Effect of epigenetic modulation on metabolites from endophytes isolated from Embelia ribes

AZ treatment induced significant, concentration, dependent alterations in the metabolite profile of P. azadirachtae, with the most pronounced effects observed at the P1AZ concentration. Multivariate and clustering analyses revealed clear metabolic differentiation between treated and control cultures. A total of 47 targeted metabolites were detected under AZ treatment, including nine previously silent metabolites consistently induced across all concentrations. Notably, AZ exposure enhanced the production of phomophyllin A and phaseolorine, indicating the selective activation of cryptic biosynthetic pathways in P. azadirachtae. SB treatment significantly altered the secondary metabolite profile of P. azadirachtae in a dose-dependent manner. Metabolomic analysis detected 47 compounds in SB-treated cultures, with the most pronounced metabolic changes observed at the P50SB and P500SB concentrations. SB exposure activated a previously silent biosynthetic gene cluster responsible for the production of 11 metabolites. Furthermore, log fold-change analysis demonstrated significant and consistent upregulation of six metabolites across most SB treatments, highlighting SB's effectiveness in activating cryptic secondary metabolism in P. azadirachtae. In AZ-treated D. phaseolorum cultures, epigenetic alteration triggered 11 metabolites. Log fold change analysis reported significant upregulation of two metabolites. In D. phaseolorum, SB treatments detected 46 targeted compounds across different concentrations. The treatment activated 11 previously silent bioactive metabolites. and significantly increased the levels of three metabolites compared with controls. These findings demonstrate that the epigenetic modulators AZ and SB altered secondary metabolite profiles in fungal endophytes, indicating their potential to activate silent biosynthetic pathways. These findings support their use as exploratory tools for metabolite discovery, while highlighting the need for multi-omics and structural validation in future work.