Nano-Zn (nZnO) has been increasingly applied in different sectors, but the mechanisms of their uses as nutritional sources are less well understood. Our study presented a regulatory mechanism of intestinal microbiota and structure mediated by nano-Zn, which subsequently improved the health and growth of fish. Fish diets were supplemented with 60 mg Zn/kg ZnSO4 (metal salt as the control group), 60 mg Zn/kg nZnO (powder), or 170 mg Zn/kg nZnO (powder) and then fed to the golden pompanos for 5 weeks. We employed a new analytical amplicon sequence variant (ASV) method to identify the bacterial species and achieved the first in situ spatial quantification of fish tissue samples. Our results demonstrated that 60 mg Zn/kg of dietary nZnO promoted the probiotics colonization (Lactic-acid bacilli spp) in the intestine. At a higher nZnO (170 mg Zn/kg) exposure, Brevinema and Mycoplasma colonized in the fish intestine as pro-inflammatory microorganisms, which activated the C5 isoprenoid biosynthesis pathway and NAD biosynthesis. Furthermore, dietary nZnO (60 mg Zn/kg) up-regulated the expression of genes related to intestinal mucus secretion and accelerated the goblet cell renewal in the intestinal villi. At 170 mg Zn/kg nZnO group, fish intestine significantly down-regulated occludin and mucin gene expression while displayed lower villus height, villus area, and goblet cell numbers, which ultimately led to abnormal digestion and absorption and immune functions. Mantel test confirmed that intestinal microbial abundance was significantly correlated with the changes in the intestinal structure, while the value of villi/crypt ratio decreased with increasing Virbrio abundance, which were validated by the key genes and serum biochemical indexes. Finally, nZnO could regulate the glucose and lipid metabolism of fish by regulating microorganisms. Our results provided important insights into the interaction between nZnO and fish intestinal microbial community and host.

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