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The widespread application of TiO2 nanoparticles (NPs) as additives in foods such as gum, candy and puddings has dramatically increased the human ingestion and accumulation of these nanomaterials. Although the toxicity of TiO2 NPs has been extensively studied, their impact on gut microbiota in vivo still needs further research. In this study, TiO2 NPs with two main crystalline phases anatase and rutile were orally administrated to mice for 28 days. The dynamic influences of anatase and rutile on gut microbiota structures were investigated at doses equivalent to those consumed by people who love to eat candies. The results showed that titanium accumulated in the spleen, lung, and kidney but had no significant effects on organ histology. Gavage of rutile NPs but not anatase NPs resulted in longer intestinal villi and irregular arrangement of villus epithelial cells. Treatment with TiO2 NPs did not decrease gut microbiota diversity but shifted their structures in a time-dependent manner. Rutile NPs had a more pronounced influence on the gut microbiota than anatase NPs. The most influenced phylum was Proteobacteria, which was significantly increased by rutile but not by anatase. At the genus level, Prevotella was significantly decreased by both the TiO2 NPs, Rhodococcus was enriched by rutile NPs, and Bacteroides was increased by anatase NPs. Overall, these results suggested that chronic overconsumption of TiO2 NP-containing foods is likely to deteriorate the gastrointestinal tract and change the structures of microbiota. The crystalline phases may play an important role in mediating the intestinal impact of TiO2 NPs.