Genomic and phenotypic comparison of Saccharomyces cerevisiae and Saccharomyces boulardii

Abstract Saccharomyces boulardii is a widely used probiotic yeast with clinical efficacy against certain gastrointestinal disorders. Although genomically related to S. cerevisiae , the extent to which S. boulardii harbors distinct probiotic-relevant traits remains incompletely defined, particularly across commercially distributed strains. Here, we performed comparative genomic, physiological, and functional analyses of five S. boulardii strains and three S. cerevisiae strains, including baker’s and laboratory variants. S. boulardii strains shared conserved genetic features and exhibited a conserved chromosomal inversion on chromosome XVI, lower copy numbers of CAZyme genes, and lineage-specific amino acid substitutions in central and tryptophan catabolism pathways—potentially underlying elevated production of immunomodulatory metabolites. S. boulardii strains also exhibited enhanced acid tolerance, elevated acetate and succinate production, and robust immunomodulatory activity, including suppression of IL-8 secretion and NF-κB, and consistent activation of the aryl hydrocarbon receptor (AhR) compared to S. cerevisiae . In contrast , S. cerevisiae strains displayed greater bile salt tolerance and faster growth under aerobic and anaerobic conditions at both 30°C and 37°C but lacked consistent anti-inflammatory effects or AhR agonism. Metabolic and immunological phenotypes varied with oxygen availability and strain background. Despite high genomic similarity, S. cerevisiae and S. boulardii exhibit distinct functional capacities relevant to probiotic efficacy. These findings help define species- and strain-specific features that inform the development and regulatory evaluation of next-generation yeast probiotics. Importance The yeast Saccharomyces boulardii is widely used as a probiotic to support human gut health, yet the reasons behind its beneficial effects remain unclear. This study compares S. boulardii with its close relative, Saccharomyces cerevisiae , which is commonly used in baking and research but does not show consistent health benefits. By examining multiple strains, we found that S. boulardii possesses unique features that may explain its ability to survive harsh gut conditions and influence the body’s immune responses. In contrast, S. cerevisiae grows faster and withstands bile better but lacks the same protective effects. These findings highlight how small genetic and physiological differences between related organisms can lead to distinct impacts on health. Understanding these differences provides a foundation for developing next-generation probiotics and for setting standards in their evaluation and use.