NextGen microbial natural products discovery

Small-molecule secondary metabolites isolated from microorganisms and plants provide the chemical scaffolds of a large fraction of today’s pharmaceuticals. Evolutionary forces shaped the molecular complexity of these natural products that contribute to the exquisite binding of these compounds to biological targets. Starting with the discovery of penicillin by Fleming, we have seen a rapid increase in the discovery and production of natural products and derivatives thereof as antibiotics and other drugs. But once the ‘easy to access’ bioactive compounds have been isolated, the drug discovery pipeline slowed down beginning in the 1990s. Pharmaceutical companies turned away from natural products as screening programmes led to the rediscovery of known structures and development of structurally complex natural products into drugs using synthetic methods proved to be challenging and too expensive if no reliable biological sources were available. Considering the urgent need for the development of new drugs to combat multidrug-resistant pathogens and overcome long-term side-effects and/or reduction in effectiveness of current drugs, unlocking nature’s treasure trough of smallmolecule chemodiversity will be crucial for next-generation drug development (Gerwick and Moore, 2012; Basmadjian et al., 2014; Genilloud, 2014). Driven by advances in sequencing, gene synthesis, bioinformatics and metabolomics, the natural products discovery process is beginning to undergo a major transformation – away from the tedious isolation, screening and dereplication process to in silico-based bioprospecting approaches that seek to eventually transform genomic information directly into biosynthetic outputs (Lewis, 2013; Deane and Mitchell, 2014). The explosion in the number of available microbial genome sequences has given us a glance at the hidden natural product biosynthetic capacity of these organisms. Based on known sequence information for enzymes involved in synthesizing, e.g. the scaffolds of bioactive polyketides, non-ribosomal peptides or terpenes, numerous gene clusters (fungi) and operons (bacteria) can be identified in microbial genomes that are silent and for which no secondary metabolite products have been identified. This also includes many well-studied natural products producers such as Streptomyces and Aspergillus strains that express only a subset of their secondary metabolome under typical laboratory growth conditions (Brakhage, 2013; Doroghazi and Metcalf, 2013; Lim and Keller, 2014; Rebets et al., 2014). Our sequencing capacity is outpacing – by orders of magnitude – our ability to identify natural products gene cluster and most importantly, translate this sequence information into screenable molecules. The number of sequenced microbial genome sequences is rapidly approaching 5000 sequenced genomes, of which a large majority is bacterial genomes with only a few hundred fungal genomes available. With this large number of sequences available, the question becomes ‘How does one most effectively search this vast sequence space for interesting natural products pathways?’ One approach commonly used is to focus on a few groups of bacteria of fungi known to produce bioactive natural products and comprehensively identify within their genomes natural products biosynthetic operons or gene cluster, and then target the most diverse biosynthetic gene cluster for characterization. In many cases, products of target gene clusters are not produced at all or only at very low levels under laboratory growth conditions, requiring gene cluster activation either through exogenous stimuli or manipulation of genetic control elements which may be strain specific and a laborious undertaking. In the case that a strain is genetically tractable, gene disruption can then be used to specifically characterize biosynthetic gene functions. This ‘reverse discovery’ approach has been quite successfully used in genome-driven bioprospecting for a number of natural products identified in bacteria and some filamentous fungi (Lewis, 2013; Deane and Mitchell, 2014; Jensen et al., 2014). Such ‘reverse discovery strategies’, however, are limited to microorganisms that can be cultivated in the laboratory and that can be genetically manipulated, leaving out enormous biosynthetic diversity found in unculturable microbial species such as many higher fungi (see below) and from complex microbial ecosystems. Recent work has shown that metagenomic libraries from microbial ecosystems can be successfully arrayed and screened for large biosynthetic gene clusters of interest based on homology to conserved regions of known Microbial Biotechnology (2015) 8(1), 26–28 doi:10.1111/1751-7915.12184 bs_bs_banner