ABSTRACT
Over the last 20 years, the field of natural products has seen a dramatic resurgence. It is not a coincidence that this revival coincides with the drastic decrease in cost and marked increase in ease of DNA sequencing. The abundance of microbial genomes available today illuminates the fact that these organisms have a vastly greater biosynthetic capacity than previously thought. Many of these biosynthetic pathways are orphans, meaning they correspond with no identified natural product. This chapter highlights current methods employed to induce and detect the products of orphan pathways. Strategies to evoke upregulation of biosynthetic pathways include genetic manipulation, media manipulation, and biotic interactions. Given that natural product pathways likely evolved to offer the producing organism a competitive advantage, it is plausible that many energetically costly natural products are only activated in response to microbial challenge, a condition atypical in most lab studies. Microbial challenge presents obstacles in terms of detecting changes in metabolic profiles of cultures in response to co-cultivation. This requires highly sensitive analytical methods, including comparative metabolite profiling by HPLC-UV or LC/MS, spatially resolved MS, MALDI MS, nanospray DESI MS, and NMR. Promising future research opportunities include emulating the natural habitats of microorganisms to probe ecological impacts of biotic interactions, cultivation-independent methods for evaluation of pathway induction, and identification of the ecological functions of these secondary metabolites.
