The key findings of the present study were that 45 d of spore-based probiotic supplementation was associated with a significant change in post-prandial expression of 15 mRNAs associated with gastrointestinal tract barrier function (four mRNAs: BATF3, CCR6, CXCR6, and PDCD2), gastrointestinal immunity (four mRNAs: CLEC5A, IL7, CARD9, and FCER1G), and future IBD risk (eight mRNAs: PD-L1, CSF1R, FAS, BID, FADD, GATA3, and KIR3DL). This evidence concerns the gene BATF3 and inflammatory bowel disease.