Evaluation of Oral Cavity DNA Extraction Methods on Bacterial and Fungal Microbiota
Publication in refereed journal

香港中文大學研究人員
替代計量分析
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摘要The objective of this study was to evaluate the most effective method of DNA extraction of oral mouthwash samples for use in microbiome studies that utilize next generation sequencing (NGS). Eight enzymatic and mechanical DNA extraction methods were tested. Extracted DNA was amplified using barcoded primers targeting the V6 variable region of the bacterial 16S rRNA gene and the ITS1 region of the fungal ribosomal gene cluster and sequenced using the Illumina NGS platform. Sequenced reads were analyzed using QIIME and R. The eight methods yielded significantly different quantities of DNA (p < 0.001), with the phenol-chloroform extraction method producing the highest total yield. There were no significant differences in observed bacterial or fungal Shannon diversity (p = 0.64, p = 0.93 respectively) by extraction method. Bray-Curtis beta-diversity did not demonstrate statistically significant differences between the eight extraction methods based on bacterial (R-2 = 0.086, p = 1.00) and fungal (R-2 = 0.039, p = 1.00) assays. No differences were seen between methods with or without bead-beating. These data indicate that choice of DNA extraction method affect total DNA recovery without significantly affecting the observed microbiome.
著者Rosenbaum, Usyk, Chen, Zolnik, Jones, Waldron, Dowd, Thorpe, Burk
期刊名稱Scientific Reports
出版年份2019
月份2
日期6
卷號9
期次1
出版社Nature Research
文章號碼1531
國際標準期刊號2045-2322
語言英式英語

上次更新時間 2021-22-02 於 23:32