The oral microbiome is a complex community of bacteria, fungi, and viruses that inhabit the oral cavity. Microbes of the oral microbiome are implicated in health and disease. We collected 220 unstimulated saliva samples from patients with periodontal disease and varying degrees of dental caries, as well as from subjects with no signs of oral disease. Metagenomic analysis of saliva revealed significantly higher abundance of periodontal pathogens in people with gum disease, and significantly higher abundance of cariogenic species in people with dental caries. We also found that salivary microbiome diversity was significantly higher in people with periodontal disease, but not in those with only caries. Furthermore, oral microbiome diversity is affected by oral hygiene habits such as flossing frequency, but not brushing frequency. Clustering and differential analysis allowed us to identify specific commensal species, such as Prevotella pallens and Veillonella atypica , which are signi...
