Saccharomyces boulardii CNCM I-745 mitigates antibiotic-induced gut microbiome functional alterations independently of the host.

The probiotic Saccharomyces boulardii CNCM I-745 (Sb) is widely prescribed to alleviate antibiotic-induced diarrhea, yet its mode of action, particularly its potential direct effects on the gut microbiome, remains incompletely defined. This study aimed to evaluate whether Sb can directly mitigate antibiotic-induced gut microbiota dysbiosis and influence downstream host immune response. Using both static (MiPro) and dynamic (SHIME®) in vitro gut microbiota models, we assessed the effects of Sb supplementation under antibiotic treatment with amoxicillin/clavulanic acid (AMC) or vancomycin (Van). Quantitative microbiome profiling integrated with targeted metabolomics showed that Sb helped stabilize bacterial biomass, partially preserved metabolic functions, and restored the production of immunoregulatory metabolites propionate and indole-3-propionic acid under AMC treatment. In addition, ex vivo exposure of primary human immune cells (PBMCs) and intestinal mucosal tissue to microbiota modulated by Sb led to a significant reduction in pro-inflammatory cytokine secretion compared to microbiota not supplemented with Sb. Collectively, these results support a beneficial role for S. boulardii CNCM I-745 in preserving directly gut microbiome function and supporting host immune homeostasis during antibiotic treatment, particularly under AMC exposure. Our findings advance the understanding of probiotic-antibiotic-gut microbiome interactions, thereby guiding future optimization of microbiome-targeted adjuvant therapies.