Genomic and functional characterization of Weissella viridescens HDY-8 as a candidate probiotic from Thai fermented fish

Weissella viridescens strain HDY-8 was isolated from traditional Thai fermented fish with chili paste and characterized using genomic and phenotypic approaches. Whole-genome sequencing with Oxford Nanopore technology produced a complete single-contig genome of 1.63 Mb with a GC content of 41.2%, containing 1550 coding sequences, 79 tRNA genes, 25 rRNA genes, and 1 tmRNA gene. Average Nucleotide Identity (ANI) analysis placed HDY-8 within the W. viridescens cluster, showing 98.0–99.5% similarity, confirming its close genomic relatedness to the species. Functional annotation showed enrichment of genes related to carbohydrate, protein, and amino acid metabolism. Several exopolysaccharide (EPS) biosynthesis genes were identified, along with conserved terpene precursor and type III polyketide synthase (T3PKS) clusters, but no bacteriocin gene clusters. Safety evaluation revealed no functional acquired antimicrobial resistance genes in the HDY-8 genome. Disk diffusion testing showed measurable inhibition zones for multiple antibiotics, whereas no inhibition zone was observed for vancomycin, consistent with the intrinsic vancomycin resistance commonly reported in Weissella spp. In addition, only three virulence-associated genes ( bsc3, hasC, clpC ) were detected, which are primarily associated with stress tolerance, and hemolysis testing indicated γ-hemolysis, confirming non-hemolytic activity. HDY-8 exhibited strong auto-aggregation (>80% at 24 h) and high co-aggregation with pathogens (>90% at 24 h), supporting probiotic-associated traits. Therefore, these findings demonstrate that HDY-8 possesses the core genomic features of W. viridescens with strain-specific traits. The absence of hemolytic activity and virulence genes, combined with strong aggregation abilities, supports its safety and suggests its potential as a candidate for probiotic applications.