Comparative exometabolomic insights into indigenous Philippine plant-derived lactic acid bacteria

Lactic acid bacteria (LAB) are increasingly explored as sources of bioactive metabolites with potential applications in food, health, and postbiotic development. However, indigenous plant-associated LAB remain comparatively underexplored. The cell-free supernatants of Lactobacillus paracasei 7060 from the salt-tolerant Nypa fruticans, Limosilactobacillus fermentum PJG11 from the indigenous tuber Dioscorea luzonensis Schauer, and Lentilactobacillus hilgardii DSB22 from the endemic bamboo Dendrocalamus merrillianus Elmer were subjected to ethyl acetate extraction and analyzed using UHPLC–Q-TOF-MS-based untargeted metabolomics. Multivariate and univariate analyses were used to characterize extracellular metabolic variation, complemented by pathway enrichment and functional genomic analyses. The exometabolomes were dominated by features putatively classified as amino acid derivatives and diketopiperazines but differed markedly in the abundance of key discriminatory features. Comparative abundance analysis against the MRS control identified enrichment of features putatively annotated as L-glutamic acid, fumaric acid, and indole-3-lactic acid across strains, alongside pyroglutamyl-isoleucine and perlolyrine, metabolites with limited reported associations with LAB. Strain-discriminatory features included β-carbolines in L. paracasei 7060, indole-3-lactic acid in L. hilgardii DSB22, and leucyl–proline in L. fermentum PJG11. Functional genomic and flux-based analyses of L. fermentum PJG11 provided metabolic context for selected observations, including candidate routes associated with leucyl-proline, fumarate, glutamate, and indole-3-lactic acid. The 1-acetyl-β-carboline-related feature was detected in both MRS and bacterial cultures, whereas the feature putatively assigned to perlolyrine was detected only in bacterial cultures, although its origin remains unresolved. Overall, the findings demonstrate extracellular metabolic diversity among indigenous Philippine LAB and identify metabolites warranting further targeted and functional investigation.