Microbial biotransformation of plant-derived metabolites: mechanisms, pathways, and multi-omics integration

Covering: 2000 to 2026Plant-derived metabolites in foods and herbal medicines are frequently transformed by microbial communities before they reach systemic circulation. Consequently, the chemical forms responsible for biological activities often differ from the compounds originally present in plant matrices. This review examines the microbial biotransformation of plant metabolites through a mechanism-focused framework that integrates enzymology, reaction chemistry, and community-level context. We organize known transformations into recurring reaction classes, including hydrolytic activation, redox remodeling, functional-group tailoring, and scaffold rearrangement. We also discuss how omics approaches enable pathway attribution and enzyme prioritization in complex microbial communities. Finally, we highlight the emerging strategies that modulate these transformations through dietary composition, fermentation, and metabolite-focused interventions.