Kwa Wit Thun, Sim Choon Kiat, Low Adrian, Lee Jonathan Wei Jie
Centre for Translational Medicine, Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore.
Institute for Health Innovation and Technology (iHealthtech), National University of Singapore, E7, 15 Kent Ridge Crescent, Singapore 119276, Singapore.
Microorganisms. 2024 Nov 25;12(12):2417. doi: 10.3390/microorganisms12122417.
Automated nucleic acid extractors are useful instruments for the high-throughput processing of bio-samples and are expected to improve research throughput in addition to decreased inter-sample variability inherent to manual processing. We evaluated three commercial nucleic acid extractors Bioer GenePure Pro (Bioer Technology, Hangzhou, China), Maxwell RSC 16 (Promega Corporation, Madison, WI, USA), and KingFisher Apex (ThermoFisher Scientific, Waltham, MA, USA) based on their DNA yield, DNA purity, and 16S rRNA gene amplicon results using both human fecal samples and a mock community (ZymoBIOMICS Microbial Community Standard (Zymo Research Corp., Irvine, CA, USA)). Bead-beating provided incremental yield to effectively lyse and extract DNA from stool samples compared to lysis buffer alone. Differential abundance analysis and comparison of prevalent bacterial species revealed a greater representation of Gram-positive bacteria in samples subjected to mechanical lysis, regardless of sample type. All three commercial extractors had differences in terms of yield, inter-sample variability, and subsequent sequencing readouts, which we subsequently share in the paper and believe are significant considerations for all researchers undertaking human fecal microbiota research.
自动化核酸提取仪是用于生物样本高通量处理的有用仪器，除了能减少手工处理固有的样本间变异性外，还有望提高研究通量。我们评估了三款商用核酸提取仪，分别是博日基因纯Pro（中国杭州博日科技有限公司）、麦克斯韦RSC 16（美国威斯康星州麦迪逊市普洛麦格公司）和凯杰飞鱼Apex（美国马萨诸塞州沃尔瑟姆市赛默飞世尔科技公司），评估内容包括它们的DNA产量、DNA纯度以及使用人类粪便样本和模拟群落（ZymoBIOMICS微生物群落标准品，美国加利福尼亚州尔湾市Zymo Research公司）得到的16S rRNA基因扩增子结果。与单独使用裂解缓冲液相比，珠磨法能增加产量，有效裂解并从粪便样本中提取DNA。差异丰度分析和常见细菌种类的比较显示，无论样本类型如何，经过机械裂解的样本中革兰氏阳性菌的占比更高。所有三款商用提取仪在产量、样本间变异性以及后续测序读数方面都存在差异，我们将在本文中分享这些差异，并认为对于所有从事人类粪便微生物群研究的研究人员来说，这些差异都是需要重点考虑的因素。
