Epidemiologic studies use various biosample collection methods to study associations between human oral microbiota and health outcomes. However, the agreement between the different methods is unclear. We compared a commercially available OMNIgene ORAL kit to three alternative collection methods: Saccomanno’s fixative, Scope mouthwash, and nonethanol mouthwash. Oral samples were collected from 40 individuals over 4 visits. Two samples were collected from each subject per visit: one with OMNIgene and one with an alternative method. DNA was extracted using the DSP DNA Virus Pathogen kit, and the V4 region of the 16S rRNA gene was PCR amplified and sequenced using MiSeq. Oral collection methods were compared based on alpha and beta diversity metrics and phylum- and genus-level relative abundances. All alpha diversity metrics were significantly lower for Saccomanno’s fixative than for OMNIgene (P < 0.001), whereas the two mouthwashes were more similar to OMNIgene. Principal-coordinate analysis (PCoA) using the Bray-Curtis and weighted UniFrac beta diversity matrices showed large differences in the microbial compositions of samples collected with Saccomanno’s compared to those with OMNIgene and the mouthwashes. Clustering by collection method was not observed in unweighted UniFrac PCoA plots, suggesting differences in relative abundances but not specific taxa detected by the collection methods. Relative abundances of most taxa were significantly different between OMNIgene and the other methods at each taxonomic level, with Saccomanno’s showing the least agreement with OMNIgene. There were clear differences in oral microbial communities between the four oral collection methods, particularly for Saccomanno’s fixative.

中文翻译：

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使用多种方法收集的口腔微生物群的比较和新流行病学研究的建议。

流行病学研究使用各种生物样品收集方法来研究人类口腔微生物群与健康结果之间的关联。但是，不同方法之间的协议尚不清楚。我们将市售的OMNIgene ORAL试剂盒与三种替代的收集方法进行了比较：Saccomanno的固定剂，Scope漱口水和非乙醇漱口水。在4次访问中从40位个体中收集了口腔样本。每次访视时从每个受试者中收集两个样本：一个样本包含OMNIgene，另一个样本包含另一种方法。使用DSP DNA病毒病原试剂盒提取DNA，并使用MiSeq对16S rRNA基因的V4区进行PCR扩增和测序。根据alpha和beta多样性指标以及门类和属类相对丰度比较了口腔收集方法。P<0.001），而两次漱口水更类似于OMNIgene。使用Bray-Curtis和加权UniFracβ多样性矩阵进行的主坐标分析（PCoA）显示，与使用OMNIgene和漱口水相比，用Saccomanno's收集的样品的微生物成分差异很大。在未加权的UniFrac PCoA图中未观察到通过收集方法进行聚类的现象，这表明相对丰度存在差异，但收集方法未检测到特定分类群。在每个分类学水平上，OMNIgene和其他方法之间大多数分类单元的相对丰度差异显着，Saccomanno与OMNIgene的一致性最小。四种口腔采集方法之间的口腔微生物群落存在明显差异，尤其是对于萨科曼诺固定剂而言。