Pathway-Weighted Multidimensional Scaling in Exometabolomic Profiling of Lactiplantibacillus plantarum Strains by LC–MS/MS

The aim of the study was a comparative analysis of the exometabolomic profiles of Lactiplantibacillus plantarum strains of diverse origin using liquid chromatography with tandem mass spectrometric detection (LC–MS/MS) combined with a pathway-weighted multidimensional data analysis approach. Culture supernatants of L. plantarum strains, including biobanked strains and an isolate obtained from kombucha, were analyzed by LC–MS/MS under both hydrophilic interaction and reversed-phase chromatographic conditions. Interstrain differences were assessed using principal component analysis (PCA), partial least squares discriminant analysis (PLS-DA), and classical multidimensional scaling (MDS) with metabolite-specific weighting factors proportional to their involvement in metabolic reactions. PCA and PLS-DA provided only coarse separation of strain-specific metabolomic profiles and could not fully resolve them under conditions of high intragroup variability. In contrast, pathway-weighted MDS allowed the construction of a biochemically interpretable metric space reflecting metabolomic distances between the strains. The results demonstrate that combining tandem mass spectrometry with pathway-weighted multidimensional scaling offers a powerful approach to a detailed comparison of metabolomic profiles of closely related bacterial strains and supports the rational selection of producers of biologically active compounds.