The primary focus of the lab is metagenomics. Microorganisms dominate the biosphere and the vast majority of them are recalcitrant to cultivation and hence their potential remains hidden. Considering the number of biocatalysts and therapeutic agents derived from the negligible number of cultivable bacterial population, the undiscovered bacterial population holds a treasure of novel bioactive compounds, having tremendous application potential. The estuaries, mangroves and forests of Kerala are rich biodiversity hotspots and the microbial resources of these environments have never been studied in detail. The generation of metagenomic libraries using the DNA from various environments and functional screening of the clones revealed several potential industrial and therapeutic enzymes and antimicrobial molecules. Further, we concentrated on therapeutic enzymes and discovered a novel asparginase from a forest soil metagenomic library with improved properties, than the enzyme currently used for Acute lymphoblastic leukemia therapy. Increasingly invasive fungal infections have become a public health concern and hence there is a growing need for novel drugs with specific antifungal activity. Currently, we are screening the metagenomic libraries for potential antifungal molecules. The libraries are also being screened for potential enzymes involved in the degradation of synthetic polymers. We are also into studies assessing the bacterial diversity of various environments including the rhizosphere microbiome and human gut microbiome through 16S gene targeted Next Generation Sequencing and functional approaches. We are also interested in bacterial biopolymers and isolated several bacteria producing Polyhydroxybutyric acid (PHB), a biodegradable thermoplastic from various environments in Kerala. The PHB biosynthetic gene cluster from a high yielding isolate has been cloned and a recombinant system producing the biopolymer was developed in E. coli.
The studies envisage construction of metagenomic libraries from various environments and screen them for genes conferring various functional attributes. The approach will help in the isolation of novel genes leading to the discovery of enzymes with immense industrial and therapeutic potential and new antimicrobial molecules remain hidden, in the genomes of microorganisms without culturing them. During the functional screening of a library generated form forest soil, a clone depicting L-asparginase activity was further characterised. The genetic element responsible for the enzyme production in the clone was sub cloned and generated a recombinant system overproducing the enzyme. The enzyme production was optimised and scaled up in a laboratory fermenter. The activity of recombinant enzyme was found to be much higher compared to the commercially available E. coli asparaginase used in leukemia therapy. The enzyme was characterised in-vitro and observed better substrate affinity and improved cytotoxicity on Acute lymphoblastic leukemia cell lines, proving the enhanced therapeutic potential of the enzyme. In-vivo cytotoxicity studies on blab/c mice depicted that the recombinant asparaginase preparation is non-toxic to various tissue samples. These findings indicate the suitability of the soil metagenome derived recombinant asparaginase to be developed as a better drug in the treatment of acute lymphoblastic leukemia.
The knowledge on the bacterial diversity in different environments is limited, since many of them cannot be cultured by current culture-based traditional methods. In our lab, we analyzed the complex genomes of microbial niches through culture-independent molecular techniques by sequencing the 16S rRNA and phylogenetic analysis to unravel the structure of natural microbial communities. So far, we have looked into the bacterial diversity of Arctic sediments, forest soils, wetland sediments and rice rhizosphere.
Climate has far reaching impacts on biological systems in the biosphere. Microbes act as climate engineers by playing the pivotal role in geochemical cycles. Wetlands are important ecosystems in methane cycle, as the methanotrophs residing serve as methane filter and limit methane emissions, one of the crucial factors responsible for global warming and climate change. Yet, little is known about the diversity of the methanotrophs in the wetlands, and only a few isolates are known. The study envisages assessing the biodiversity of methanotrophic communities in the wetland ecosystems in Kerala through metagenomic approach and to evaluate their biodegradation potential. During the study, isolated three methylotrophs from the wetland and assessed their methanol dehydrogenase activity responsible for methanol oxidation in-vitro and the genes involved in methanol metabolism, mxaF and xoxF were characterised. Among the isolates, Methylobacterium radiotolerans KUT39 recorded the highest enzyme activity.
The human gastrointestinal environment harbours a complex microbial ecosystem. Since majority of the gut microbes are culture reluctant, the metagenomic approach along with next generation sequencing is the most pertinent method to get a comprehensive knowledge on gut microbial ecology and how they influence on health and diseases. The incidence of diabetes in Indian population and particularly in Kerala is showing an increasing trend. Hence, it is worthwhile to look into the role of gut microbiota as an etiology in high incidence of diabetes apart from the lifestyle and genetic predisposition. The investigation is an attempt to analyse the diversity and function of the gut microbiota from type 2 diabetic patients, as represented in stool samples though metagenomic approach. One common observation during the study is that the gut bacteria belonged mainly to two phyla, Firmicutes and Bacteroidetes, with a smaller representation of Proteobacteria and Actinobacteria. The prominent group was found to be Bacteriodetes in all the samples, represented mostly by the genus Prevotella without significant variation between the healthy and diabetic subjects. Firmicutes represented 33% of the gut bacterial community and are mostly represented by Clostridia. The genera Ruminococcus, Veillonella, Klebsiella, Akkermansia, Streptococcus, Lactobacillus, Serratia, Citrobacter, Clostridium, Enterobacter and Desulfovibrio were underrepresented in diabetic people in comparison with healthy subjects.
PHB [Poly(3-hydroxybutyric acid)] is a biodegradable thermoplastic accumulated by several microorganisms as carbon and energy reservoir. They are immunologically compatible with human tissue and can be used as biodegradable carriers for controlled drug release and are currently used in industry and medicine. The main limitations for the bulk production of bioplastics are its high production and recovery costs. Generation of recombinant organisms for the biosynthesis of PHB will improve the production and reduce the costs. PHB accumulating bacteria were screened out from various environmental conditions and the high yielding Bacillus aryabhattai was selected for cloning. PHB biosynthetic gene cluster of this bacterium was amplified, characterised and engineered a recombinant E. coli. for heterologous expression of the genes and polymer production. The recombinant PHB was characterised for their various physico-chemical properties.
Previous/ Completed Research Grants
Metagenomic analysis of gut microbiome from type 2 diabetic subjects in Kerala - a preliminary study
Kerala State Council for Science, Technology and Environment [KSCSTE] 2014-2017
Studies on the distribution and diversity of methanotrophic microbial communities, mitigating methane emission in Kuttanad wetland ecosystem, Kerala
Department of Environment and Climate Change, Govt. of Kerala 2013-2016
A novel site specifically targeting nanoparticle based oral - drug and siRNA releasing polymer systems for colon cancer (Co-PI).
Department of Biotechnology [DBT] 2010-2013
Generation of metagenomic libraries for screening novel bioactive compounds
Kerala State Council for Science, Technology and Environment [KSCSTE] 2008-2009
Detection and molecular characterization of microbial population from different polluted zones caused by coir retting
Department of Biotechnology [DBT] 2002-2004
Molecular characterization of the pesticide/heavy metal compounds degrading microorganisms isolated from the Kuttanad and other waterbodies of Kerala
Department of Biotechnology [DBT] 2001-2003