Division of Urogynecology, Department of Obstetrics and Gynecology, Oregon Health and Science University, Portland, OR, 97239, USA.
Division of Bioinformatics and Computational Biomedicine, Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, OR, 97239, USA.
Sci Rep. 2021 Mar 17;11(1):6186. doi: 10.1038/s41598-021-85482-1.
The urinary microbiome has been increasingly characterized using next-generation sequencing. However, many of the technical methods have not yet been specifically optimized for urine. We sought to compare the performance of several DNA isolation kits used in urinary microbiome studies. A total of 11 voided urine samples and one buffer control were divided into 5 equal aliquots and processed in parallel using five commercial DNA isolation kits. DNA was quantified and the V4 segment of the 16S rRNA gene was sequenced. Data were processed to identify the microbial composition and to assess alpha and beta diversity of the samples. Tested DNA isolation kits result in significantly different DNA yields from urine samples. DNA extracted with the Qiagen Biostic Bacteremia and DNeasy Blood & Tissue kits showed the fewest technical issues in downstream analyses, with the DNeasy Blood & Tissue kit also demonstrating the highest DNA yield. Nevertheless, all five kits provided good quality DNA for high throughput sequencing with non-significant differences in the number of reads recovered, alpha, or beta diversity.
尿液微生物组学已越来越多地采用下一代测序技术进行描述。然而，许多技术方法尚未专门针对尿液进行优化。我们旨在比较几种用于尿液微生物组学研究的 DNA 分离试剂盒的性能。总共 11 份随机尿液样本和一份缓冲液对照样本被分成 5 等份，并使用 5 种商业 DNA 分离试剂盒平行处理。定量 DNA 并对 16S rRNA 基因的 V4 片段进行测序。对数据进行处理以鉴定微生物组成，并评估样本的 alpha 和 beta 多样性。测试的 DNA 分离试剂盒从尿液样本中得到的 DNA 产量有显著差异。使用 Qiagen Biostic Bacteremia 和 DNeasy Blood & Tissue 试剂盒提取的 DNA 在下游分析中显示出最少的技术问题，而 DNeasy Blood & Tissue 试剂盒的 DNA 产量也最高。然而，所有五个试剂盒都为高通量测序提供了高质量的 DNA，回收的读取数、alpha 或 beta 多样性方面没有显著差异。
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