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.

Impact of 16S rRNA gene redundancy and primer pair selection on the quantification and classification of oral microbiota in next-generation sequencing

“…On the other hand, the identification, at least at the species level, is highly desirable in 16S rRNA sequencingbased studies of the oral microbiota (14). This is because it has been demonstrated how different species from the same genus are associated with different oral conditions (15)(16)(17). Our results revealed that Porphyromonas catoniae is a core species linked to dental and periodontal health, while Porphyromonas endodontalis is associated with dental and periodontal pathology.…”

Impact of Probiotics on the Salivary Microbiota and Salivary Levels of Inflammation-Related Proteins during Short-Term Sugar Stress: A Randomized Controlled Trial

“…Indeed, saliva, which can be sampled with ease and non-invasively, portrays the composition of the oral microbiota and harbors relevant inflammatory markers [13,14]. Importantly, the composition of the salivary microbiota and salivary levels of inflammatory markers have been demonstrated not only to reflect oral health status [15,16], but also to be susceptible to external stress such as oral hygiene discontinuation, smoking and diet [17][18][19]. Therefore, analysis of the salivary microbiota and salivary levels of inflammatory markers is an elegant model system to study the impact of coordinated perturbations on oral homeostasis.…”

The salivary microbiome shows a high prevalence of core bacterial members yet variability across human populations

“…In this study, we extracted the 16S rRNA gene amplicon sequencing data of healthy human saliva from 47 studies (Figure 1A) [15, 16,48, 67-110]. We abstracted data from subjects who had no diagnosed disease state, hereafter named “healthy”.…”