Concurrent identification of Natural Antibiotics-Producing Gene Clusters and Culture Conditions

Modern metagenomics studies on diverse microbiomes revealed immense repertoires of potential natural products/antibiotics to be tapped into.However, identifying such secondary metabolites (SMs) directly from a complex microbiome remains rarely successful due to two major technicalchallenges: i) difficulty in dissecting complex microbiome samples and massive metagenomics data, and ii) difficulty in culturing the uncultivablebacteria to induce normally silent biosynthetic gene clusters (BGCs). Carrera Bioscience proposes a strategy to enrich antimicrobial-expressingBGCs from mixed bacteria samples both experimentally and bioinformatically via a high throughput screen (HTS). About 4000 culture conditionswill be screened for induction of antimicrobial activities followed by high throughput transcript amplicon sequence analysis targeting the major SMsynthases. A panel of bacterial strains with antibiotic-producing potential derived from healthy dolphin fecal microbiota will be used as sourcemicrobes to demonstrate the feasibility of this strategy. This approach will significantly reduce the complexity of initial bioinformatics analysescompared to whole genome mining or even genome-based targeted amplicon analysis. At the same time, it is capable of identifying cultureconditions that can activate antibiotics expression from normally silent BGCs. The responsible microorganisms and gene clusters will be verifiedand refined by a secondary screen and genome/transcriptome-based analyses.