DNA Extraction for Streamlined Metagenomics of Diverse Environmental Samples

作者：Clarisse A. Marotz, Amnon Amir, Greg C. Humphrey, James Gaffney, Grant Gogul, Rob Knight · 发表于：BioTechniques · 年份：2017 · DOI：10.2144/000114559 · 被引用次数：190 · 研究领域：Genomics and Phylogenetic Studies、Environmental DNA in Biodiversity Studies、Microbial Community Ecology and Physiology

A major bottleneck for metagenomic sequencing is rapid and efficient DNA extraction. Here, we compare the extraction efficiencies of three magnetic bead-based platforms (KingFisher, epMotion, and Tecan) to a standardized column-based extraction platform across a variety of sample types, including feces, oral, skin, soil, and water. Replicate sample plates were extracted and prepared for 16S rRNA gene amplicon sequencing in parallel to assess extraction bias and DNA quality. The data demonstrate that any effect of extraction method on sequencing results was small compared with the variability across samples; however, the KingFisher platform produced the largest number of high-quality reads in the shortest amount of time. Based on these results, we have identified an extraction pipeline that dramatically reduces sample processing time without sacrificing bacterial taxonomic or abundance information.