Over the past many years I have led the development of several synthetic biology tools and functional genomics technologies to better characterize microbial 'dark-matter' and use that information for a number of biotechnological applications. Very recently, I led the development of a high-throughput functional genomics technology named Dual Barcoded Shotgun Expression Library Sequencing (Dub-seq, winner of R&D100 award-2017), that uses barcoded shotgun expression libraries and increases the throughput of functional screens in the presence of antibiotics, metals and stresses. Recently, we expanded these high-throughput methods to study bacteriophages, and host factors involved in phage infection and resistance. These studies offer a rational approach in formulating antibiotic and phage cocktails for treating bacterial infections. Using the same technology platform, we have uncovered the specificity of interaction between phage-tail-like-bacteriocins and bacterial predators with prey bacteria. These studies have not only filled an important technology gap in mapping the resistance landscape at a scale that has not been possible before but also enabled gene-function annotations in both phages and bacterial predators and target host bacteria
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