Chennai: Researchers from the Indian Institute of Technology Madras (IIT Madras) and leading US institutions have identified and reconstructed 1.3 million virus genomes from freshwater lakes. This is now the largest freshwater virus genome study of its kind.
This groundbreaking research by IIT Madras and US researchers, published in Nature Microbiology, is based on over two decades of environmental DNA data and has significant implications for human health, ecology and environmental management.
The study, led by Dr Karthik Anantharaman, visiting professor at IIT Madras’ Wadhwani School of Data Science and AI, and Associate Professor at the University of Wisconsin-Madison, used advanced machine learning tools to decode microbial life from 465 lake water samples collected from Madison, Wisconsin.
It is considered the longest DNA-based environmental monitoring effort ever undertaken.
The research spotlights the growing field of “phage therapy”, a promising approach that employs viruses, specifically phages, to eliminate drug-resistant bacteria.
In addition to potential medical applications, the study demonstrates how viruses can stabilise ecosystems, much like apex predators do in animal food chains.
“This study fills a major gap in our understanding of viral communities in natural environments,” said Dr Anantharaman. “By tracking how viruses evolve and respond to environmental changes, we can better predict future outbreaks and manage ecosystems.”
Using metagenomics to sequence environmental DNA, researchers discovered that viral populations display seasonal cycles and return year after year, offering predictive insights into ecological behaviour.
Strikingly, they found 578 viral genes that play roles in photosynthesis and methane metabolism, showing how viruses “steal” and repurpose host genes for their survival and impact on biogeochemical cycles.
The findings also reveal that viral evolution is shaped by pollution indicators like carbon and ammonium levels, highlighting the broader environmental relevance of viral studies.
Such data could one day help restore polluted lakes by using viruses to prevent harmful algal blooms and waterborne bacterial outbreaks.
Welcoming the research, Prof Karthik Raman from IIT Madras said, “Viruses are often misunderstood. Many actually help maintain ecological balance and microbial health, making them key allies in understanding both nature and disease.”
