| Summary: | Fish gut microbiota were potentially influenced by habitat changes. However, the fish gut has been shown to have a filtering effect on habitat microorganisms. Here, we hypothesized that the filtering of fish gut microbiota could counteract the effect of dam construction on the gut microbiota composition. To test this hypothesis, we collected water and <i>Rhinogobio cylindricus</i> individuals from four sampling sites located upstream of the Three Gorges Dam (TGD) and analyzed the microbiota composition in the water samples (n = 48) and <i>R. cylindricus</i> gut samples (n = 89) by high-throughput sequencing of the 16S rRNA gene. A total of 6,772,720 (49,435.91 ± 3762.80) high-quality sequences were obtained from 137 samples. The microbiota in the water environment was significantly more diverse than that in the gut of <i>R. cylindricus</i>. The β-diversity of microbiota in the water was significantly lower than that in the gut of <i>R. cylindricus</i>. The water microbiota composition varied greatly according to the distribution of the sampling sites upstream of the TGD, but the gut microbiota of <i>R. cylindricus</i> did not show the same pattern. Rather, the gut microbiota of <i>R. cylindricus</i> were not significantly affected by the TGD. This consistency in the internal tract of <i>R. cylindricus</i> is presumedly a result of a filtering effect on the water microorganisms. Our study furthers our understanding of the stabilization mechanism of the gut microbiota composition of fish and the impact of dams on river ecosystems.
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