Challenging old microbiological treasures for natural compound biosynthesis capacity

Abstract

Strain collections are a treasure chest of numerous valuable and taxonomically validated bioresources. The Leibniz Institute DSMZ is one of the largest and most diverse microbial strain collections worldwide, with a long tradition of actinomycetes research. Actinomycetes, especially the genus <i>Streptomyces</i>, are renowned as prolific producers of antibiotics and many other bioactive natural products. In light of this, five <i>Streptomyces</i> strains, DSM 40971^T, DSM 40484^T, DSM 40713^T, DSM 40976^T, and DSM 40907^T, which had been deposited a long time ago without comprehensive characterization, were the subject of polyphasic taxonomic studies and genome mining for natural compounds based on <i>in vitro</i> and <i>in silico</i> analyses. Phenotypic, genetic, and phylogenomic studies distinguished the strains from their closely related neighbors. The digital DNA-DNA hybridization and average nucleotide identity values between the five strains and their close, validly named species were below the threshold of 70% and 95%-96%, respectively, determined for prokaryotic species demarcation. Therefore, the five strains merit being considered as novel <i>Streptomyces</i> species, for which the names <i>Streptomyces kutzneri</i> sp. nov., <i>Streptomyces stackebrandtii</i> sp. nov.<i>, Streptomyces zähneri</i> sp. nov.<i>, Streptomyces winkii</i> sp. nov., and <i>Streptomyces kroppenstedtii</i> sp. nov. are proposed. Bioinformatics analysis of the genome sequences of the five strains revealed their genetic potential for the production of secondary metabolites, which helped identify the natural compounds cinerubin B from strain DSM 40484^T and the phosphonate antibiotic phosphonoalamide from strain DSM 40907^T and highlighted strain DSM 40976^T as a candidate for regulator-guided gene cluster activation due to the abundance of numerous "<i>Streptomyces</i> antibiotic regulatory protein" (SARP) genes.