Multi-omic investigation identifies key antifungal biochemis

Abstract
The use of multi-omic approaches has significantly advanced the exploration of microbial traits, leading to the discovery of new bioactive compounds and their mechanisms of action. Streptomyces sp. MH71 is known for its antifungal properties with potential for use in crop protection. Using genomic, transcriptomic, and metabolomic analyses, the antifungal metabolic capacity of Streptomyces sp. MH71 was investigated. After 96 hours of liquid fermentation, cell-free spent media showed inhibitory activity against the fungal phytopathogen Verticillium dahliae, with the lowest IC50 value being 0.11 % (v/v) after 144 h. Through whole-genome sequencing, we obtained a near-complete genome of 11 Mb with a G+C content of 71 % for Streptomyces sp. MH71. Genome mining identified 50 putative biosynthetic gene clusters, six of which produced known antimicrobial compounds. To link antifungal activity with candidate biosynthetic pathways, a transcriptomic approach was applied to understand antifungal induction in MH71 cells during the observed increase in antifungal activity. This approach revealed 2774 genes that exhibited differential expression, with significant upregulation of genes involved in biosynthesis of secondary metabolites during the stationary growth phase. Metabolomic analyses using LC-MS and GC-MS of secreted compounds identified a cocktail of potent antifungal metabolites, including volatiles with antifungal activity. By combining genome mining, bioactivity data, transcriptomics, and metabolomics, we describe in detail the gene expression and metabolite products driving antifungal activity during microbial fermentation.

组学方法的广泛应用显著推进了微生物性状的深度挖掘，促进了新型生物活性化合物及其作用机制的发现。链霉菌MH71（Streptomyces sp. MH71）具有显著的抗真菌特性，在作物保护领域展现出良好的应用潜力。本研究利用基因组学、转录组学和代谢组学分析，系统解析了链霉菌MH71的抗真菌代谢潜能。经96小时液体发酵后，无细胞发酵液对植物病原真菌大丽轮枝菌（Verticillium dahliae）表现出显著抑制活性，其中144小时发酵液的半数抑制浓度（IC₅₀）最低可达0.11%（v/v）。全基因组测序获得该菌株近完整基因组，大小为11 Mb，G+C含量为71%。基因组挖掘鉴定出50个推定生物合成基因簇（BGCs），其中6个可产生已知抗菌化合物。为建立抗真菌活性与候选生物合成通路的关联，采用转录组学方法探究MH71在抗真菌活性增强时期的诱导表达特征，共鉴定出2774个差异表达基因（DEGs），其中与次生代谢产物生物合成相关的基因在稳定生长期显著上调。采用液相色谱-质谱联用（LC-MS）和气相色谱-质谱联用（GC-MS）技术对分泌型代谢物进行代谢组学分析，鉴定出一系列强效抗真菌代谢物，包括具有抗真菌活性的挥发性物质（VOCs）。通过整合基因组挖掘、生物活性数据、转录组学和代谢组学，本研究详细阐述了微生物发酵过程中驱动抗真菌活性的基因表达谱与代谢产物流动态。