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. 2024 Jun 14:15:1408479.
doi: 10.3389/fmicb.2024.1408479. eCollection 2024.

Genomes and secondary metabolomes of Streptomyces spp. isolated from Leontopodium nivale ssp. alpinum

Fabian Malfent  1   2 , Martin Zehl  3 , Rasmus H Kirkegaard  4   5 , Martina Oberhofer  1 , Sergey B Zotchev  1
Affiliations

Genomes and secondary metabolomes of Streptomyces spp. isolated from Leontopodium nivale ssp. alpinum

Fabian Malfent et al. Front Microbiol. .

Abstract

Bacterial endophytes dwelling in medicinal plants represent an as yet underexplored source of bioactive natural products with the potential to be developed into drugs against various human diseases. For the first time, several Streptomyces spp. were isolated from the rare and endangered traditional medicinal plant Leontopodium nivale ssp. alpinum, also known as Edelweiss. In the search for novel natural products, nine endophytic Streptomyces spp. from Edelweiss were investigated via genome sequencing and analysis, followed by fermentation in different media and investigation of secondary metabolomes. A total of 214 secondary metabolite biosynthetic gene clusters (BGCs), of which 35 are presumably unique, were identified by the bioinformatics tool antiSMASH in the genomes of these isolates. LC-MS analyses of the secondary metabolomes of these isolates revealed their potential to produce both known and presumably novel secondary metabolites, whereby most of the identified molecules could be linked to their cognate BGCs. This work sets the stage for further investigation of endophytic streptomycetes from Edelweiss aimed at the discovery and characterization of novel bioactive natural products.

Keywords: Edelweiss; Streptomyces; endophytes; genome mining; secondary metabolites.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

FIGURE 1
FIGURE 1
Phylogenetic tree based on the genome sequences from nine Streptomyces spp. isolated from Edelweiss and the closest related type strains (nearest neighbors) in the TYGS database (Type Strain Genome Server, Leibniz Institute, DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany) (Meier-Kolthoff and Göker, 2019).
FIGURE 2
FIGURE 2
Summary of the Edelweiss isolates’ origin, isolation medium, genome size, number of contigs, and BGCs. BGCs shaded the same color represent BGCs shared between two or more of these isolates. Non-shaded BGCs are unique for each isolate. BGCs presumed to be unique are marked by a star sign (*). BGCs putatively specifying the biosynthesis of the identified secondary metabolites by high-resolution LC-MS are marked in bold. Detailed antiSMASH-based BGC analyses are given in Supplementary Tables 4–12. PDA, potato dextrose agar; ISP2, international Streptomyces project 2 agar medium; HVA, humic acid vitamin agar.
FIGURE 3
FIGURE 3
Numbers and types of biosynthetic gene clusters (BGCs) identified in Streptomyces endophytes. NRPS, nonribosomal peptide synthetases; PKS, polyketide synthases; RiPP, ribosomally synthesized and post-translationally modified peptides.
FIGURE 4
FIGURE 4
Secondary metabolites tentatively identified using high-resolution LC-MS in the extracts of Streptomyces sp. LN549.
FIGURE 5
FIGURE 5
Secondary metabolites tentatively identified using high-resolution LC-MS in the extracts of Streptomyces sp. LN699.
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