Batch-dependent microbiota variation in mixed vegetable fermentations shapes the probiotic potential of autochthonous multifunctional cultures

Fermented vegetables (FVs) are valuable sources of lactic acid bacteria (LAB), which can be employed as functional cultures to enhance the quality, stability and probiotic potential of traditional food products. In this study, the selection of LAB strains with both technological and probiotic properties was supported by a parallel investigation of the microbiota and mycobiota in six FVs mixtures. Metataxonomic analysis and culture-based isolation were consistent in displaying a succession of LAB species through fermentation. Leuconostoc (Lc.) mesenteroides dominated the early stages, followed by lactobacilli species such as Latilactobacillus (Lat.) sakei, Levilactobacillus (Lev.) brevis and Lactiplantibacillus (Lpb.) plantarum from the middle to the late fermentation stages. The majority of LAB isolates were identified as Lc. mesenteroides and Lpb. plantarum, with the latter displaying superior probiotic performances in vitro, including high tolerance to bile salts and resistance to simulated human gastrointestinal conditions. Differences in microbial composition were observed between the two experimental batches (A and B), regardless of the vegetable composition. Notably, batch A showed more homofermentative conditions across all FVs, as confirmed by the organic acids profile. Remarkably, most of the promising probiotic Lpb. plantarum strains were isolated from the homofermentative FVs. By leveraging a complementary metataxonomic approach, this study demonstrates how batch-to-batch variability can influence the probiotic potential of FVs and guide the selection of functional LAB cultures.