Study of inter- and intra-individual variations in the salivary microbiota

Background Oral bacterial communities contain species that promote health and others that have been implicated in oral and/or systemic diseases. Culture-independent approaches provide the best means to assess the diversity of oral bacteria because most of them remain uncultivable. Results The salivary microbiota from five adults was analyzed at three time-points by means of the 454 pyrosequencing technology. The V1-V3 region of the bacterial 16S rRNA genes was amplified by PCR using saliva lysates and broad-range primers. The bar-coded PCR products were pooled and sequenced unidirectionally to cover the V3 hypervariable region. Of 50,708 obtained sequences, 31,860 passed the quality control. Non-bacterial sequences (2.2%) were removed leaving 31,170 reads. Samples were dominated by seven major phyla: members of Firmicutes, Proteobacteria, Actinobacteria, Bacteroidetes and candidate division TM7 were identified in all samples; Fusobacteria and Spirochaetes were identified in all individuals, but not at all time-points. The dataset was represented by 3,011 unique distinct sequences of ~215 nucleotides and 359 phylotypes defined at =97% identity. We compared saliva samples from different individuals in terms of the phylogeny of their microbial communities. Conclusions Based on the presence and absence of unique phylotypes defined at 100% identity, samples from each subject formed distinct clusters. Among individual taxa, phylum Bacteroidetes and order Clostridiales (Firmicutes) were the best indicators of intraindividual similarity of the salivary flora over time. Candidates for individual and universal microbial core were identified at different taxon levels. These results point to the persistence of subject-specific strains whose frequency fluctuates between the time points.