Unique genetic basis of the distinct antibiotic potency of high acetic acid production in the probiotic yeast <i>Saccharomyces cerevisiae</i> var. <i>boulardii</i>

Abstract

The yeast <i>Saccharomyces boulardii</i> has been used worldwide as a popular, commercial probiotic, but the basis of its probiotic action remains obscure. It is considered conspecific with budding yeast <i>Saccharomyces cerevisiae</i>, which is generally used in classical food applications. They have an almost identical genome sequence, making the genetic basis of probiotic potency in <i>S. boulardii</i> puzzling. We now show that <i>S. boulardii</i> produces at 37°C unusually high levels of acetic acid, which is strongly inhibitory to bacterial growth in agar-well diffusion assays and could be vital for its unique application as a probiotic among yeasts. Using pooled-segregant whole-genome sequence analysis with <i>S. boulardii</i> and <i>S. cerevisiae</i> parent strains, we succeeded in mapping the underlying QTLs and identified mutant alleles of <i>SDH1</i> and <i>WHI2</i> as the causative alleles. Both genes contain a SNP unique to <i>S. boulardii</i> (<i>sdh1</i> ^F317Y and <i>whi2</i> ^S287*) and are fully responsible for its high acetic acid production. <i>S. boulardii</i> strains show different levels of acetic acid production, depending on the copy number of the <i>whi2</i> ^S287* allele. Our results offer the first molecular explanation as to why <i>S. boulardii</i> could exert probiotic action as opposed to <i>S. cerevisiae</i> They reveal for the first time the molecular-genetic basis of a probiotic action-related trait in <i>S. boulardii</i> and show that antibacterial potency of a probiotic microorganism can be due to strain-specific mutations within the same species. We suggest that acquisition of antibacterial activity through medium acidification offered a selective advantage to <i>S. boulardii</i> in its ecological niche and for its application as a probiotic.