The results of immune tolerance induced by the oral administration of brain protein (BP) and BP combined with probiotics in the BP and combined groups compared with the Sham, SBI group. (A) The rats of the sham, SBI, BP, and combined groups were sacrificed at 3, 7, and 14 days. (B) ELISA results of IL-6, TNF-α, and IL-17 among the SBI, BP, and combined groups at 1, 3, 7, and 14 days. (C) Iba and GFAP expression scoring of microglia and astrocytes measured at 3 days after SBI compared with those of the BP and combined groups. (D) Comparison of alpha-diversity indices (Chao1 index taxonomic units) among the sham, SBI, BP, and combined groups at 3 days. **Indicates p < 0.01 by the Wilcoxon rank-sum test. (E) Bar plots depicting relative abundances of bacterial taxa in the sham, SBI, BP, and combined groups. (F) Relative abundances of Lactobacillus among the sham, SBI, BP, and combined groups. (G) Relative abundances of Allobaculum among the sham, SBI, BP, and combined groups. (H) The differences of FITC-Dextran fluorescence intensity among the Sham, SBI, BP, and combined groups. (I) Representative images of occludin and claudin immunofluorescence staining in the colon and small intestinal tissues among the SBI, BP, and combined groups at 3 days. We demonstrated dramatically increased intestinal permeability (H) by a mechanism associated with reduced expression of epithelial tight junction proteins such as claudin and occludin (I). This effect was completely restored by the oral administration of BP and probiotics. These data suggest that gut bacteria are involved in the control of intestinal permeability and in the occurrence of immune tolerance. *p < 0.05; **p < 0.01; and ***p < 0.001.