Abstract:[Background] Epimedium pubescens Maxim., a traditional medicinal plant, contains flavonoids as its primary bioactive constituents. The bioavailability of certain highly glycosylated flavonoids is limited due to high glycosylation. Biotransformation enables directional preparation of low-glycosylated flavonoids, representing a potential strategy to enhance the druggability of active components. [Objective] To screen functional strains capable of efficiently converting epimedin C to icariin, characterize their key enzyme systems, and improve substrate tolerance/conversion efficiency through microbial domestication. [Methods] We isolated strains from the rhizosphere microbiota and the phyllosphere microbiota of Epimedium by habitat-specific sampling. A thin layer chromatography (TLC)-HPLC system was established for the monitoring of transformation products. The phylogenetic analysis (16S rRNA gene) and glycosidase activity profiling were employed to identify the strain and functional enzymes, respectively. Single-factor experiments were conducted to optimize the crude enzyme reaction parameters (temperature, pH, substrate concentration, and enzyme activity). Six rounds of gradient stress domestication (0.01-0.12 g/mL aqueous extract of Epimedium) were implemented to evaluate the adaptive evolution of the strain. [Results] Bacillus sp. MY202402-3 was isolated, with its crude enzymes demonstrating notable α-L-rhamnosidase (18.7 U/mL) and β-glucosidase (3.3 U/mL) activities. In the medium containing 0.01 g/mL aqueous extract, the average epimedin C conversion rate and the average baohuoside Ⅰ yield reached 88.10% and 21.13%, respectively. The optimal reaction conditions of the crude enzyme were 50 ℃, pH 7.5, 1.2 mg/mL substrate, and 10 U/mL enzyme, under which the epimedin C conversion rate and the icariin purity reached 95.20% and 96.78%, respectively, within 2 h. Post-domestication, the conversion rate improved to 90.93% in the medium containing 0.10 g/mL aqueous extract, and the baohuoside Ⅰ yield reached 26.96% in the system containing 0.08 g/mL aqueous extract of Epimedium. [Conclusion] The integrated microbial screening-domestication strategy significantly enhances epimedin C biotransformation efficiency, providing insights for improving the bioavailability of herbal extracts. Concentration-dependent optimization demonstrates scalable industrial potential. As the Bacillus strain reported for Epimedium flavonoid transformation, MY202402-3 expands the application scope of Bacillus.