Mingxin Xie

The intestine, particularly the gut microbiota, and the liver play key roles in digestion, nutrient transformation, and immune regulation in fish. However, limited information is available regarding how different ornamental fish species regulate these systems under identical aquaculture conditions. Therefore, this study systematically compared gut microbiota diversity, structural variation, and predicted ecological functions among eight ornamental fish species reared in the same environment, using 16S rRNA high-throughput sequencing combined with digestive enzyme indices and histological analysis of intestinal and liver tissues. The results showed that goldfish (Carassius auratus) and crucian carp exhibited efficient digestive and absorptive capacities, supported by a thickened muscularis and prominent mucosal layers (p < 0.001). High goblet cell density was observed in red swordtail (Xiphophorus hellerii) and Mickey Mouse platy (Xiphophorus hellerii × X. maculatus) (p < 0.001). Larger hepatocyte perimeter and area were observed in red swordtail (p = 0.022, p = 0.015), whereas platinum mini parrot cichlid and sapphire mini parrot cichlid showed significant hepatocyte vacuolization. Microbial analysis showed that the eight fish species had similar α diversity indices, while the gut microbial profiles of Mickey Mouse platy and golden crucian carp differed the most. At the genus level, beneficial taxa such as Lactococcus, Paracoccus, and Cetobacterium were significantly enriched in red swordtail, sailfin molly, and goldfish, respectively, whereas opportunistic pathogens, including Edwardsiella, Aeromonas, and Acinetobacter, were enriched in Mickey Mouse platy, sapphire mini parrot cichlid, and golden crucian carp, respectively (p < 0.05). Functional prediction based on KEGG pathways indicated that sailfin molly and Mickey Mouse platy exhibited the broadest functional enrichment, primarily involving amino acid metabolism, fatty acid metabolism, and antibiotic biosynthesis. Crucian carp and golden crucian carp showed higher activity in amino acid biosynthesis and glycolysis/gluconeogenesis pathways. The two parrot cichlid species were characterized by enrichment in biofilm formation pathways of pathogenic bacteria and amino sugar and nucleotide sugar metabolism pathways. Goldfish and red swordtail were mainly associated with quorum sensing and ABC transporter pathways. These results provide a theoretical foundation for optimizing aquaculture conditions for ornamental fish and improving fish health and production efficiency.