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. 2017 Jul 19;85(8):e00106-17.
doi: 10.1128/IAI.00106-17. Print 2017 Aug.

Microbiomes of Site-Specific Dental Plaques From Children With Different Caries Status

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Free PMC article

Microbiomes of Site-Specific Dental Plaques From Children With Different Caries Status

Vincent P Richards et al. Infect Immun. .
Free PMC article

Abstract

The oral microbiota associated with the initiation and progression of dental caries has yet to be fully characterized. The Human Oral Microbe Identification Using Next-Generation Sequencing (HOMINGS) approach was used to analyze the microbiomes of site-specific supragingival dental plaques from children with different caries status. Fifty-five children (2 to 7 years of age) were assessed at baseline and at 12 months and grouped as caries free (CF), caries active with enamel lesions (CAE), and caries active with dentin carious lesions (CA). Plaque samples from caries-free tooth surfaces (PF) and from enamel carious lesions (PE) and dentin carious lesions (PD) were collected. 16S community profiles were obtained by HOMINGS, and 408 bacterial species and 84 genus probes were assigned. Plaque bacterial communities showed temporal stability, as there was no significant difference in beta diversity values between the baseline and 12-month samples. Irrespective of collection time points, the microbiomes of healthy tooth surfaces differed substantially from those found during caries activity. All pairwise comparisons of beta diversity values between groups were significantly different (P < 0.05), except for comparisons between the CA-PF, CAE-PE, and CA-PE groups. Streptococcus genus probe 4 and Neisseria genus probe 2 were the most frequently detected taxa across the plaque groups, followed by Streptococcus sanguinis, which was highly abundant in CF-PF. Well-known acidogenic/aciduric species such as Streptococcus mutans, Scardovia wiggsiae, Parascardovia denticolens, and Lactobacillus salivarius were found almost exclusively in CA-PD. The microbiomes of supragingival dental plaque differ substantially among tooth surfaces and children of different caries activities. In support of the ecological nature of caries etiology, a steady transition in community species composition was observed with disease progression.

Keywords: bacteria; biofilms; caries; children; dental plaque; microbiome; supragingival.

Figures

FIG 1
FIG 1
(A) Constrained analysis of principal coordinates (CAP) of plaque bacterial communities using distance-based redundancy analysis (db-RDA). (B) Neighbor-joining phylogeny based on pairwise PERMANOVA components for beta diversity. Branch lengths represent the degrees to which bacterial communities are differentiated. Groups shaded in green showed no significant differences in beta diversity values. CF, caries-free children; CAE, caries-active children with enamel carious lesions; CA, caries-active children with dentin carious lesions; PF, supragingival plaque from caries-free tooth surfaces; PE, plaque from active, enamel carious lesions; PD, plaque from active, dentin carious lesions.
FIG 2
FIG 2
(A) Distribution of the 60 most abundant taxa (out of 492 taxa) among the four plaque groups. *, taxon showing a significant difference in abundance among the groups; sp, species probe; g, genus probe. The left chart shows the mean taxon counts for each of the plaque groups expressed as a proportion of the sum of the means. The right chart shows the sum of the means (see Table 1 for a description of the taxa captured by the genus probes). (B and C) Two line charts showing the frequencies of certain taxa that, in addition to showing significant differences in abundances among the groups, also showed strong and progressive increases or decreases in frequency as caries progressed. Frequency is expressed as a proportion of the sum of the means.
FIG 3
FIG 3
Levels of alpha diversity for the different groups of site-specific plaque samples. (A) Box-and-whisker plots showing alpha diversity levels for the different groups of site-specific plaque samples. (B) Pairwise t tests for significant differences in alpha diversity values among the different groups of site-specific plaque samples. P values were corrected by using FDR analysis; *, significant P values.
FIG 4
FIG 4
Distribution of the 30 most frequently detected taxa among the CF-PF samples (A) and CA-PD samples (B).

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