Integrated Multi-Omics and Molecular Docking Analysis of Malate Degradation by Lactiplantibacillus plantarum S4 During Sea Buckthorn Juice Fermentation

Sea buckthorn juice (SBJ) is nutritionally valuable, but its high malic acid content contributes to excessive sourness that limits consumer acceptance. In this study, the deacidification phenotypes of two lactic acid bacterial isolates, Lactiplantibacillus plantarum S4 and Lacticaseibacillus paracasei YJ2, were compared using fermentation phenotyping, sensory evaluation, enzyme assays, untargeted metabolomics, transcriptomics, and molecular docking. After 96 h of fermentation, S4 degraded 91.98% of malic acid, compared with 69.50% for YJ2, and exhibited higher viable-cell counts and overall sensory acceptability under the tested conditions. S4 also showed higher crude-extract malate-conversion activity under MLE-favoring conditions. Molecular docking predicted more favorable interactions of malate with S4-derived MleP and MleS than with the corresponding YJ2 proteins; however, these analyses did not directly measure MleP-mediated transport or MleS-specific catalytic flux. Metabolomic profiling showed lower abundance of malic acid and several other organic acids in S4-fermented SBJ, together with increased abundance of succinic acid, 2-oxoglutaric acid, phenyllactic acid-related metabolites, D-octopine, and N-lactoyl-phenylalanine. Transcriptomic analysis revealed differences between S4 and YJ2 in carbohydrate metabolism, glycolysis, pyruvate metabolism, energy generation, and late-stage cellular maintenance. Integration of these datasets supports a working model in which malate-associated conversion, central-carbon redistribution, organic-acid remodeling, and acid-stress adaptation may contribute to the greater malate-removal phenotype of S4. Because only one isolate of each species was examined, the observed differences should be interpreted as differences between S4 and YJ2 rather than as species-level effects.