Triaging of Culture Conditions for Enhanced Secondary Metabolite Diversity from Different Bacteria

Abstract

Over the past decade, the one strain many compounds (OSMAC) approach has been established for the activation of biosynthetic gene clusters (BGCs), which mainly encode the enzymes of secondary metabolite (SM) biosynthesis pathways. These BGCs were successfully activated by altering various culture conditions, such as aeration rate, temperature, and nutrient composition. Here, we determined the biosynthetic potential of 43 bacteria using the genome mining tool antiSMASH. Based on the number of BGCs, biological safety, availability of deposited cultures, and literature coverage, we selected five promising candidates: Bacillus amyloliquefaciens DSM7, Corallococcus coralloides DSM2259, Pyxidicoccus fallax HKI727, Rhodococcus jostii DSM44719, and Streptomyces griseochromogenes DSM40499. The bacteria were cultivated under a broad range of OSMAC conditions (nutrient-rich media, minimal media, nutrient-limited media, addition of organic solvents, addition of biotic additives, and type of culture vessel) to fully assess the biosynthetic potential. In particular, we investigated so far scarcely applied OSMAC conditions to enhance the diversity of SMs. We detected the four predicted compounds bacillibactin, desferrioxamine B, myxochelin A, and surfactin. In total, 590 novel mass features were detected in a broad range of investigated OSMAC conditions, which outnumber the predicted gene clusters for all investigated bacteria by far. Interestingly, we detected mass features of the bioactive compounds cyclo-(Tyr-Pro) and nocardamin in extracts of DSM7 and DSM2259. Both compounds were so far not reported for these strains, indicating that our broad OSMAC screening approach was successful. Remarkably, the infrequently applied OSMAC conditions in defined medium with and without nutrient limitation were demonstrated to be very effective for BGC activation and for SM discovery.

Combining OSMAC Approach and Untargeted Metabolomics for the Identification of New Glycolipids with Potent Antiviral Activity Produced by a Marine Rhodococcus

“…As a fact, through culture media variation (i.e., varying the concentration of carbon, nitrogen, phosphorous, inorganic salts, etc. ), it is possible to upregulate or trigger the production of certain secondary metabolites produced by talented microorganisms [7,[46][47][48]. In this study, the OSMAC strategy associated to bioassays allowed the selection of a specific growth condition expressing unique, structurally related metabolites, as highlighted by molecular networking (MN).…”

In Vitro Production and Exudation of 20-Hydroxymaytenin from Gymnosporia heterophylla (Eckl. and Zeyh.) Loes. Cell Culture

“…Acquisition by the DAD detector was performed at 400 nm and by the mass spectrometer, in positive mode from 90 to 900 m/z. The source parameters were established similar to previous publications [ 53 , 54 , 55 ]: 4 bar for nebulizing gas pressure, 12 L/min for a dry gas (N2) flow, 220 °C for the desolvation gas (N2) temperature, and 4.5 kV for a capillary voltage.…”

Bivariate OSMAC Designs Expand the Secondary Metabolite Production Space in Corallococcus Coralloides

“…Although a high number of BGCs can be found in the genome of C. coralloides (Figure S1), none of the predicted compounds were detected up to now [11]. Thus, the activation of the biosynthetic potential requires a different approach.…”

“…coralloides possesses a large genome of 10.08 Mbp and 33 BGCs coding for potential SMs and accordingly has a large biosynthetic potential [11] (and new genome analysis for this study). However, in our previous study, we found that C. coralloides produced only 35 new MFs in response to various OSMAC stimuli [11]. Previous experience suggests that the number of new MFs should be much higher in terms of genome size and the number of BGCs predicted.…”

“…In our previous study, C. coralloides was included in a multitude of OSMAC screening conditions. However, none of the 12 known BGCs and other predicted genomic features were activated using a single elicitor [11]. We assumed that the exposure to single stimuli was not sufficient for the activation of its BGCs.…”