Context
There is an increasing concern that the scientific world is undergoing a reproducibility crisis. Microbiomics is one of the fields that is facing the biggest challenges, because substantial bias can be introduced at each step of the workflow [1]. This has led researchers to question and validate their methodology using mock-microbial community standards, such as the ZymoBIOMICS® Microbial Community Standard (Zymo Research Corp., Irvine, CA). The ZymoBIOMICS® standard contains ten well-characterized organisms (i.e., 5 gram-positive, 3 gram-negative, and 2 yeast) that are mixed at defined proportions. This standard is comprised of microbes of various sizes and cell wall toughness, which makes it ideal for evaluating each step of the microbiomics workflow.
It has been reported that the choice of cell lysis technique during the nucleic acid extraction step can significantly influence results of Next Generation Sequencing (NGS) based microbiome analysis [2]. Mechanical lysis using bead beating-based homogenization has become the Gold Standard. Thanks to its powerful 3D-movement, the Precellys® Evolution offers great homogenization capabilities within a few seconds. Here, we use the ZymoBIOMICS® Microbial Community standard to show that the Precellys® Evolution bead-beating homogenizer combined with the ZymoBIOMICS® DNA/RNA Miniprep Kit can achieve complete lysis without compromising RNA integrity enabling accurate metagenome and microbiome analysis. Additionally, we evaluate the quality of the nucleic acid extracted with this workflow from this standard and 3 additional samples, including Gram-positive and Gram-negative bacteria and human fecal matter samples.
