Challenging old microbiological treasures for natural compound biosynthesis capacity

Area of Science:

• Microbiology
• Genomics
• Natural Product Discovery

Background:

• Strain collections are vital bioresource repositories.
• The Leibniz Institute DSMZ houses a diverse microbial collection with a history of actinomycetes research.
• Actinomycetes, particularly Streptomyces, are known for producing antibiotics and bioactive compounds.

Purpose of the Study:

• To taxonomically characterize five long-deposited Streptomyces strains from the DSMZ collection.
• To explore the potential for natural compound production in these strains through genome mining.
• To establish the taxonomic status of these strains, potentially identifying new species.

Main Methods:

• Polyphasic taxonomic studies including phenotypic, genetic, and phylogenomic analyses.
• In vitro and in silico analyses for genome mining of natural compounds.
• Digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) calculations.

Main Results:

• The five strains (DSM 40971^T, DSM 40484^T, DSM 40713^T, DSM 40976^T, and DSM 40907^T) were phylogenetically and phenotypically distinct from known species.
• dDDH and ANI values were below established thresholds for species demarcation.
• Genome analysis revealed the potential for secondary metabolite production, identifying cinerubin B and phosphonoalamide, and highlighting SARP gene clusters.

Conclusions:

• The five strains represent novel Streptomyces species: Streptomyces kutzneri sp. nov., Streptomyces stackebrandtii sp. nov., Streptomyces zähneri sp. nov., Streptomyces winkii sp. nov., and Streptomyces kroppenstedtii sp. nov.
• These novel species possess a genetic capacity for producing diverse secondary metabolites.
• Strain DSM 40976^T is a promising candidate for further investigation into regulator-guided gene cluster activation for novel antibiotic discovery.