Odontobutis potamophila, a small fish of high economic value in the middle-lower Yangtze River, is currently farmed under two principal systems: recirculating aquaculture and rice-crayfish-Odontobutis potamophila integrated culture. Previous research has emphasized water-saving or yield-increasing aspects, yet systematic comparisons of how these systems modulate the species’ intestinal microbiota remain scarce, constraining optimization and dissemination of healthy production strategies. In this study, two culture modes of Recirculating aquaculture system and rice-crayfish-Odontobutis potamophila integrated culture were set up in the same season and the same region. The composition, diversity, and potential function of gut microbiota were analyzed. At the same time, the blood physiological and biochemical indexes were measured to systematically evaluate the effects of the two culture modes on the intestinal microbial function of O. potamophila. The results showed that there was no significant difference in the dominant phylum of gut microbiota between the two culture modes, but there was a significant difference in the composition of dominant genus. LEfSe analysis found that the composition of the core gut microbiota was significantly different between the two culture modes. A total of five significantly different pathways were identified by the differential analysis of KEGG pathway level 3, all of which were significantly up-regulated under the rice-crayfish-Odontobutis potamophila integrated culture. The up-regulation of these metabolic pathways can enhance the function of energy metabolism and lipid metabolism of the gut microbiota of O. potamophila. The five blood physiological and biochemical indexes (ALT, AST, TG, T-CHO, and GLU) of O. potamophila in recirculating aquaculture system were significantly higher than those in rice-crayfish-Odontobutis potamophila integrated culture. The specific microbiota was significantly correlated with blood glucose, blood lipid, and liver enzyme levels, indicating that gut microbiota may be an important microecological factor causing the difference in blood physiological and biochemical indexes. This study confirmed that different culture modes can reshape the intestinal microbial community of fish, and then regulate the metabolic pressure and physiological health of the body, providing a scientific basis for selecting appropriate management strategies for different culture modes.
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