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This study aims to evaluate the effects of probiotic Bacillus coagulans 13,002 (BCS) and prebiotic fructo-oligosaccharides (FOS) on mice treated with the alkylating agent cyclophosphamide (CTX). We found that both BCS and FOS, especially BCS, significantly alleviated CTX-induced injury by modulating intestinal-derived and fecal microbiota. BCS and BCS + FOS increased serum immunoglobulin levels, which were reduced by CTX. In addition, BCS and BCS + FOS upregulated IFN-γ and IL-4, which protect mucosal barriers and the balance of Th1/Th2. BCS promoted the gr