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Abstract In this study, the tilapia was orally vaccinated by the attenuated Streptococcus agalactiae (S. agalactiae) strain YM001, and the distribution and the pathological effect of strain YM001 in different intestinal segments of tilapia were evaluated by real-time PCR(qPCR), immunohistochemistry(IHC) and histomorphology. The qPCR results showed that the number of bacteria was the highest in the intestinal tracts at 12 h post oral gavage in the YM001 group, then began to decrease sharply and eliminated at 7 d. And the number of bacteria was highest in the foregut, hindgut, and rectum at 12 h, 24 h, and 3 d, respectively. IHC indicated that bacteria mainly distributed in the margin epithelium and the goblet cells at 12 h - 24 h, and in the submucosa and muscle layer in the YM001 group in 3 d post gavage, then almost disappeared at 7 d. Histological examination of intestines post gavage displayed that an inflammation was observed at 7 d in the YM001 group and the intestinal structure was fully recovered at 15 d. and the intestinal structure was fully recovered at 15 d. Conclusion: The attenuated S. agalactiae vaccine strain YM001 could enter the intestinal tissue after oral gavage and had a strong spatial and temporal selectivity in the intestinal tract, which could cause obvious mucosal immune response and mild pathological reaction, but the pathological change could be gradually repaired with the extinction of bacteria in the body. Highlights • The attenuated S. agalactiae vaccine strain YM001 could enter the intestinal tissue. • The strain YM001 had a strong spatial and temporal selectivity in the intestinal tract. • Fish can be repaired with the extinction of bacteria in the body. [ABSTRACT FROM AUTHOR]