) Shannon-Wiener diversities of the DRs in PD (red box), PH (blue box) and all (white box). (D) Shannon-Wiener diversities of the spacers. (E) Bray-Curtis diversities of the DRs. (F) Bray-Curtis diversities of the spacers. The boxes represent the interquartile range between the first and third quartiles. The whiskers denote the lowest and highest values within the interquartile ranges of the first and third quartiles. The thick lines inside the boxes represent the medians.
Mentions: 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.Figure 1

View Article: PubMed Central - PubMed

Affiliation: Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China.

AUTOMATICALLY GENERATED EXCERPT
Please rate it.

Clustered regularly interspaced short palindromic repeats (CRISPR), which are widely present in prokaryotic genomes (Grissa et al., ), belong to a family of DNA sequences characterized as short direct repeats (DR) separated by spacers (Jansen et al., )... 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., )... 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... To classify these CRISPR elements, DRs and spacers were respectively aligned to bacteria and phage genomes in NCBI non-redundant (NR) database... When the oral microbial flora of patients suffered from chronic periodontitis encountered bacteriophages corresponding to the distinctive spacers hold only by healthy people, it is easier to be attacked and might not maintain a stable bacterial community, and microbiota disequilibrium was exactly the reason causing or increasing the susceptibility of periodontal diseases (Curtis et al., )... However, Streptococcus and Prevotella, which usually account for the dominant of oral microbiota, are not the leading contributors of DRs... This result suggests the abundance of CRISPRs of microbial community in human oral cavities is not only determined by the amount of bacteria, but also closely related with species composition... Porphyromonas gingivalis, Tannerella forsythia and Treponema denticola were also widely known as ‘the red complex’ to be involved in the periodontal diseases (Darveau, )... Although we found that the DR abundance of several genera (e.g., Prevotella, Selenomonas, Treponema and Tannerella) in PD samples was a little higher than that in PH samples, we did not observe any of them with significant difference by Mann-Whitney U test... In conclusion, by systematical analysis of CRISPR using whole genome sequencing data for oral microbiome, we found the composition of DRs and spacers are significantly different between PD and PH... Discrete dots indicated the bacteriophages that can better separate the samples (PSD 603 KB) The most variegated DRs (classified to bacterial genera by BLASTX) between the PD and PH samples... Red color represented PD (n = 9) and blue color represented PH (n = 9) samples... Scales on x-axis represent relative abundance (PSD 529 KB)

No MeSH data available.


Related in: MedlinePlus