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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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Evenness of the CRISPR DRs and spacers in PD and PH samples. (A) Top 30 most abundant bacterial genera of DR source. Area of each bubble represented the relative abundance (by dividing total reads numbers of each sample and then normalized to 100,000) of DRs for each sample (column) and each genus (row). Red color represented PD (n = 9) and blue color represented the PH (n = 9) samples. (B) The most variegated spacers (classified to phage species by BLASTX) between the PD and PH groups (n = 9). Scales on x-axis represent relative abundance.
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Fig2: Evenness of the CRISPR DRs and spacers in PD and PH samples. (A) Top 30 most abundant bacterial genera of DR source. Area of each bubble represented the relative abundance (by dividing total reads numbers of each sample and then normalized to 100,000) of DRs for each sample (column) and each genus (row). Red color represented PD (n = 9) and blue color represented the PH (n = 9) samples. (B) The most variegated spacers (classified to phage species by BLASTX) between the PD and PH groups (n = 9). Scales on x-axis represent relative abundance.

Mentions: To characterize the subjects that play a role of defense, we ranked the DRs based on the relative abundance of DRs-assigned genera. The relative abundance of each genus was calculated by dividing total reads numbers of each sample and then normalized to 100,000. Top 30 most abundant genera of DR source were shown in the bubble chart (Fig. 2A), which accounted for 98.8% of the entire DRs. Common bacteria of human oral cavities such as Corynebacterium, Actinobacillus, Capnocytophaga, Streptococcus and Prevotella, were all included in this consortia. 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. Previous studies have reported that some bacteria were highly abundant in periodontitis, such as Prevotella, Selenomonas and Treponema (Wang et al., 2013). Porphyromonas gingivalis, Tannerella forsythia and Treponema denticola were also widely known as ‘the red complex’ to be involved in the periodontal diseases (Darveau, 2010). 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. This reveals that the ability of defense to phages is at least not weaker in healthy people than in patients.Figure 2


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)

Evenness of the CRISPR DRs and spacers in PD and PH samples. (A) Top 30 most abundant bacterial genera of DR source. Area of each bubble represented the relative abundance (by dividing total reads numbers of each sample and then normalized to 100,000) of DRs for each sample (column) and each genus (row). Red color represented PD (n = 9) and blue color represented the PH (n = 9) samples. (B) The most variegated spacers (classified to phage species by BLASTX) between the PD and PH groups (n = 9). Scales on x-axis represent relative abundance.
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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Fig2: Evenness of the CRISPR DRs and spacers in PD and PH samples. (A) Top 30 most abundant bacterial genera of DR source. Area of each bubble represented the relative abundance (by dividing total reads numbers of each sample and then normalized to 100,000) of DRs for each sample (column) and each genus (row). Red color represented PD (n = 9) and blue color represented the PH (n = 9) samples. (B) The most variegated spacers (classified to phage species by BLASTX) between the PD and PH groups (n = 9). Scales on x-axis represent relative abundance.
Mentions: To characterize the subjects that play a role of defense, we ranked the DRs based on the relative abundance of DRs-assigned genera. The relative abundance of each genus was calculated by dividing total reads numbers of each sample and then normalized to 100,000. Top 30 most abundant genera of DR source were shown in the bubble chart (Fig. 2A), which accounted for 98.8% of the entire DRs. Common bacteria of human oral cavities such as Corynebacterium, Actinobacillus, Capnocytophaga, Streptococcus and Prevotella, were all included in this consortia. 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. Previous studies have reported that some bacteria were highly abundant in periodontitis, such as Prevotella, Selenomonas and Treponema (Wang et al., 2013). Porphyromonas gingivalis, Tannerella forsythia and Treponema denticola were also widely known as ‘the red complex’ to be involved in the periodontal diseases (Darveau, 2010). 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. This reveals that the ability of defense to phages is at least not weaker in healthy people than in patients.Figure 2

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.