Effective approaches to discover new microbial metabolites in a large strain library

Abstract

Natural products have provided many molecules to treat and prevent illnesses in humans, animals and plants. While only a small fraction of the existing microbial diversity has been explored for bioactive metabolites, tens of thousands of molecules have been reported in the literature over the past 80 years. Thus, the main challenge in microbial metabolite screening is to avoid the re-discovery of known metabolites in a cost-effective manner. In this perspective, we report and discuss different approaches used in our laboratory over the past few years, ranging from bioactivity-based screening to looking for metabolic rarity in different datasets to deeply investigating a single Streptomyces strain. Our results show that it is possible to find novel chemistry through a limited screening effort, provided that appropriate selection criteria are in place.

N-Acetyl-Cysteinylated Streptophenazines from Streptomyces

“…Current results stem from a study aimed at identifying small-molecule elicitors that would trigger production of secondary metabolites. Using 21 randomly chosen Streptomyces strains from the NAICONS collection of 45 000 actinomycete strains, 10 we cultivated them in medium-scale liquid cultures in a single medium but in separate experiments and analyzed the metabolite fingerprints of the corresponding extracts by LC-MS/MS (K.V., unpublished results). During the course of this study, we realized that the available data set could be “mined” for metabolites that fulfilled the following properties: (i) they were not detected in any of the 14 000 metabolic fingerprints contained in the NMFL; (ii) they did not cluster together with any of the annotated metabolites in the GNPS platform; 6 (iii) they coeluted with few other metabolites by reversed-phase HPLC; and (iv) they were observed in extracts obtained from biological replicates of the same strain performed at different times ( Figure 1 ).…”

N-acetyl-cysteinylated streptophenazines from Streptomyces

“…Current results stem from a study in aimed at identifying small molecule elicitors that would trigger production of secondary metabolites. Using 21 randomly chosen Streptomyces strains from the NAICONS' collection of 45 000 actinomycete strains 10 , we cultivated them in medium-scale liquid cultures in a single medium but in separate experiments and analyzed the metabolite fingerprints of the corresponding extracts by LC-MS/MS (K.V., unpublished results). During the course of this study, we realized that the available dataset could be "mined" for metabolites that fulfilled the following properties: i) they were not detected in any of the 14 000 metabolic fingerprints contained in the NMFL; ii) they did not cluster together with any of the annotated metabolites in the GNPS platform 6 ; iii) they co-eluted with few other metabolites in reverse phase HPLC; and iv) they were observed in extracts obtained from biological replicates of the same strain performed at different times (Figure 1).…”

“…Relying on the assumption that novel chemistry is detected relatively rarely when exploring well-established microbial taxa 3 , it should nevertheless be possible to pinpoint medically valuable metabolites by exploring a sufficiently large dataset of metabolites. In this respect, NAICONS' metabolic fingerprint library (NMFL), derived from about 14 000 extracts obtained from about four thousand actinomycete strains 10 , offers a great opportunity for "rarity-based" prioritization of metabolites to discover novel antimicrobials. Recently, a metabolomics-guided approach has enabled the discovery of the unusual biaryl-linked tripeptides produced by some Planomonospora strains and permitted the finding that the associated biosynthetic gene clusters (BGCs) are widespread among actinobacteria, although the corresponding metabolites have so far escaped detection 11 .…”

The Natural Products Atlas 2.0: a database of microbially-derived natural products

“…COCONUT ( 1 ), LOTUS ( 2 )), inconsistent dereplication methodologies and high rates of rediscovery still plague natural products discovery programs. ( 3 ). The Natural Products Atlas aims to address these issues by collating a standardized database of all known microbial natural product structures, source organisms and citations.…”