This study aimed to explore the genetic and functional diversity of Lactiplantibacillus plantarum (Lpb. plantarum) strains from wild fermented foods to identify traits that are useful for food innovation. The growing demand for clean-label, plant-based, and functionally enriched fermented foods exposes the limitations of current industrial fermentation practices, which rely on standardized lactic acid bacteria (LAB) strains with limited metabolic plasticity. This constraint hinders the development of new food formulations and the replacement of conventional additives. To address this gap, 343 LAB strains were analyzed, including 69 Lpb plantarum strains, isolated from five minimally processed, spontaneously fermented matrices: fermented millet, kombucha, and sourdough (plant-based), wild fermented mountain milk, and natural whey starter (animal-based). Whole-genome sequencing was performed to assess phylogenetic relationships and to annotate genes encoding carbohydrate-active enzymes (CAZymes) and antimicrobial compounds. The results revealed a marked strain-level diversity. Glycoside hydrolase (GH) families GH13 and GH1 were widely distributed, while GH25 and GH32 showed variable presence across clusters. Strains grouped into clusters enriched with plant-based isolates exhibited distinct CAZyme profiles adapted to complex carbohydrates. Clusters with animal-based strains exhibited a broader gene repertoire related to bacteriocin biosynthesis. These findings highlight the untapped potential of wild fermented food environments as reservoirs of Lpb. plantarum with unique genomic traits. Harnessing this diversity can expand the functional capabilities of starter cultures, promoting more sustainable, adaptive, and innovative fermentation systems. This study underscores the strategic value of underexploited microbial niches in meeting the evolving demands of modern food production.
