Abstract
Live biotherapeutic products (LBPs) are a promising therapeutic class due to their ability to perform metabolic functions in close proximity to their animal host. Of these, Saccharomyces boulardii (Sb) stands out due to its ability to secrete high titers of proteins, long shelf life when freeze-dried, resistance to both phage and antibiotics, and palatability. Despite growing evidence of Sb’s suitability as an LBP, knowledge regarding its physiological responses to the gut environment remains very limited. Here, we colonize germ-free mice with Sb and measure Sb’s transcriptome in the cecum and colon. We find that in the germ-free gut, Sb’s transcriptome is distinct from its transcriptome during axenic culture and is characterized by upregulation of genes involved in fatty acid oxidation, such as POX1, FOX2, SPS19, PXA1, and PXA2, and amino acid intake, including SNO1 and SNZ1, and GDH3. Moreover, the result indicated that Sb utilizes a multi-faceted adaptation strategy, characterized by SNF1/AMPK-driven metabolic flexibility, TOR suppression for stress adaptation, and MSN2/MSN4 activation for resistance to oxidative and osmotic stress. We further compare estimates of promoter activity between this work and prior studies of promoter activity in Sb. Taken together, this work sheds light on the physiology of Sb during passage through the gut and suggests routes to improve its therapeutic properties. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-026-12661-7.