Challenging old microbiological treasures for natural compound biosynthesis capacity

• Published in: Frontiers in bioengineering and biotechnology Vol. 12; p. 1255151
• Main Authors: Nouioui, Imen, Zimmermann, Alina, Hennrich, Oliver, Xia, Shuning, Rössler, Oona, Makitrynskyy, Roman, Pablo Gomez-Escribano, Juan, Pötter, Gabriele, Jando, Marlen, Döppner, Meike, Wolf, Jacqueline, Neumann-Schaal, Meina, Hughes, Chambers, Mast, Yvonne
• Format: Journal Article
• Language: English
• Published: Switzerland Frontiers Media S.A 01.02.2024
• Subjects: actinomycetes; antibiotic; Bioengineering and Biotechnology; biosynthetic gene cluster; novel species; polyphasic taxonomy; Streptomyces; antibiotic; Streptomyces; biosynthetic gene cluster; actinomycetes; novel species; polyphasic taxonomy
• ISSN: 2296-4185; 2296-4185
• DOI: 10.3389/fbioe.2024.1255151

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 Streptomyces , are renowned as prolific producers of antibiotics and many other bioactive natural products. In light of this, five Streptomyces 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 in vitro and in silico 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 Streptomyces species, for which the names Streptomyces kutzneri sp. nov., Streptomyces stackebrandtii sp. nov. , Streptomyces zähneri sp. nov. , Streptomyces winkii sp. nov., and Streptomyces kroppenstedtii 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 “ Streptomyces antibiotic regulatory protein” (SARP) genes.