Temporal stability of the oral microbiota: A longitudinal study of the dental, tongue, and salivary bacterial consortia

Every individual harbors a distinct oral microbiome that is influenced by environmental changes and shifts dramatically during the transition to disease. Examining baseline variation within and between individuals over time is critical to understanding this disease transition. Here we examined the temporal stability of supragingival plaque, tongue dorsum, and salivary microbial communities of healthy individuals. Ten subjects were sampled over 90 days and oral bacterial communities were profiled by high-throughput 16S rRNA gene sequencing. In all cases, supragingival plaque consortia were distinct from tongue dorsum and salivary communities. Overall, 97% of bacterial operational taxonomic units (OTUs) found in saliva were also detected in tongue samples, whereas only 2% of salivary OTUs were associated with supragingival plaque. Relative to other sites, the tongue dorsum also exhibited the highest relative temporal stability in bacterial composition. Because of the temporal variability in intra-individual microbiota, pooling of data from at least three time-points was required to capture the majority of an individual’s diversity at all time points. Using machine learning, we could also identify each subject by their microbial profiles alone with 95% accuracy, owing to each individual’s distinct oral microbial profiles. We also identified a core set of bacterial OTUs from all samples that classified within six genera: Streptococcus, Fusobacterium, Haemophilus, Neisseria, Prevotella, and Rothia. A set of 14 additional core OTUs were present in the majority of subjects, sites, and time-points, affiliated with the Campylobacter, Bergeyella, and Porphyromonas genera. This study characterizing a baseline and examining temporal shifts of the healthy core microbiota provides an useful prospect to examine dysbiosis during disease. While this knowledge can be harnessed to develop novel prognostics and diagnostics for disease conditions, the intra-individual differences in oral microbiota also highlight the need for an individualized approach to bacterial surveillance in dentistry.