Oral specimens as a tool for accurate metagenomic analysis: A pilot study.

Abstract
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.

摘要
急性口腔黏膜损伤及其他炎症过程似乎与口腔微生物群失调相关。开展口腔微生物组变化的相关研究，促使我们提出假说：何种样本能够最具代表性地呈现完整的人类口腔微生物组全貌。
本研究为观察性横断面研究。6名健康成年受试者各提供3种不同类型的样本，包括唾液、口腔冲洗液及黏膜活检组织。我们采用Illumina MiSeq技术，对18份样本的16S rRNA（16S ribosomal RNA）V3-V4区域进行测序。
受试者年龄为27±6.3岁。相较于全未刺激唾液及口腔黏膜组织样本，口腔冲洗液样本的细菌α多样性（alpha diversity）更高（p=0.005）。但唾液样本中鉴定出的物种相对丰度达56%，口腔冲洗液样本为30%，而组织样本仅为1%。三类样本的β多样性（beta diversity）存在显著差异。
本研究发现不同样本类型的口腔微生物组组成存在差异。若需获得更高的α多样性，应选择口腔冲洗液样本；而若需获取足量细菌DNA以开展大体积样本分析，则全未刺激唾液样本更为合适。