Valorization of Grape Seed By-Products by Lactiplantibacillus plantarum FBL002 Fermentation: Multi-Omics Insights into β-Glucosidase-Mediated Polyphenol Biotransformation and Antioxidant Enhancement

Grape seeds are a major by-product of grape processing and a rich source of polyphenolic compounds, yet their value remains underutilized. In this study, 12 lactic acid bacteria (LAB) strains were evaluated in a grape seed-based fermentation system to compare their tolerance, metabolic performance, and ability to promote polyphenol release. Among them, Lactiplantibacillus plantarum FBL002 showed the best overall performance. The strain maintained strong viability and metabolic activity at 5% grape seed concentration and released polyphenols more effectively than the other tested strains. The resulting fermentation broth also showed pronounced intracellular antioxidant activity. To clarify the basis of this phenotype, we further combined metabolomic, genomic, and transcriptomic analyses. Fermentation caused substantial shifts in phenolic metabolites, characterized by a decrease in glycosylated forms and an increase in more bioactive aglycones. Genome annotation revealed an enrichment of β-glucosidase-related genes in FBL002, and transcriptomic analysis showed that these genes were markedly upregulated during fermentation. This pattern was closely associated with the enhanced release of polyphenols. Together, these findings identify β-glucosidase as a key driver of grape seed polyphenol biotransformation by FBL002 and support the sustainable, high-value use of grape seeds in functional foods and cosmetic applications.