The probiotic yeast has been extensively studied for the prevention and treatment of diarrheal diseases, and it is now commercially available in some countries. displays notable phenotypic characteristics, such as a high optimal growth temperature, high tolerance against acidic conditions, and the inability to form ascospores, which differentiate from The majority of prior studies stated that exhibits sluggish or halted galactose utilization. Nonetheless, the molecular mechanisms underlying inefficient galactose uptake have yet to be elucidated. When the galactose utilization of a widely used strain, ATCC MYA-796, was examined under various culture conditions, the strain could consume galactose, but at a much lower rate than that of While all genes were present in the genome, according to analysis of genomic sequencing data in a previous study, a point mutation (G1278A) in , which codes for phosphoglucomutase, was identified in the genome of the strain. As the point mutation resulted in the truncation of the Pgm2 protein, which is known to play a pivotal role in galactose utilization, we hypothesized that the truncated Pgm2 might be associated with inefficient galactose metabolism. Indeed, complementation of in restored galactose utilization. After reverting the point mutation to a full-length in by Cas9-based genome editing, the growth rates of wild-type (with a truncated gene) and mutant (with a full-length) strains with glucose or galactose as the carbon source were examined. As expected, the mutant (with a full-length ) was able to ferment galactose faster than the wild-type strain. Interestingly, the mutant showed a lower growth rate than that of the wild-type strain on glucose at 37°C. Also, the wild-type strain was enriched in the mixed culture of wild-type and mutant strains on glucose at 37°C, suggesting that the truncated might offer better growth on glucose at a higher temperature in return for inefficient galactose utilization. Our results suggest that the point mutation in might be involved in multiple phenotypes with different effects. is a probiotic yeast strain capable of preventing and treating diarrheal diseases. However, the genetics and metabolism of this yeast are largely unexplored. In particular, molecular mechanisms underlying the inefficient galactose metabolism of remain unknown. Our study reports that a point mutation in, which codes for phosphoglucomutase, is responsible for inferior galactose utilization by After correction of the mutated via genome editing, the resulting strain was able to use galactose faster than a parental strain. While the mutation made the yeast use galactose slowly, investigation of the genomic sequencing data of other strains revealed that the mutation is evolutionarily conserved. Interestingly, the mutation was beneficial for growth at a higher temperature on glucose. We speculate that the mutation was enriched due to selection of in the natural habitat (sugar-rich fruits in tropical areas).