Altered oral viral ecology in association with periodontal disease

Abstract

The human oral cavity is home to a large and diverse community of viruses that have yet to be characterized in patients with periodontal disease. We recruited and sampled saliva and oral biofilm from a cohort of humans either periodontally healthy or with mild or significant periodontal disease to discern whether there are differences in viral communities that reflect their oral health status. We found communities of viruses inhabiting saliva and the subgingival and supragingival biofilms of each subject that were composed largely of bacteriophage. While there were homologous viruses common to different subjects and biogeographic sites, for most of the subjects, virome compositions were significantly associated with the oral sites from which they were derived. The largest distinctions between virome compositions were found when comparing the subgingival and supragingival biofilms to those of planktonic saliva. Differences in virome composition were significantly associated with oral health status for both subgingival and supragingival biofilm viruses but not for salivary viruses. Among the differences identified in virome compositions was a significant expansion of myoviruses in subgingival biofilm, suggesting that periodontal disease favors lytic phage. We also characterized the bacterial communities in each subject at each biogeographic site by using the V3 hypervariable segment of the 16S rRNA and did not identify distinctions between oral health and disease similar to those found in viral communities. The significantly altered ecology of viruses of oral biofilm in subjects with periodontal disease compared to that of relatively periodontally healthy ones suggests that viruses may serve as useful indicators of oral health status.

Importance: Little is known about the role or the constituents of viruses as members of the human microbiome. We investigated the composition of human oral viral communities in a group of relatively periodontally healthy subjects or significant periodontitis to determine whether health status may be associated with differences in viruses. We found that most of the viruses present were predators of bacteria. The viruses inhabiting dental plaque were significantly different on the basis of oral health status, while those present in saliva were not. Dental plaque viruses in periodontitis were predicted to be significantly more likely to kill their bacterial hosts than those found in healthy mouths. Because oral diseases such as periodontitis have been shown to have altered bacterial communities, we believe that viruses and their role as drivers of ecosystem diversity are important contributors to the human oral microbiome in health and disease states.

FIG 1

Bar graphs of the mean percentages of contigs (± the standard errors) with viral homologues in the NR database from all of the subjects. Panels: A, saliva; B, subgingival plaque; C, supragingival plaque.

FIG 2

PCOA of beta diversity present in the viromes of each subject at each biogeographic site. Relatively periodontally healthy subjects are represented in white, and subjects with significant periodontal disease are represented in black. Circles represent saliva, squares represent subgingival plaque, and triangles represent supragingival plaque. Panels: A, saliva; B, subgingival and supragingival plaque.

FIG 3

Pie charts of bacteriophage families present in the saliva (A) and subgingival (B) or supragingival plaque (C) samples of relatively periodontally healthy subjects (left) and those with disease (right). Asterisks indicate significant differences (P ≤ 0.05) between the proportions of virus families identified in periodontally healthy subjects and those with disease.

FIG 4

PCOA of beta diversity present in the bacterial communities of each subject at each biogeographic site. Panels: A, classified by biogeographic site; B, classified by oral health status.

FIG 5

Bar plots (means ± standard errors of the means) of putative viral host taxonomy (A and C) and bacterial taxonomy based on 16S rRNA (D to F) at the phylum level. Each phylum is shown on the x axis, and the percentage of contigs or OTUs identified belonging to the observed phyla is shown on the y axis. Panels A and D represent saliva, panels B and E represent subgingival plaque, and panels C and F represent supragingival plaque. White bars represent relatively periodontally healthy subjects, and black bars represents subjects with significant periodontal disease. Asterisks indicate significant differences (P ≤ 0.05) between phyla in periodontally healthy subjects and those with disease.