Genetic basis for probiotic yeast phenotypes revealed by nanopore sequencing

Abstract

Probiotic yeasts are emerging as preventative and therapeutic solutions for disease. Often ingested via cultured foods and beverages, they can survive the harsh conditions of the gastrointestinal tract and adhere to it, where they provide nutrients and inhibit pathogens like Candida albicans. Yet, little is known of the genomic determinants of these beneficial traits. To this end, we have sequenced 2 food-derived probiotic yeast isolates that mitigate fungal infections. We find that the first strain, KTP, is a strain of Saccharomyces cerevisiae within a small clade that lacks any apparent ancestry from common European/wine S. cerevisiae strains. Significantly, we show that S. cerevisiae KTP genes involved in general stress, pH tolerance, and adherence are markedly different from S. cerevisiae S288C but are similar to the commercial probiotic yeast species S. boulardii. This suggests that even though S. cerevisiae KTP and S. boulardii are from different clades, they may achieve probiotic effect through similar genetic mechanisms. We find that the second strain, ApC, is a strain of Issatchenkia occidentalis, one of the few of this family of yeasts to be sequenced. Because of the dissimilarity of its genome structure and gene organization, we infer that I. occidentalis ApC likely achieves a probiotic effect through a different mechanism than the Saccharomyces strains. Therefore, this work establishes a strong genetic link among probiotic Saccharomycetes, advances the genomics of Issatchenkia yeasts, and indicates that probiotic activity is not monophyletic and complimentary mixtures of probiotics could enhance health benefits beyond a single species.

Keywords: FLO genes; Issatchenkia occidentalis strain ApC; Saccharomyces cerevisiae strain KTP; probiotic traits associated genes.

Fig. 1.

Analysis and placement of S. cerevisiae KTP. a) A colony of S. cerevisiae KTP imaged under a microscope after 24 h incubation on a YPD agar plate. b) Scanning electron micrograph of S. cerevisiae KTP. c) Global phylogenetic position of the KTP strain in comparison to other S. cerevisiae strains.

Fig. 2.

Analysis and placement of I. occidentalis ApC. a) A colony of I. occidentalis ApC imaged under a microscope after 24 h incubation on a YPD agar plate. b) Scanning electron micrograph of I. occidentalis ApC. c) Phylogenetic position of I. occidentalis ApC in the Pichiaceae family.

Fig. 3.

Comparing the genomes of S. cerevisiae S288c, S. boulardii unique28, and S. cerevisiae KTP. a) BUSCO genome completeness assessment of the 3 strains. The white text shows the completeness score for each assembly. b) Venn diagram of orthologous proteins shared or unique to the 3 strains. c) Whole genome alignment with ProgressiveMauve. Colored blocks indicate regions of high similarity. Red vertical lines designate a new contig in the genome assembly. Blocks below the center line are aligned sequences in the reverse direction. White vertical lines within blocks represent the localized areas that have not aligned. d) Word cloud of the top BLASTp descriptions for the unique KTP proteins. e) Number of BLASTp hits for the unique KTP proteins according to the top strain found. f) Ethanol production of S. cerevisiae KTP after 30 h of fermentation in YP with either 10% or 20% glucose.

Fig. 4.

Percent identity to proteins implicated in probiotic phenotypes. BLASTp hits from the S. cerevisiae KTP and S. boulardii unique28 strains with less than 80% query coverage are shown with black diagonal lines.