In this proposal, we aim to validate the human gut microbiome and arid soil as a source of antibiotic natural products (NPs ) by using a metagenomic NP discovery platform developed at Radiant Genomics. Recent studies suggest that the genomes of uncultivated microorganisms, like their cultivated counterparts, encode an enormous number of NPs. Gaining systematic access to NPs using standard, cultivation-dependent approaches, however, remains challenging as <1% of microbial diversity has been successfully cultured in a laboratory setting. In the interest of expanding the list of currently-available antibiotic pharmacophores, our company has built a metagenomic platform (which overcomes cultivation barriers) for discovering, producing, and diversifying NPs from complex microbiomes. At its core, this platform consists of a world-class pipeline for sequencing, assembling, refactoring, and expressing full-length NP gene clusters from complex environments, including uncultivated microbes. Our system identifies NP-encoding gene clusters using both a sequence-guided search engine and a droplet microfluidics-based antibacterial screening technology that has capacity to analyze >10^7 clones/day. Because our libraries are renewably cloned, we can rapidly isolate, assemble, refactor and heterologously express selected gene clusters in our panel of metabolically-optimized, gram(+ and -) industrial host strains, resulting in high-throughput, systematic identification of novel NPs.
