Untapped Mycobiota: A Scoping Review of Endophytic Fungi in Medicinal Plants from Malaysia

Endophytic fungi from Malaysian medicinal plants constitute a metabolically prolific yet underexplored reservoir for natural product discovery. This scoping review of 56 studies published between 2015 and 2025 identified a fundamental methodological divergence within the field: while phenotypic bioactivity screening dominates the literature (>87% of studies), it is weakly supported by chemical characterization (<25%) and entirely disconnected from genomic investigation (0% biosynthetic gene cluster studies). This phenotype-first paradigm has largely confined the field to descriptive reporting, limiting mechanistic understanding and translational potential. Collectively, the evidence reveals a substantial disconnect between reported bioactivities and their underlying biosynthetic foundations. To address this limitation, a practical genotype-to-phenotype workflow is proposed that integrates strain prioritisation, multi-omics-guided activation, chemical mapping, and mechanism-oriented validation. By linking genomic potential with metabolite production and biological function, this framework provides a roadmap for advancing fungal natural product discovery beyond conventional phenotype-driven screening. Adoption of such approaches may improve the identification of chemically novel and biologically relevant metabolites while supporting the sustainable development of Malaysia’s endophytic fungal resources for biotechnological and pharmaceutical applications.