Saccharomyces cerevisiae, commonly known as baker’s yeast, is extensively utilized across multiple industries due to its unique and versatile traits and metabolic capabilities. However, concerns have arisen regarding its potential as an opportunistic pathogen, particularly when used in probiotic applications in the case of immunosuppressed patients. By studying how yeasts adapt to the mammalian hosts, we may know more about potential concerns and even mitigate these. To address this issue, this study investigates the evolution of Saccharomyces cerevisiae following injection into a mouse model. The experiment aims to understand how the yeast strain adapts and evolves within a host environment, shedding light on its pathogenic potential and providing insights into its suitability for pharmaceutical use. Through a comprehensive analysis of mutations and genome structure changes of isolates recovered after experimental mouse infection, this study aims to contribute valuable information to the ongoing discussions surrounding the safety and efficacy of Saccharomyces cerevisiae.