Relationship between dental and periodontal health status and the salivary microbiome: bacterial diversity, co-occurrence networks and predictive models

Abstract

The present study used 16S rRNA gene amplicon sequencing to assess the impact on salivary microbiome of different grades of dental and periodontal disease and the combination of both (hereinafter referred to as oral disease), in terms of bacterial diversity, co-occurrence network patterns and predictive models. Our scale of overall oral health was used to produce a convenience sample of 81 patients from 270 who were initially recruited. Saliva samples were collected from each participant. Sequencing was performed in Illumina MiSeq with 2 × 300 bp reads, while the raw reads were processed according to the Mothur pipeline. The statistical analysis of the 16S rDNA sequencing data at the species level was conducted using the phyloseq, DESeq2, Microbiome, SpiecEasi, igraph, MixOmics packages. The simultaneous presence of dental and periodontal pathology has a potentiating effect on the richness and diversity of the salivary microbiota. The structure of the bacterial community in oral health differs from that present in dental, periodontal or oral disease, especially in high grades. Supragingival dental parameters influence the microbiota's abundance more than subgingival periodontal parameters, with the former making a greater contribution to the impact that oral health has on the salivary microbiome. The possible keystone OTUs are different in the oral health and disease, and even these vary between dental and periodontal disease: half of them belongs to the core microbiome and are independent of the abundance parameters. The salivary microbiome, involving a considerable number of OTUs, shows an excellent discriminatory potential for distinguishing different grades of dental, periodontal or oral disease; considering the number of predictive OTUs, the best model is that which predicts the combined dental and periodontal status.

Figure 1

Principal Coordinate Analysis (PCoA), including PERMANOVA test values in the comparison between different grades of dental, periodontal and oral health (graphic made using the phyloseq package, version 1.34.0).

Figure 2

Number of OTUs of the salivary core microbiome present in different grades of dental, periodontal and oral health, as well as their respective relative abundance values.

Figure 3

Main module of the co-occurrence network associated with grade 0 of the overall oral health scale (node = 79; degree = 1723) (graphic made using the igraph package, version 1.2.4.1).

Figure 4

Main module of the co-occurrence network associated with grade 2,3 of the overall oral health scale (node = 38; degree = 280) (graphic made using the igraph package, version 1.2.4.1).

Figure 5

Main module of the co-occurrence network associated with grade 0 of the dental health subscale (node = 113; degree = 1444) (graphic made using the igraph package, version 1.2.4.1).

Figure 6

Main module of the co-occurrence network associated with grade 0 of the dental health subscale (node = 101; degree = 2663) (graphic made using the igraph package, version 1.2.4.1).

Figure 7

Potential of the salivary microbiome to discriminate the different grades of dental and periodontal health and the combination of both: ROC curves and AUC values (graphics made using the MixOmics package, version 1.6.3).