Characterization of bacteriophage communities and CRISPR profiles from dental plaque - PubMed (original) (raw)

Characterization of bacteriophage communities and CRISPR profiles from dental plaque

Mayuri Naidu et al. BMC Microbiol. 2014.

Abstract

Background: Dental plaque is home to a diverse and complex community of bacteria, but has generally been believed to be inhabited by relatively few viruses. We sampled the saliva and dental plaque from 4 healthy human subjects to determine whether plaque was populated by viral communities, and whether there were differences in viral communities specific to subject or sample type.

Results: We found that the plaque was inhabited by a community of bacteriophage whose membership was mostly subject-specific. There was a significant proportion of viral homologues shared between plaque and salivary viromes within each subject, suggesting that some oral viruses were present in both sites. We also characterized Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) in oral streptococci, as their profiles provide clues to the viruses that oral bacteria may be able to counteract. While there were some CRISPR spacers specific to each sample type, many more were shared across sites and were highly subject specific. Many CRISPR spacers matched viruses present in plaque, suggesting that the evolution of CRISPR loci may have been specific to plaque-derived viruses.

Conclusions: Our findings of subject specificity to both plaque-derived viruses and CRISPR profiles suggest that human viral ecology may be highly personalized.

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Figures

Figure 1

Figure 1

Percentages of contigs with viral homologues (Panels A and B) and mappings of virome reads to select bacterial genomes (Panels C and D). Homologues to genes involved in virulence are represented in purple, replication and integration in yellow, and all others including structural and hypothetical genes in orange. Contigs from saliva are shown in Panel A and contigs from dental plaque are shown in Panel B. Read mappings of virome reads from subject #4 to Streptococcus pseudopneumoniae IS7493 is shown in Panel C and read mappings from subject #3 to Streptococcus gallolyticus UCN34 is shown in Panel D. Putative ORFs are represented by yellow arrows and the annotation provided above each ORF. Those ORFs without annotation represent hypothetical coding sequences. The relative proportion of reads and location where the reads map is demonstrated in blue in Panel C and gold in Panel D. Coordinates within each genome also are demonstrated at the top of each diagram.

Figure 2

Figure 2

Mappings of virome reads from each subject to select viruses. Panel A - the virome read mappings from subject #1 dental plaque to Actinomyces phage AV-1, Panel B - the virome read mappings from subject #2 to Streptococcus phage DP-1, Panel C – the virome read mappings from subject #3 to Enterobacteria phage P7, and Panel D – the virome read mappings from subject #4 to Enterobacteria phage Lambda. The _y_-axis demonstrates the total number of reads mapping to individual segments of each virus.

Figure 3

Figure 3

Heatmap of virome contigs (Panel A) and principal coordinates analysis of virome contigs (Panel B) and bacteria 16S rRNA (Panel C) from each subject and biogeographic site. Panel A - Each row represents a unique homologue, and the columns represent viromes from each subject and sample type. The intensity scale bar is located below the heatmap. In Panels B and C, subject #1 is represented in green, subject #2 in red, subject #3 in gold, and subject #4 in blue. Saliva is represented by squares and dental plaque by circles.

Figure 4

Figure 4

Heatmap and principal coordinates analysis of SGI (Panels A and C) and SGII (Panels B and D) CRISPR spacer groups from all subjects and sample types. Panels A and B - Each row represents a unique CRISPR spacer group, and the columns represent each subject and biogeographic site. The intensity scale bar is located to the right of each heatmap. Panels C and D - Principal coordinates analysis of CRISPR spacer groups. Subject #1 is represented in green, subject #2 in red, subject #3 in gold, and subject #4 in blue. Saliva is represented by squares and plaque by circles.

Figure 5

Figure 5

Radial diagram of SGI (Panel A) and SGII (Panel B) CRISPR spacer groups with streptococcal homologues. The relative number of CRISPR spacer groups homologous to each sequence is drawn to scale. Yellow represents streptococcal viruses, green represents streptococcal genomes, and red represents streptococcal plasmids.

Figure 6

Figure 6

Diagram of CRISPR spacers with exact matches and their locations along the genomes of several streptococcal bacteriophage. SGII CRISPR spacer mappings are shown in Panels A, C, and E, while SGI CRISPR spacer mappings are shown in Panels B, D, and F. Bacteriophage SM-1 is shown in Panels A and B, phage PH-10 is shown in Panels C and D, and phage CP-1 is shown in Panels E and F. The genes in each phage and their orientation are shown in yellow, and matches to each gene and their relative locations along each gene are shown in red. Putative functions assigned to each gene are demonstrated above each gene, and the relative length of each phage is shown at the top of each panel.

Figure 7

Figure 7

Heatmap (Panel A) and principal coordinates analysis (Panel B) of CRISPR spacer-virome read matches for all subjects and sample types. Each heatmap row represents reads from the viromes from each subject, and columns represent each subject and sample type. In Panel B, subject #1 is represented in green, subject #2 in red, subject #3 in gold, and subject #4 in blue. Saliva is represented by squares and plaque by circles. Grey outlines represent SGI CRISPR spacers and black outlines represent SGII CRISPR spacers.

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