Comparison of direct boiling method with commercial kits for extracting fecal microbiome DNA by Illumina sequencing of 16S rRNA tags
Comparison of direct boiling method with commercial kits for extracting fecal microbiome DNA by Illumina sequencing of 16S rRNA tags
复制标题
通过 Illumina 测序 16S rRNA 标签提取粪便微生物组 DNA 的直接煮沸法与商业试剂盒的比较
DOI：
10.1016/j.mimet.2013.07.015
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发表时间：
2013-12-01
影响因子：
2.2
通讯作者：
Zhou, Hong-Wei
中科院分区：
文献类型：
--
作者：
Peng, Xin;Yu, Ke-Qiang;Zhou, Hong-Wei
低成本和高通量能力是使用下一代测序（NGS）技术来确定宏基因组16S rRNA标签序列的主要优点。这些方法极大地改变了我们对人类健康和环境科学领域中微生物的看法。然而，使用商业试剂盒的DNA提取具有成本高和时间限制的缺点。在本研究中，我们评估了使用直接煮沸法与5种不同的商业提取方法（例如，Qiagen和MO BIO试剂盒。使用UniFrac距离和聚类的主坐标分析（PCoA）表明，直接煮沸各种粪便浓度得到的细菌群落模式与大多数商业试剂盒中获得的细菌群落模式相似，MO BIO方法除外。粪便浓度煮沸法影响的估计et多样性指数，否则结果一般煮沸和商业方法之间的可比性。通过直接煮沸测定的操作分类单位（OTU）与大多数商业方法测定的频率高度一致。即使是MO BIO试剂盒的那些也是通过直接煮沸法以高置信度获得的。本研究表明，直接煮沸法可用于测定粪便微生物组，使用这种方法将显着降低成本，提高样品制备效率，用于研究肠道微生物组多样性。(C)2013爱思唯尔有限公司版权所有。
Low cost and high throughput capacity are major advantages of using next generation sequencing (NGS) techniques to determine metagenomic 16S rRNA tag sequences. These methods have significantly changed our view of microorganisms in the fields of human health and environmental science. However, DNA extraction using commercial kits has shortcomings of high cost and time constraint. In the present study, we evaluated the determination of fecal microbiomes using a direct boiling method compared with 5 different commercial extraction methods, e.g., Qiagen and MO BIO kits. Principal coordinate analysis (PCoA) using UniFrac distances and clustering showed that direct boiling of a wide range of feces concentrations gave a similar pattern of bacterial communities as those obtained from most of the commercial kits, with the exception of the MO BIO method. Fecal concentration by boiling method affected the estimation of et-diversity indices, otherwise results were generally comparable between boiling and commercial methods. The operational taxonomic units (OTUs) determined through direct boiling showed highly consistent frequencies with those determined through most of the commercial methods. Even those for the MO BIO kit were also obtained by the direct boiling method with high confidence. The present study suggested that direct boiling could be used to determine the fecal microbiome and using this method would significantly reduce the cost and improve the efficiency of the sample preparation for studying gut microbiome diversity. (C) 2013 Elsevier B.V. All rights reserved.