Genomic and phenotypic characterization of Weissella paramesenteroides WP12 from fermented fish sauce (Budu) reveals promising strain for food fermentation and probiotic applications

This research provides an extensive genomic analysis of Weissella paramesenteroides WP12, a strain with significant potential for food fermentation. The 2.07 Mb genome comprises a circular chromosome and two plasmids, encoding 2301 protein-coding sequences, 25 rRNA genes, 77 tRNA genes, and one tmRNA gene. Functional annotation identified essential genes involved in carbohydrate metabolism, aminopeptidase activity, and maltose transport, emphasizing the fermentative abilities of this strain. Key metabolic pathways, such as glycolysis, pentose phosphate pathway, and pyruvate metabolism, are well-represented, highlighting the robust capacity of the strain for sugar utilization and energy production. Safety evaluations performed in silico indicate the absence of antibiotic resistance and virulence genes. Moreover, the comparative analysis of secondary metabolite gene clusters across 47 W. paramesenteroides showed that most strains, including WP12, predominantly encode Type III Polyketide Synthase (T3PKS), confirming its safety for use in food products. The genome also lacks genes associated with biogenic amine production, reducing the risk of foodborne toxicity. Pangenome analysis of 47 strains revealed a unique gene repertoire of WP12, including pepN and malK which are important for efficient fermentation. Additionally, the presence of a cold shock RNA helicase gene suggests its capability to withstand environmental stresses, especially in diverse fermentation conditions. Comparative genomics demonstrated that the WP12 harbors unique carbohydrate-active enzymes (CAZymes) not found in other strains, potentially enhancing its fermentative performance. The analysis identified 1929 genes shared across all strains, representing core genes essential for fundamental biological functions. The strain also possesses genes linked to exopolysaccharide (EPS) production, a feature absent in some other strains. These EPS-related genes enhance the ability of this strain to improve the texture and stability of fermented foods. The phenotypic analysis demonstrated that WP12 exhibits strong probiotic characteristics, including tolerance to gastrointestinal conditions such as low pH and bile salts. The strain showed robust auto-aggregation and co-aggregation abilities, achieving up to 70% co-aggregation with foodborne pathogens, which suggests its potential to inhibit pathogen colonization. WP12 also exhibited broad-spectrum antibacterial activity, primarily through acid-mediated inhibition of various foodborne pathogens. These findings highlight W.paramesenteroides WP12 as a promising candidate for biotechnological applications in the food industry, particularly for the development of innovative and enhanced fermented food products.