Beyond Buro: Genomics and assays revealed the probiotic and antifungal traits of Limosilactobacillus fermentum from Philippine burong isda (fermented fish)

In the Philippines, fermented foods are recognized as rich sources of lactic acid bacteria (LAB) with potential probiotic properties. However, traditional research methods often overlook the advantages offered by genome-based techniques. This study addresses this gap by applying genomics and performing in vitro assays to investigate the probiotic potential of Limosilactobacillus fermentum BIL20 and BIL24, isolated from burong isda, a traditional fermented fish product from Arayat, Pampanga. The BIL genomes revealed a single AMR gene, vanTG , with no nearby integration or excision mobile genetic elements, no plasmids, and no resistance to 85 antibiotics, suggesting minimal virulence potential. Genes associated with probiotic traits—including acid and bile salt resistance, cell aggregation and adhesion, antipathogenic activity, immunomodulation, and vitamin biosynthesis—were identified. Furthermore, 15 families of carbohydrate-active enzymes, under glycoside hydrolases and glycosyltransferases, were predicted in both genomes. The isolates exhibited growth across a range of pH levels (4, 5, 7, and 9) and bile salt concentrations (0.3–1.5 %). Metabolites extracted from the BIL cultures inhibited the growth of clinically relevant pathogens, such as Candida albicans and Aspergillus fumigatus . Notably, the antifungal cyclic dipeptide cyclo(leucylprolyl) was identified in the metabolome of the BIL extracts. This study contributes to the limited body of literature from the Philippines that applies genomics and conducts probiotic assays on fermented food-derived LAB isolates, which effectively reveals their promising probiotic characteristics and potential health benefits. • Integrates genomics and assays to characterize LAB from Philippine fermented foods. • Various probiotic-related genes were identified in the L. fermentum genomes. • In vitro assays confirmed L. fermentum ’s bile salt and pH tolerance. • L. fermentum extracts exhibited antifungal activity, which may be attributed to cyclo(leucylprolyl). • Genomics revealed L. fermentum’s minimal virulence and AMR potential.