SysFungiNet: A Multi-Omics Data Fusion Framework with Explainable AI for Bioactive Prioritization

Macrofungi signify an extensive reservoir of bioactive metabolites. Still, their chemical description is stalled by fragmented analytical pipelines and low reproducibility. This study introduces SysFungiNet, a unified, FAIR-compliant systems-bioinformatics framework designed to accelerate bioactives discovery in non-model fungi. Unlike existing pipelines, SysFungiNet integrates LC-MS/MS metabolomics, transcriptomics, and genomic data with explainable artificial intelligence and molecular docking validation. By reconstructing biosynthetic pathways for Ganoderma lucidum and Craterellus cornucopioides, the framework achieved a Pathway Completeness Index of 0.86. An ensemble machine-learning model predicted bioactivity with an F1-score of 0.91, identifying 312 annotated metabolites. Crucially, decision-making was transparent, with SHAP analysis identifying specific chemical substructures driving predicted immunomodulation. The framework prioritized five high-confidence candidates, including a putative novel terpenoid, Cornucopiolide, which showed high binding affinity (−9.4 kcal/mol) to human immune receptors in silico. Benchmarking against MetaFungi and PhytoOmics demonstrated superior annotation accuracy and reproducibility. SysFungiNet offers a scalable, open-source ecosystem for transforming fungal bioprospecting into an evidence-driven process.