Characterization of bacteriophage communities and CRISPR profiles from dental plaque

Abstract

BackgroundDental 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.ResultsWe 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.ConclusionsOur findings of subject specificity to both plaque-derived viruses and CRISPR profiles suggest that human viral ecology may be highly personalized.

Viruses comprise an extensive pool of mobile genetic elements in eukaryote cell cultures and human clinical samples

“…Oropharynx and urinary tract differ significantly with regard to temperature, osmolarity, pH, oxygenation, or secreted immune factors. Phage diversity differs significantly between ecological niches (68, 69). Nevertheless, relative abundances of bacteria thriving under different environmental conditions do not necessarily predict the relative abundances of their phages (68, 69).…”

“…Phage diversity differs significantly between ecological niches (68, 69). Nevertheless, relative abundances of bacteria thriving under different environmental conditions do not necessarily predict the relative abundances of their phages (68, 69). In contrast, replication of eukaryotic viruses in specialized cells, for example, explains the detection of influenza viruses in the oropharynx but not in the urinary tract.…”

Ecology of the Oral Microbiome: Beyond Bacteria

“…The bacteriophages are vastly greater in number, and thus will be the primary focus of this section of the review. The human oral virome is highly varied between individuals and surprisingly stable over time, even compared to the oral bacteriome [18, 65, 69]. Furthermore, sharing of living environment may have an important role in determining the ecology of the human oral virome, as members of the same household had remarkably similar viromes [66].…”

“…In a classic Red Queen dynamic, the genetic arms race invoked by coevolution of phage and host bacteria likely serves to prevent novel bacteria and phage from establishing in the oral community [75]. Several recent studies have explored CRISPRs transcribed in the oral cavity and their protective effects against invading phage [69, 77, 78]. On the other hand, recent investigations suggest that oral phage may employ anti-CRISPR proteins to inactivate the bacterial immune system, preventing the eradication of phage by bacteria, and allowing phage to persist within the oral microbiome [79, 80].…”

CRISPR‐Cas systems in oral microbiome: From immune defense to physiological regulation

“…The oral microbiome contains approximately 700 prokaryote species, which play an important role in the human microbial community and human health (Zarco, Vess, & Ginsburg, ). Studies have demonstrated that a substantial number of CRISPR spacer sequences match the sequences of viruses present in plaque and saliva (Naidu, Robles‐Sikisaka, Abeles, Boehm, & Pride, ; Pride, Salzman, & Relman, ). The transcription of oral CRISPR loci is also relatively ubiquitous (Lum et al, ).…”