A comparison of DNA/RNA extraction protocols for high-throughput sequencing of microbial communities.
Justin P ShafferClarisse MarotzPedro Belda-FerreCameron MartinoStephen WandroMehrbod EstakiRodolfo A SalidoCarolina S CarpenterLivia S ZaramelaJeremiah J MinichMacKenzie BryantKarenina SandersSerena FraraccioGail AckermannGregory HumphreyAustin D SwaffordSandrine Miller-MontgomeryRob KnightPublished in: BioTechniques (2021)
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.
Keyphrases
- microbial community
- nucleic acid
- sars cov
- antibiotic resistance genes
- high throughput
- respiratory syndrome coronavirus
- circulating tumor
- high throughput sequencing
- single cell
- cell free
- coronavirus disease
- single molecule
- randomized controlled trial
- risk assessment
- human health
- healthcare
- drinking water
- real time pcr
- gram negative
- heavy metals