Searching for Genomic Signatures of Probiotic Potential in Novel Saccharomyces Cerevisiae Strains: Comparative Analysis Against S288C and Saccharomyces cerevisiae var. boulardii

Background Saccharomyces cerevisiae var. boulardii is the only yeast approved for medical use as a probiotic. Traditionally, screening for new strains with probiotic potential has relied on time-consuming biochemical and physiological assays. More recently, genomic approaches have been introduced, yet the genetic determinants of probiotic properties remain poorly understood. This study provides a comprehensive genomic characterization of two environmental S. cerevisiae strains, WUT3 and WUT151, previously shown to exhibit probiotic-relevant phenotypes. Results We performed de novo assembly and annotation, followed by comparative genomics against the reference strain S288C and the probiotic S. cerevisiae var. boulardii CNCM I-745 (SB). Mitochondrial DNA, often overlooked, revealed substantial variation in the COX1 region ( AI4 and BI2 genes). We observed redundancy among the hexose transporter family ( HXT ) and the frequent deletion of the ASP3 cluster. The largest divergence was noticed in proteins and genes associated with the nucleus, particularly those involved in transcriptional regulation. Besides, the protein-level comparison revealed low similarity of transport proteins. Phylogenomically, WUT strains appeared more closely related to S. cerevisiae than to SB. However, WUT strains harbor a few unique genes of unknown function that are absent in S288C. Conclusions The genomic divergences between WUT3, WUT151, and S288C are consistent with their distinct phenotypes. We did not find any clear genomic features that could be considered characteristic of probiotics with certainty, but we did discover some differentiating CDSs of unknown function. Furthermore, our study demonstrates that combining multidirectional in silico analysis with experimental validation is essential for elucidating complex genomic concepts.