Ph.D. candidate
Abhinaba Chakraborty
Microbiology Laboratory, Department of Botany, Siksha-Bhavana, Visva-Bharati, Santiniketan, Birbhum, West Bengal
Title: A rapid, cost-effective, efficient method for total RNA extraction from pure bacterial cultures and complex microbiomes and its effectiveness in deciphering functionally active microbial populations
Name(s): Abhinaba Chakraborty (Presenting author), Bomba Dam (Corresponding author)
Microbiology Laboratory, Department of Botany, Siksha-Bhavana (Institute of Science), Visva-Bharati (A central university and an institution of National importance), Santiniketan, Birbhum, West Bengal, India
Extraction of high-quality RNA from microbial samples, especially complex microbiomes like the gut, remains a significant challenge. The instability of RNA, coupled with the abundance of RNases and the difficulty of lysing microbial cells, often results in degraded or low-yield RNA, hampering downstream applications. To overcome this critical bottleneck, we developed a simple, rapid, cost-effective, and efficient microbial RNA extraction method, which is equally effective for pure cultures and complex microbiomes. The method utilises low pH (4.7) and high temperature to lyse the cells, followed by rapid cooling to induce misfolded renaturation of genomic DNA and proteins. During the phase separation step, RNA remains in the aqueous phase and is subsequently precipitated using chilled isopropanol. The RNA suspended in double-distilled water (pH 6.5) remained stable for six months at -20 °C. Further, we compared amplicon microbiome profiles generated from metagenomic DNA and cDNA (synthesised from extracted meta-RNA) derived from the broiler gut, taken as a model system. Our findings reveal that cDNA-based amplicon microbiome composition more accurately deciphers the metabolically active population in gut environments, aligning with culture-based enumeration of viable microbes. This proof-of-concept study underscores the importance of meta-RNA approaches for functional microbiome analysis and provides a reliable RNA isolation method that can be broadly adopted for studies aimed at resolving active microbial community structure.
Biography of the presenting author
Abhinaba Chakraborty is final year PhD student. He has already given the pre-PhD seminar and is soon to graduate from the course. He has already published 9 research articles in reputable international journals.
Full name: Abhinaba Chakraborty
Contact number: +91 8250830483
Email: chakrabortyabhinaba04@gmail.com
Researchgate: https://www.researchgate.net/profile/Abhinaba-Chakraborty-4
Google Scholar: https://scholar.google.com/citations?user=DKXs4VwAAAAJ&hl=en
ORCID: 0000-0002-5689-0108
Session name/ number: 6. Bioinformatics and Microbiome
Category: Oral presentation