Challenging old microbiological treasures for natural compound biosynthesis capacity

Imen Nouioui; Alina Zimmermann; Oliver Hennrich; Shuning Xia; Oona Rössler; Roman Makitrynskyy; Juan Pablo Gomez-Escribano; Gabriele Pötter; Marlen Jando; Meike Döppner; Jacqueline Wolf; Meina Neumann-Schaal; Chambers Hughes; Yvonne Mast

doi:10.3389/fbioe.2024.1255151

Challenging old microbiological treasures for natural compound biosynthesis capacity

Front Bioeng Biotechnol. 2024 Feb 1:12:1255151. doi: 10.3389/fbioe.2024.1255151. eCollection 2024.

Authors

Imen Nouioui¹, Alina Zimmermann^{1

2}, Oliver Hennrich¹, Shuning Xia^{2

3}, Oona Rössler¹, Roman Makitrynskyy¹, Juan Pablo Gomez-Escribano¹, Gabriele Pötter¹, Marlen Jando¹, Meike Döppner¹, Jacqueline Wolf¹, Meina Neumann-Schaal^{1

4}, Chambers Hughes^{2

3}, Yvonne Mast^{1

2

4

5}

Affiliations

¹ Department Bioresources for Bioeconomy and Health Research, Leibniz Institute DSMZ -German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
² German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany.
³ Department of Microbiology, Biotechnology, Faculty of Science, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany.
⁴ Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany.
⁵ Technische Universität Braunschweig, Institut für Mikrobiologie, Braunschweig, Germany.

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 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.

Keywords: Streptomyces; actinomycetes; antibiotic; biosynthetic gene cluster; novel species; polyphasic taxonomy.

Grants and funding

The authors gratefully acknowledge the funding received from the Leibniz Association (K445/2022) and the German Center of Infection Research (DZIF) TTU 09.826. SX is grateful for a PhD scholarship (202008330294) from the Chinese Scholarship Council.