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: bioRxiv : the preprint server for biology (2020)
One goal among 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 we previously established as field standards. To enable simultaneous SARS-CoV-2 and microbial community profiling, we compare the relative performance of two total nucleic acid extraction protocols and our previously benchmarked protocol. We included a diverse panel of environmental and host-associated sample types, including body sites commonly swabbed for COVID-19 testing. Here we 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
- high throughput
- antibiotic resistance genes
- respiratory syndrome coronavirus
- high throughput sequencing
- circulating tumor
- randomized controlled trial
- coronavirus disease
- cell free
- risk assessment
- human health
- drinking water
- healthcare
- social media
- gram negative
- health information
- real time pcr
- multidrug resistant