A comprehensive pangenome approach to exploring the probiotic potential of Weissella confusa

Fermented foods harbor the bacterium Weissella confusa , which has probiotic properties but can potentially act as an opportunistic pathogen in humans and animals. Using pangenome analysis, our study aimed to improve the classification and identify functional traits of publicly available W. confusa genomes, focusing on evaluating their potential as probiotics. The genomic sequence of 120 strains of W. confusa was acquired from the NCBI RefSeq database. The downloaded sequences underwent a quality verification and filtering process. Ultimately, the chosen genomes were examined for comparative genomic analysis. We employed Roary to investigate the pangenome of W. confusa . Fisher's exact test was utilized to analyze contingency tables, with a significance threshold of p = 0.05 (two-tailed). Our investigation revealed that the pangenome of W. confusa comprises 1100 core genes, 184 soft-core genes, 1407 shell genes, and 7006 cloud genes. This finding emphasizes the "open" aspect of the W. confusa pangenome. The comparison of genomes showed that there were no acquired antibiotic resistance genes. However, the strains had different amounts of prophage regions, CRISPR arrays, and plasmids. Our research identified probiotic marker genes (PMGs), with the majority (78 %) found in the core and soft-core genomes of various strains of W. confusa . An extensive investigation of the W. confusa pangenome has concluded that it could be useful as a probiotic. Further research is necessary to evaluate the potential risks thoroughly. • Comparative genomic analysis was conducted on 117 Weissella confusa strains. • No acquired antibiotic resistance genes were detected across genomes. • Pangenome analysis revealed 1100 core genes and accessory gene diversity. • About 78 % of probiotic marker genes (PMGs) were found in core/soft-core genomes. • Findings support W. confusa as a promising probiotic candidate pending safety evaluation.