Current Research Interests

The highly diverse and ubiquitous lifestyles of bacteria have always fascinated me. It is indeed remarkable that a teeny-tiny organism, invisible to naked eyes can have a great impact on our lives. From the microbiome we harbour in and out of our body to the nitrogen fixing bacteria in the environment encompass a very large collection of different bacteria. On the contrary are pathogens, which even though fractionally small compared to the former, are responsible for millions of deaths across the world. I study these ‘villainous bacteria’, responsible for several casualties worldwide. My research focusses mainly on evolution of antibiotic resistant superbugs, virulence evolution of enteric and intracellular pathogens. I use a combination of phylogenetics and comparative genomics approaches to study the evolutionary dynamics of these pathogens.

1. Detection of Footprints of Adaptive Evolution in Bacterial Genomes: With the advent of the second- and third-generation sequencing technologies, our databases are now flooded with invaluable sequence data. The wealth of bacterial genome data publicly available for us will provide a great deal of information about their evolution. In the case of antibiotic resistant or virulent pathogens, they constantly encounter a great deal of selection pressure from antibiotics, host immune response etc. In order to survive in such hostile niches, pathogens undergo positive selection to emerge as superbugs. The evolution of bacteria in such conditions are often due to accumulation of certain advantageous mutations. Those advantageous mutations which confer pathogens a selective advantage in the presence of a selection pressure are termed adaptive mutations. We use a combination of robust microevolutionary analysis and simulation under neutrality to detect footprints of adaptive evolution (due to adaptive mutations) in genome.

2. Role of Truncation Mutations in Virulence Evolution: Formation of pseudogenes via accumulation of truncation mutations are a common observation in bacterial genomes. The common belief is that, such sort of gene inactivation occurs via ‘use or lose’ dynamics, where the organism purges traits which are no longer essential for their survival in a novel niche as frequently observed in the case of host-restricted and host-adapted bacteria. It is a major defining characteristic of reductive evolution. However, preliminary data from Dr. Sujay Chattopadhyay’s lab hint at the possibility of formation of pseudogenes via accumulation of truncation mutations due to adaptive evolution. This evolutionary dynamic, unlike reductive evolution follows a ‘die or lose’ dynamics, characterized by purging of traits which can be deleterious in a novel niche. It is also described in the light of antagonistic pleiotropic theory and the concept of antivirulence. The focus of this study would be primarily on serovars of  Salmonella enterica Subspecies 1 and aims to develop a novel analytical tool to decipher the adaptive significance of gene truncations leading to a lose of protein functionality.