Comparative genomic and phenotypic decoding of probiotic mechanisms in Weissella paramesenteroides strain MW-142

Weissella paramesenteroides is a promising candidate for probiotic and fermentative applications, yet a comprehensive understanding of its genotype-to-phenotype relationship remains limited. This study employed an integrated approach combining whole-genome sequencing, comparative genomics, and phenotypic assays to decipher the genetic determinants underlying its probiotic functionalities. The complete genome of strain MW-142 (2.01 Mb, G+C 38.11%) was sequenced, revealing genes associated with the biosynthesis of lactic acid, exopolysaccharides, and antimicrobial peptides. Phenotypically, MW-142 demonstrated high tolerance to simulated gastrointestinal stress (e.g., 94% survival in gastric fluid after 3 h), potent auto-aggregation (31%), and selective antagonistic activity against pathogens like Staphylococcus aureus (14.6 mm inhibition zone). Genomically, comparative analysis uncovered 213 unique genes and a specialized carbohydrate-active enzyme repertoire, including 122 sugar transporters and 50 glycoside hydrolases, which correlate with its robust metabolic adaptability. Furthermore, functional annotation highlighted a suite of stress-response genes, providing a molecular basis for its resilience. Collectively, this study elucidates the specific genetic architecture that underpins the probiotic and metabolic prowess of W. paramesenteroides MW-142. These findings not only advance the fundamental understanding of this species but also provide a validated genetic blueprint for its targeted development as a functional probiotic culture or fermentation starter in food and pharmaceutical industries. • Conducted a comprehensive comparative genomic analysis of Weissella paramesenteroides strain MW-142, unveiling its unique genetic makeup and genomic diversity compared to other strains. • Identified a plethora of genes associated with carbohydrate, amino acid, and vitamin metabolism in MW-142, highlighting its robust metabolic potential for efficient nutrient utilization. • Uncovered key genes conferring probiotic properties to MW-142, such as those involved in acid and bile tolerance, intestinal cell adhesion, and antimicrobial activity against pathogens. • The findings provide valuable insights into the biological characteristics of Weissella paramesenteroides MW-142, paving the way for its potential applications in food fermentation and probiotic product development.