Bacillus subtilis plays a role in the inhibition of transporter ABCB1 in Caco-2 cells

•The structure of gut microbiome of patients with drug-resistant epilepsy was different from that of patients with non-drug-resistant epilepsy and healthy controls in both α diversity and β diversity of the gut microbiota based on the microbiota sequencing results.•The Phylum Firmicutes were enriched in the patients with drug-resistant epilepsy and B. subtilis was the key bacterial subtype associated with drug-resistant epilepsy.•B. subtilis downregulated the expression of transporter ABCB1 in both mRNA and protein levels in the Caco-2 cells model. Meanwhile, B. subtilis inhibited the intracellular Rhodamine 123 accumulation and reduced the efflux of antiseizure medicines from the Caco-2 cells. Therefore, this study indicated that B. subtilis played a role in the inhibition of transporter ABCB1 in Caco-2 cells in terms of expression and function.