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Genome mining and untargeted metabolomics of Streptomyces sp. D3

elucidating antifungal potential against wood-decaying fungi

,1
Shih-Wei Huang, #,1,2,3 Shang-Tse Ho,* Y u -Liang Yang* ,2,3

1 Department of Wood-Based Materials and Design, National Chiayi University, Chiayi
600041, Taiwan
2 Agricultural Biotechnology Research Center, Academia Sinica, Tainan 115201, Taiwan
3 Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan 711010, Taiwan.
* E-mail: ylyang@gate.sinica.edu.tw, stho@mail.ncyu.edu.tw

Abstract
Streptomyces is a genus of Actinobacteria well known for producing diverse secondary
metabolites with biological activities, many of which have been developed into clinical
antibiotics. With growing concerns over the environmental impacts of chemical preservatives,
eco-friendly preservatives for wood protection were urgently needed. In this study, we isolated
Streptomyces sp. D3 from soil and evaluated its inhibitory activity against four wood-decay
fungi—Fomitopsis pinicola, Laetiporus sulphureus, Trametes versicolor, and Lenzites betulina.
Inhibition assays revealed that D3 exhibited strong inhibition against the brown-rot fungi F.
pinicola and L. sulphureus, whereas effects on the white-rot fungi were insignificant. To
identify the active components, culture broth was extracted with ethyl acetate and n-butanol,
and only the butanol extract showed antifungal activity. Whole-genome sequencing and
antiSMASH analysis revealed that the biosynthetic gene clusters of D3 were predicted to
produce linearmycin and related antifungal compounds. Consistently, LC-MS/MS analysis of
the butanol crude extract confirmed the presence of linearmycin B. Guided by these findings,
the active extract was further fractionated using Sephadex LH-20 column chromatography,
followed by HPLC purification to obtain bioactive fractions. Overall, our results suggested that
Streptomyces sp. D3 was a promising biological source for developing eco-friendly wood
preservatives, especially effective against brown-rot fungi.

Figure 1. Results of the antifungal assays. The left side contained Streptomyces sp. D3, the right
side included wood-decaying fungi T. versicolor, L. betulina, F. pinicola and L.
sulphureus. (5 days post-infection)

Keywords: Biocontrol; Streptomyces spp.; Wood-decaying fungi; Linearmycin