Use of the Precellys® Evolution Homogenizer For Unbiased DNA Extraction From The Zymobiomics™ microbial Community Standard

Abstract

Microbiome profiling via Next Generation Sequencing (NGS) techniques is rapidly changing the landscape of microbiology. However, to ensure accurate microbiome measurements, it is essential to ensure the microbiome workflow is unbiased and robust [1]. For instance, it has been reported that bias in microbiomics analyses can be introduced at every step [2-4] including the DNA extraction step if microbial cells are not uniformly and completely lysed. Mechanical cell lysis using beads of various composition (bead beating) is a generally accepted method used to lyse various microbes [5] and, although a variety of mechanical lysis devices and instruments are available, their performance greatly varies [6-8]. Until recently, there has not been a convenient way to assess the efficiency of lysis afforded by any particular instrument, however, with the release of the ZymoBIOMICS™ Microbial Community Standard (Zymo Research Corp, Irvine, CA, USA) this is now possible. The ZymoBIOMICS Microbial Community is a mock microbial community standard comprised of ten well-characterized organisms (i.e., 5 grampositive, 3 gram-negative, and 2 yeast) that are mixed at defined proportions. The standard contains microbes of different cell wall recalcitrance and of different cell size making it ideal for evaluating cell lysis efficiency. In this study, the efficiency of microbial lysis with the ZymoBIOMICS Microbial Community Standard was assessed using the Precellys® Evolution tissue homogenizer combined with Cryolys® Evolution cooling unit (Bertin Instruments, Rockville, MD, USA).