A Comparison of DNA/RNA Extraction Protocols for High-Throughput Sequencing of Microbial Communities
Justin P. Shaffer, Clarisse Marotz, Pedro Belda‐Ferre, Cameron Martino, Stephen Wandro, Mehrbod Estaki, Rodolfo A. Salido, Carolina S. Carpenter, Lívia S. Zaramela, Jeremiah J. Minich, MacKenzie Bryant, Karenina Sanders, Serena Fraraccio, Gail Ackermann, Gregory Humphrey, Austin D. Swafford, Sandrine Miller‐Montgomery, Rob Knight
Abstract
One goal of microbial ecology researchers is to capture the maximum amount of information from all organisms in a sample. The recent COVID-19 pandemic, caused by the RNA virus SARS-CoV-2, has highlighted a gap in traditional DNA-based protocols, including the high-throughput methods the authors previously established as field standards. To enable simultaneous SARS-CoV-2 and microbial community profiling, the authors compared the relative performance of two total nucleic acid extraction protocols with the authors' previously benchmarked protocol. The authors included a diverse panel of environmental and host-associated sample types, including body sites commonly swabbed for COVID-19 testing. Here the authors present results comparing the cost, processing time, DNA and RNA yield, microbial community composition, limit of detection and well-to-well contamination between these protocols.