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Production of pimpled or sandpaper-shelled eggs (SE) is a major problem in aged hens. Probiotics can improve eggshell quality; however, the relationship between SE production and gut bacteria remains unclear. Here, 1200 450-d-old Hy-line hens were assigned to four groups (300 hens each), with the control group fed basal diet and treatment groups fed basal diet plus 500, 1000, and 1500 mg/kg of Clostridium butyricum and Bacillus subtilis, respectively. After 4 weeks, probiotics significantly decreased the SE rate from 42.51% to 28.02%. To address why probiotics reduced SE rate, the hens that only produced normal eggs (NE) or SE based on a 2-week assessment were assigned to three groups (NE, SE, and SEP groups; 10 hens each), with the NE and SE groups fed a basal diet and SEP group fed a basal diet plus 1000 mg/kg probiotics. After 4 weeks, ileal tissues from eight birds/group were collected for histomorphological and gene expression analyses, and the ileal content was collected from five birds/group for 16S rDNA sequencing analysis. The data showed that probiotics significantly increased the villus length and ratio of villus length to crypt depth. Quantitative PCR analysis indicated that there were no significant differences in the expression of genes related to tight junctions, nutrient transport, and calcium absorption among the groups (except TRPV6, P < 0.001). The 16S rDNA sequencing analysis indicated that the alpha-diversity of gut bacteria in the SEP group was the highest among the groups. The Firmicutes phylum was dominant in the NE and SEP groups, whereas the Proteobacteria phylum was dominant in the SE group. Together, these results suggest that probiotics can significantly influence A d v a n c e V i e w P r o o f s