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

Period of Performance: 09/09/2015 - 03/18/2017


Phase 1 SBIR

Recipient Firm

Carrera Bioscience
PO Box 100 Array
Ithaca, NY 14850
Firm POC
Principal Investigator


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 technical challenges: i) difficulty in dissecting complex microbiome samples and massive metagenomics data, and ii) difficulty in culturing the uncultivable bacteria to induce normally silent biosynthetic gene clusters (BGCs). Carrera Bioscience proposes a strategy to enrich antimicrobial-expressing BGCs from mixed bacteria samples both experimentally and bioinformatically via a high throughput screen (HTS). About 4000 culture conditions will be screened for induction of antimicrobial activities followed by high throughput transcript amplicon sequence analysis targeting the major SM synthases. A panel of bacterial strains with antibiotic-producing potential derived from healthy dolphin fecal microbiota will be used as source microbes to demonstrate the feasibility of this strategy. This approach will significantly reduce the complexity of initial bioinformatics analyses compared to whole genome mining or even genome-based targeted amplicon analysis. At the same time, it is capable of identifying culture conditions that can activate antibiotics expression from normally silent BGCs. The responsible microorganisms and gene clusters will be verified and refined by a secondary screen and genome/transcriptome-based analyses.