Scale-up and Optimization of Natural Product Fermentation Processes using Mass-Guided Metabolite Fingerprinting

Microbial secondary metabolites represent a rich, chemically-diverse source of bioactive compounds that have been exploited for applications in human medicine, agriculture, and industry [1-3]. Natural product fermentation bioprocesses have remained an important tool in efforts to acquire chemical diversity in bioactive compound libraries for lead generation [4]. In recent years, natural product discovery groups have become increasingly focused on optimization of scale-up processes to successfully re-supply target-directed biological assays, and subsequent structural elucidation efforts to structurally-characterize bioactive compounds [3,5]. Changes in this workflow have been driven by wide scale adoption of miniaturized high-throughput screening technology (HTS) that has significantly reduced the sample volume that is available for parallel discovery efforts, and has increased the difficulty in achieving equivalent chemical output of bioactive metabolites during scale-up fermentation processes [6,7]. Fermentation systems supporting HTS screening efforts have subsequently been miniaturized (0.1-10mL) into formats that have enhanced their compatibility with the liquid handling and microfludic components, and have dramatically enhanced total throughput of discovery processes [8-10]. Once novel bioactive compounds have been identified using HTS approaches, the producing microorganism is transferred to larger volume fermentation