Deep sequencing of secondary meta-metabolomes: A preliminary screening tool for determining natural product diversity

Increasingly, natural product isolation strategies are circumventing culture-dependent methods for the isolation secondary metabolite genes directly from the environment. Many of these isolation strategies are undertaken with little knowledge of an environment's specific secondary metabolite potential. Next-generation sequencing technology was used to determine the diversity of non-ribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) genes within multiple environments to a depth previously not reported. A multiplexing strategy was used to amplify thousands of ketosynthase and amino acid condensation domain sequences from over thirty different environments. Sequences were differentiated according to function and taxonomic origin, as well as their distribution within distinct environments. Similar patterns of NRPS and PKS occurrence were observed between functionally similar but geographically distinct environments. Furthermore, increases in microbial diversity between environments did not influence the occurrence of these genes. It is expected that this approach will be applied to any environment enabling for the tailoring of culture-dependent and culture-independent strategies for the isolation of novel natural products.