ORIGINAL RESEARCH article
Front. Microbiol.
Sec. Systems Microbiology
Genomic determinants of antifungal activity of Streptomyces melanosporofaciens STM-2 revealed by genome mining, comparative genomics and evolutionary analysis
Muhammed Opoku Gyamfi 1
Min-Jen Zheng 1
Jyh-Yih Leu 1
Min Tseng 1
Joshua Addo 2
Ai-Ling Hour 1
Wei-Chung Cheng 1
1. Fu Jen Catholic University, New Taipei, Taiwan
2. University of New Hampshire, Durham, United States
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Abstract
Streptomyces species are prolific producers of bioactive compounds, and they play a role in biological control in agricultural systems. In the current study, we employed an integrated approach that involved physiological and biochemical characterization, genome mining, comparative genomics, and evolutionary analysis to elucidate the specific genomic determinants underlying the antifungal activity exhibited by STM-2, a novel Streptomyces melanosporofaciens strain, isolated from Chiayi County, Taiwan. Initial physiological and biochemical characterization, complemented by enzymatic screening, revealed the secretion of antifungal hydrolytic enzymes, including protease, CMCase, pectinase and xylanase, which actively play a role in fungal growth inhibition and fungal cell wall degradation. To elucidate the molecular basis of this activity, a whole-genome sequence was obtained and annotated, revealing a typical high-GC (71%) linear chromosome. Genome mining using antiSMASH predicted an extensive repertoire of 52 biosynthetic gene clusters (BGCs), encompassing type I and II PKS, NRPS, and hybrid PKS–NRPS systems, RiPPs, siderophores, terpenes, and diverse tailoring enzymes (P450s, glycosyltransferases, halogenase candidates). Again, we identified genes tentatively responsible for antifungal activity, including chitinases, β-1,3-glucanases, xylanses, pectinases, and proteases. Comparative pangenomic analysis, supported by high-resolution Average Nucleotide Identity (ANI) and digital DNA–DNA hybridization (dDDH) scores, revealed the evolutionary uniqueness of the strain, identifying an accessory genome containing unique genes specifically associated with specialized antifungal activity. Further in silico structural analysis of these unique gene products using AlphaFold2 yielded three-dimensional protein models with very high pLDDT scores, providing high-confidence structural evidence for Formatted: Not Superscript/ Subscript Commented [Ma1]: Authors' names and arrangement have been corrected their specialized functional roles. Collectively, these results provide a comprehensive understanding of the genomic determinants required for potent biocontrol activity, positioning STM-2 as a promising candidate for biocontrol and further research in biotechnological applications.
Summary
Keywords
AlphaFold2, Antifungal activity, BGC, biocontrol, Comparativegenomics, Genomics, STM-2, Streptomyces
Received
13 January 2026
Accepted
17 February 2026
Copyright
© 2026 Opoku Gyamfi, Zheng, Leu, Tseng, Addo, Hour and Cheng. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
*Correspondence: Min-Jen Zheng; Jyh-Yih Leu
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