Product-level comparison of selected lactic acid bacteria from Nepalese naturally fermented dairy products under standardized single-strain fermentation conditions

Naturally fermented dairy products are valuable sources of lactic acid bacteria (LAB), but isolation frequency and in vitro phenotypes do not necessarily predict performance in a dairy matrix. In this study, 259 LAB isolates were recovered from 24 Nepalese naturally fermented dairy products. Genomic characterization and stepwise phenotypic screening were performed on 167 isolates from the three most frequently recovered species, leading to the selection of NP8-16, NP18-7, and NP9-12 for product-level evaluation. The three strains were tested in sweetened cow milk using the same initial inoculum, fermentation temperature (42 °C), and endpoint pH. Although all products reached comparable endpoint acidification, fermentation time, endpoint culturable cell counts, and early post-ripening characteristics differed among strains. NP18-7 reached the target pH most rapidly (5.5 ± 0.2 h). During 21 d of refrigerated storage, significant strain × storage-time interactions were observed for pH, apparent viscosity, firmness, and culturable cell counts, demonstrating distinct storage trajectories. Untargeted UPLC-Q-TOF-MS/MS analysis after 24 h of post-ripening further distinguished the three products and identified 111 nonredundant differentially abundant metabolic features. Overall, comparable endpoint acidification did not correspond to comparable product performance. The comparison is restricted to the standardized process tested here and does not rank the intrinsic performance of the strains under strain-specific optimal conditions.