Digging deep into the arsenal of calcium-dependent antibiotics through highly targeted genotype-based selection

There is a pressing need for novel antibiotics in face of increasing
drug resistance. Most antibiotics in clinical use are derived from
natural products. It is generally accepted that there is still an
enormous untapped potential left, especially in soil. However, many
promising strains remain out of reach of functional exploration
because of their low abundance, compounded by limited culturability
under standard lab conditions. In this proposal, we will harness the
power of culture-independent, genotype-based selection, while
dramatically improving the lower limit of detection - aiming for singleclone
sensitivity. We will investigate the feasibility of achieving this
aim by adapting a high-throughput droplet microfluidics platform to
perform digital PCR for eDNA cosmid clone selection. To
demonstrate proof of concept, we will focus on beta-lactam
antibiotics, with the aim of discovering structurally novel building
blocks of this important class of antibiotics. Next, we will explore
whether the capabilities of the resulting platform can be expanded to
allow genotype-based selection of single cells, based on taxonomic
markers informed by publicly available metagenomics studies. This
would enable the enrichment of specific, rare, high-interest
taxonomic groups for targeted whole-genome sequencing. This
analysis is expected to yield a wealth of potentially novel antibiotic
classes, thus opening the door to truly transformative discovery of
novel natural products.