This population-based study determined the salivary microbiota composition of 2,343 adult residents of Hisayama town, Japan, using 16S rRNA gene next-generation high-throughput sequencing. Of 550 identified species-level operational taxonomic units (OTUs), 72 were common, in ≥75% of all individuals, as well as in ≥75% of the individuals in the lowest quintile of phylogenetic diversity (PD). These "core" OTUs constituted 90.9 ± 6.1% of each microbiome. The relative abundance profiles of 22 of the core OTUs with mean relative abundances ≥1% were stratified into community type I and community type II by partitioning around medoids clustering. Multiple regression analysis revealed that a lower PD was associated with better conditions for oral health, including a lower plaque index, absence of decayed teeth, less gingival bleeding, shallower periodontal pockets and not smoking, and was also associated with tooth loss. By contrast, multiple Poisson regression analysis demonstrated that community type II, as characterized by a higher ratio of the nine dominant core OTUs, including Neisseria flavescens, was implicated in younger age, lower body mass index, fewer teeth with caries experience, and not smoking. Our large-scale data analyses reveal variation in the salivary microbiome among Japanese adults and oral health-related conditions associated with the salivary microbiome.The human oral cavity is colonized by numerous and diverse microorganisms as commensals. These bacteria constitute complex microbial communities on intraoral surfaces, and dental plaque microbiota that form on the teeth are the cause of two major oral diseases, dental caries and periodontitis. Mutans streptococci are the major etiologic agent of dental caries 1 and Porphyromonas gingivalis, Tannerella forsythia and Treponema denticola are prime suspects in periodontitis 2 . Furthermore, recent studies that have used open-ended molecular approaches and the 16S rRNA gene have implicated other commensal members with the etiology of each disease, such as lactobacilli for dental caries 3 and as many as 17 species, including Filifactor alosis for periodontitis 4 .Saliva is a biological fluid secreted from the salivary glands into the oral cavity and contains bacteria shed from adhering microbial communities on various intraoral surfaces, including tooth surfaces, gingival crevices, tongue dorsum, and buccal mucosa. Oral bacteria in a planktonic state (as in saliva) are not generally regarded as direct causal agents of the oral diseases. However, intraoral transmission of pathogenic bacteria is likely to be mediated by bacteria dispersed via saliva 5,6 .The salivary microbiome, which is comprised of indigenous bacteria that are specific to each person, exhibits long-term stability (on the scale of years) [7][8][9][10] . On the other hand, oral disorders alter the structure of the teeth and their surroundings. Along with the loss of teeth, tooth decay and its treatment alter the structure of the tooth surfaces on which bacteria are attached. Gingival crevi...