Anannya Roy, Amity University Kolkata
Microbial Ecology known as environmental microbiology is the study of microorganisms’ relationship with each other as well as their environment. The main goal of researchers in this department is to capture the maximum amount of information from all organisms that are present in a given sample. Traditionally DNA-based protocols are used for such community analysis.
Today the world is suffering from the impact of the Covid-19 pandemic. The interesting fact is that the genome of SARS-Cov-2 is a positive-sense single-stranded RNA. Such RNA based organisms cannot be detected using the DNA based protocols, as a result of which recent months have seen the development of new methods. Researchers wanted to identify an extraction protocol that can extract both high-quality RNA and produce DNA output.
The traditional protocol utilized is the Quigen MagAttract PowerSoil DNA Isolation Kit referred to as ‘Power-soil .’ MagMAX Microbiome Ultra Nucleic Acid Isolation Kit, having two variants- the MagMAX 20 minute protocol and the MagMAX 2 minute protocol.
A diverse panel of samples collected from both Human and Environmental sources included 33 skin samples, six fecal samples, four water samples, two tissue samples, and much more. Then, nucleic acids were extracted in the laboratory. This was done in both ways- the traditional DNA extraction protocol and the novel protocol that could extract both RNA and DNA, after which comparisons were analyzed between the two. Metagenomic sequencing was done to identify the proteins, enzymes, genes, and biochemical pathways in the organisms.
It was observed that the new kits were similar concerning RNA efficiency, but differed according to the quantity produced. After evaluating both, based upon the time and cost, it was concluded that the MagMAX 2 minute protocol is a more efficient alternative to PowerSoil. This research provides us insights on the ongoing quest for the development of computational methods that could reduce experimental variations and explore new molecular methods for improving our understanding of microbial ecology.
Also read: Can the MMR Vaccine provide protection against COVID-19!
Source:
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, Livia S. Zaramela, Jeremiah J. Minich, MacKenzie Bryant, Karenina Sanders, Serena Fraraccio, Gail Ackermann, Gregory Humphrey, Austin D. Swafford, Sandrine Miller-Montgomery, Rob Knight https://www.biorxiv.org/content/10.1101/2020.11.13.370387v1
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