Genomic insights into the probiotic potential of dairy-associated Saccharomyces cerevisiae WUT3 and WUT151 strains.

Despite the prevalence of bacterial probiotics, yeast-based preparations offer unique therapeutic benefits that remain a key research priority. Here, we conducted a comparative genomic characterization of the dairy-associated Saccharomyces cerevisiae WUT3 and WUT151 strains, building on previous evidence showing their enhanced probiotic potential relative to the probiotic S. cerevisiae var. boulardii CNCM I-745. The genomes of WUT3 and WUT151 were compared with the reference S. cerevisiae S288C and the probiotic S. boulardii CNCM I-745. At the CDS level, both WUT strains were closer to S288C, suggesting that their probiotic properties stem from unique mechanisms rather than general genetic similarities to the probiotic strain. WUTs shared selected probiotic-related features, including ENA1 deletions, WHI2 alterations, and loss of Ty1/Ty2 regions present in S288C. Together with conserved core stress-response genes, this profile supports their tolerance to low pH, bile salts, and elevated temperature. Gene content analysis revealed redundancy within the hexose transporters and confirmed the absence of the ASP3 cluster. Indels in HSP150 and PIR3 may reflect WUT and S. boulardii cell wall variations. Overall, the probiotic potential of WUT strains does not originate from a single 'probiotic genome', but rather from a unique combination of traits dispersed throughout the S. cerevisiae species. Since no detrimental features were revealed in the analyzed genomes, these strains represent promising candidates for further clinical evaluation. Furthermore, these findings demonstrate that integrative genomic analysis is an effective strategy for the identification, selection, and characterization of candidate probiotic yeast strains.