A comparison of DNA/RNA extraction protocols for high-throughput sequencing of microbial communities
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.
Document Details
- Document Type
- Pub Defense Publication
- Publication Date
- Mar 01, 2021
- Source ID
- 10.2144/btn-2020-0153
Entities
People
- Austin D Swafford
- Cameron Martino
- Carolina S. Carpenter
- Clarisse Marotz
- Gail Ackermann
- Gregory Humphrey
- Jeremiah J Minich
- Justin P Shaffer
- Karenina Sanders
- Livia S Zaramela
- MacKenzie Bryant
- Mehrbod Estaki
- Pedro Belda-ferre
- Rob Knight
- Rodolfo A Salido
- Sandrine Miller-montgomery
- Serena Fraraccio
- Stephen Wandro
Organizations
- Crohn's & Colitis Foundation of America
- Defense Advanced Research Projects Agency
- National Institutes of Health
- United States Department of Defense
- University of California, San Diego