Metabolomic Comparison and Assessment of Co-cultivation and a Heat-Killed Inducer Strategy in Activation of Cryptic Biosynthetic Pathways

Abstract

Co-cultivation has been used as a promising tool to turn on or up-regulate cryptic biosynthetic pathways for microbial natural product discovery. Recently, a modified culturing strategy similar to co-cultivation was investigated, where heat-killed inducer cultures were supplemented to the culture medium of producer fermentations to induce cryptic pathways. In the present study, the repeatability and effectiveness of both methods in turning on cryptic biosynthetic pathways were unbiasedly assessed using UHPLC-HRESIMS-based metabolomics analysis. Both induction methods had good repeatability, and they resulted in very different induced metabolites from the tested producers. Co-cultivation generated more induced mass features than the heat-killed inducer cultures, while both methods resulted in the induction of mass features not observed using the other induction method. As examples, pathways leading to two new natural products, <i>N</i>-carbamoyl-2-hydroxy-3-methoxybenzamide (<b>1</b>) and carbazoquinocin G (<b>5</b>), were induced and up-regulated through co-culturing a producer <i>Streptomyces</i> sp. RKND-216 with inducers <i>Alteromonas</i> sp. RKMC-009 and <i>M. smegmatis</i> ATCC 120515, respectively.