This richness is considerably higher than the 34 to 72 phylotypes and the 6 to 30 genera previously described using conventional cloning and sequencing [15, 16]. The predominant taxa belonged to Firmicutes (genus Streptococcus, family Veillonellaceae, genus

Granulicatella), Proteobacteria (genus Neisseria, Haemophilus), Actinobacteria (genus Corynebacterium, Rothia, Actinomyces), Bacteroidetes (genus Prevotella, Capnocytophaga, Porphyromonas) and Fusobacteria (genus Fusobacterium) (Additional file 4). Figure 2 The relative abundance of OTUs per individual. Relative abundance of OTUs based on all unique sequences (0%, solid lines) and OTUs within genetic distances that do not exceed 3% difference (3%, dashed lines) per individual S1, S2 and S3, respectively. The x-axis indicates the individual OTUs, ranked according to their relative abundance (high MCC950 cell line to low). The S3I-201 y-axis indicates the cumulative abundance of the OTUs. About 100 “”species-level”" phylotypes (118, 97 and 112 phylotypes in the microbiome of individual S1, S2 and S3, respectively) belonged to abundant OTUs of the individual microbiome (Additional file 1). A phylotype was considered abundant if it contributed to at least 0.1% of the microbiome. These abundant phylotypes together contributed to 92 – 93% of each microbiome. As with a pooled oral microbiome [4] and

individually see more sequenced gut microbiomes [13], each individual oral microbiome in this study was dominated by a few sequences while most sequences were rare and contributed to the “”long tail”" effect (Figure 2). Overlap of three individual oral microbiomes Unique sequences Twenty-six percent (1660 sequences) of the unique sequences were found in all three microbiomes and 65% in at least

two microbiomes (Figure 3A). Of all reads, 66% belonged to sequences that were shared by three microbiomes (Table 2). Nine sequences were highly abundant (0.5 – 5.8% of the reads) across all individuals: they contributed to 11%, 9% and 21% of the microbiome of individuals S1, S2 and S3, respectively (the full list of the taxonomy and abundance of the overlapping sequences is given in Additional file 5). Two of these sequences were assigned to the genus Streptococcus, two to the family Veillonellaceae, one each to the genera Granulicatella (Firmicutes), Corynebacterium, Rothia (Actinobacteria), Porphyromonas check (Bacteroidetes) and Fusobacterium (Fusobacteria). Figure 3 The extent of overlap of oral microbiome between three individuals. The extent of overlap between subjects S1 (pink circle), S2 (light blue circle) and S3 (yellow circle) at the level of A) unique sequences, B) OTUs clustered at 3% difference and C) higher taxa (genus or more inclusive taxon). The data was obtained by combining all samples of the respective individual microbiome. The Venn Diagrams show that 26% of the unique sequences, 47% of the OTUs and 72% of the higher taxa were common (area in grey) to the three individuals.