Approaches to Capturing and Designing Biologically Active Small Molecules Produced by Uncultured Microbes

Bacteria are one of the most important sources of bioactive natural products for drug discovery. Yet, in most habitats only a small percentage of all existing prokaryotes is amenable to cultivation and chemical study. There is strong evidence that the uncultivated diversity represents an enormous resource of novel biosynthetic enzymes and secondary metabolites. In addition, many animal-derived drug candidates that are structurally characterized but difficult to access seem to be produced by uncultivated, symbiotic bacteria. This review provides an overview about established and emerging techniques for the investigation and exploitation of the environmental metabolome. These include metagenomic library construction and screening, heterologous expression, community sequencing, and single-cell methods. Such tools, the advantages and shortcomings of which are discussed, have just begun to reveal the full metabolic potential of free-living and symbiotic bacteria, providing exciting new avenues for natural product research and environmental microbiology.