Sani, Rajesh

• Ph.D., Institute of Microbial Technology/Panjab University

• M.S.C., Indore University

• B.S.C., Meerut University

This proposal aims to establish a genome-enabled discovery platform for identifying thermophile-derived small-molecule inhibitors targeting pathogenic biofilms. Pathogenic biofilms formed by Staphylococcus aureus and Escherichia coli contribute significantly to persistent infections and antibiotic tolerance, underscoring the need for alternative anti-pathogenic strategies. Thermophilic microorganisms represent an underexplored source of chemically stable and structurally novel metabolites with potential anti-biofilm activity. 

Using the extensive thermophile collection housed in the MASON laboratory at South Dakota Mines, 15 representative thermophiles will be cultured under defined thermophilic conditions and subjected to whole-genome sequencing using in-house Nanopore technology. Genomes will be annotated to identify biosynthetic gene clusters and KEGG-defined metabolic pathways, enabling systematic prediction of small-molecule candidates. These genome-derived predictions will be curated into a relational database that links strains, pathways, biosynthetic features, and predicted metabolites. Computational prioritization will be performed using molecular docking against key biofilm-associated targets from S. aureus and E. coli.

Three top-ranked candidates will be experimentally validated using crude lysate preparations in standardized in vitro biofilm assays to assess biofilm-specific inhibition. By integrating genomics, computation, and experimental validation, this project will generate a scalable discovery pipeline and a ranked set of thermophile-derived anti-biofilm candidates, positioning the work for future metabolite purification, mechanistic studies, and translational funding opportunities.

This pilot study will generate preliminary data supporting future NIH R15/STRR proposals and academic-year research. The project emphasizes hands-on student training in small molecule discovery, biofilm assays, anti-pathogenic biofilm modulation while aligning with SD INBRE's mission of fostering biomedical research and undergraduate mentorship in South Dakota.