Oral specimens as a tool for metagenomic analysis: A pilot study
Acute oral mucosal damage, as well as other inflammatory processes seem to be related to dysbiosis of the oral microbiome. The need to study changes in the oral microbiome led us to hypothesize what type of sample would provide the most representative picture of the entire human oral microbiome. An observational, and cross-sectional study was carried out. Six healthy adult participants provided 3 different sample types each, that included saliva, oral rinse and mucosal biopsy tissue.  We performed 16S rRNA sequencing of the V3-V4 region of the 18 samples using Illumina MiSeq technology.  Participants were 27 ± 6,3 years old. Bacterial alpha diversity was higher in oral rinse samples compared to whole unstimulated saliva and oral mucosa tissue (p=0,005). However, saliva specimens showed a 56% relative abundance of identified species followed by a 30% in oral rinse and only 1% in tissue samples. Beta diversity was clearly different among the three types of specimens. This study found differences on oral microbiome composition for each type of sample. Oral rinse should be chosen when higher alpha diversity is needed, whereas whole unstimulated saliva should be more appropriate for larger volume of bacterial DNA.