Genetic basis for probiotic yeast phenotypes revealed by nanopore sequencing

Area of Science:

• Microbiology
• Genomics
• Yeast Biology

Background:

• Probiotic yeasts offer preventative and therapeutic disease solutions by surviving the gastrointestinal tract and inhibiting pathogens.
• Understanding the genomic basis of beneficial probiotic yeast traits, such as adherence and nutrient provision, is crucial for their application.
• Limited genomic data exists for many food-derived probiotic yeast isolates, hindering a full understanding of their mechanisms.

Purpose of the Study:

• To sequence and analyze the genomes of two food-derived probiotic yeast isolates with demonstrated ability to mitigate fungal infections.
• To identify the genomic determinants responsible for the beneficial traits of these probiotic yeasts.
• To compare the genetic mechanisms of probiotic activity between different yeast species and clades.

Main Methods:

• Whole-genome sequencing of two distinct probiotic yeast strains: Saccharomyces cerevisiae KTP and Issatchenkia occidentalis ApC.
• Comparative genomic analysis to identify genes related to stress tolerance, pH adaptation, and adherence.
• Phylogenetic analysis to determine the evolutionary relationships of the sequenced strains.

Main Results:

• Saccharomyces cerevisiae KTP, from a unique clade, possesses genes for stress, pH tolerance, and adherence distinct from common strains but similar to Saccharomyces boulardii, suggesting convergent evolution of probiotic mechanisms.
• Issatchenkia occidentalis ApC, a rarely sequenced species, exhibits significant genomic dissimilarity, inferring a different probiotic mechanism compared to Saccharomyces strains.
• The study establishes a genetic link among probiotic Saccharomycetes and advances Issatchenkia genomics.

Conclusions:

• Probiotic activity is not monophyletic, with different yeast species potentially achieving benefits through distinct genetic pathways.
• S. cerevisiae KTP and S. boulardii may utilize similar genetic strategies for probiotic effects despite differing evolutionary origins.
• Complementary mixtures of different probiotic yeast species could offer enhanced health benefits beyond single-strain applications.