Functional expression of dental plaque microbiota

Abstract

Dental caries remains a significant public health problem and is considered pandemic worldwide. The prediction of dental caries based on profiling of microbial species involved in disease and equally important, the identification of species conferring dental health has proven more difficult than anticipated due to high interpersonal and geographical variability of dental plaque microbiota. We have used RNA-Seq to perform global gene expression analysis of dental plaque microbiota derived from 19 twin pairs that were either concordant (caries-active or caries-free) or discordant for dental caries. The transcription profiling allowed us to define a functional core microbiota consisting of nearly 60 species. Similarities in gene expression patterns allowed a preliminary assessment of the relative contribution of human genetics, environmental factors and caries phenotype on the microbiota's transcriptome. Correlation analysis of transcription allowed the identification of numerous functional networks, suggesting that inter-personal environmental variables may co-select for groups of genera and species. Analysis of functional role categories allowed the identification of dominant functions expressed by dental plaque biofilm communities, that highlight the biochemical priorities of dental plaque microbes to metabolize diverse sugars and cope with the acid and oxidative stress resulting from sugar fermentation. The wealth of data generated by deep sequencing of expressed transcripts enables a greatly expanded perspective concerning the functional expression of dental plaque microbiota.

Keywords: biofilm; caries; dental plaque; oral microbiota; transcriptome.

Figure 1

Dendrogram of twin pairs based on RNA expression patterns.

Figure 2

Transcript abundance of representative genera in dental plaque biofilms. Pie chart representing the proportions of transcripts mapping to 27 genera observed in 19 twin pairs.

Figure 3

Abundance of the dental plaque core microbiota. Box and whisker plot. Outliers shown as dots represent values 1.5 times great or less than the upper and lower quartile, respectively.

Figure 4

Spearman Correlation matrix of the dental plaque core microbiota. Blue indicates positive correlation and yellow indicates negative correlation.

Figure 5

Functional Networks. Positively correlated (green) and anti-correlated (red) transcripts define networks. The thickness of lines indicates the strength of the correlation.

Figure 6

Functional Network in dental plaque microbiota, complex I. The y-axis displays read counts on a log scale. The x-axis displays subjects in the order shown in Table 1.

Figure 7

Functional Network in dental plaque microbiota, complex III. The y-axis displays read counts on a log scale. The x-axis displays subjects in the order shown in Table 1.

Figure 8

Functional role categories expressed in dental plaque biofilm.