Analysis of the salivary microbiome using culture-independent techniques

We explored the bacterial community composition in the saliva sample using metagenomic whole genome shotgun (WGS) sequencing, the extraction of 16S rRNA gene fragments from metagenomic sequences (16S-WGS) and high-throughput sequencing of PCR-amplified bacterial 16S rDNA gene (16S-HTS) regions V1 and V3.The hierarchical clustering of data based on the relative abundance of bacterial genera revealed that distances between 16S-HTS datasets for V1 and V3 regions were greater than those obtained for the same V region with different numbers of PCR cycles. Datasets generated by 16S-HTS and 16S-WGS were even more distant. Finally, comparison of WGS and 16S-based datasets revealed the highest dissimilarity.The analysis of the 16S-HTS, WGS and 16S-WGS datasets revealed 206, 56 and 39 bacterial genera, respectively, 124 of which have not been previously identified in salivary microbiomes. A large fraction of DNA extracted from saliva corresponded to human DNA. Based on sequence similarity search against completely sequenced genomes, bacterial and viral sequences represented 0.73% and 0.0036% of the salivary metagenome, respectively. Several sequence reads were identified as parts of the human herpesvirus 7.Analysis of the salivary metagenome may have implications in diagnostics e.g. in detection of microorganisms and viruses without designing specific tests for each pathogen.The microbiota in the mouth has a significant impact on both the oral and general health. Bacterial species associated with periodontal health and those that are more prevalent in periodontal disease have been identified [1]. The salivary microbiota is a potential diagnostic indicator of several diseases. For instance, a caries-free oral status in children is associated with a significant shift in the relative abundance of Porphyromonas catoniae and Neisseria flavescens in saliva [2]. Increased salivary counts of Capnocytophaga gingivalis, Prevotella melaninogenica and Streptococcus mitis are associated w