Exploratory comparison of extracellular proteomic, metabolomic, and lipidomic profiling of inulin-fortified gelatin capsule waste gel fermented by Lactiplantibacillus plantarum

Abstract

This exploratory study evaluated whether partial replacement of sucrose with inulin was associated with differences in the proteomic, metabolomic, and lipidomic profiles of gelatin capsule waste gel fermented by Lactiplantibacillus plantarum. A sucrose-based Control and an INU-50 formulation, in which 50% of sucrose was replaced with inulin, were compared using parallel proteomic, untargeted metabolomic, and untargeted lipidomic profiling. The Control and INU-50 groups separated clearly across all datasets. Proteomic analysis identified four proteins with higher abundance in the INU-50 formulation, including proteins putatively associated with carbohydrate transport, pentose phosphate metabolism, purine biosynthesis, and translation-related functions. Untargeted metabolomics detected 1885 molecular features, among which 426 differential features with putative metabolite annotations were identified in the original exploratory analysis. These features were mainly linked to carbohydrate metabolism, sugar interconversion, amino sugar and nucleotide sugar metabolism, cofactor metabolism, and intermediary carbon pathways. Untargeted lipidomics detected 6005 lipid-related molecular features, including 563 differential features with putative annotations, associated with fatty acid metabolism, glycerophospholipid-related compounds, cardiolipin-related species, ceramide-associated molecules, and secondary metabolite-linked lipid features. Integrated analysis indicated that the observed protein abundance patterns and extracellular molecular features were associated with differences between the two fermented formulations. These findings provide an exploratory molecular dataset describing associations between inulin fortification and complementary omics profiles during gelatin capsule waste fermentation. Because non-fermented controls and targeted validation were not included, mechanistic interpretation should be considered cautiously.