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As an omnivorous fish, wild tilapia feed on both animal and plant foods, depending on what is available. To understand the nutritional function of the gut microbiota of tilapia, we used shotgun metagenomic sequencing, untargeted metabolomics analysis, and 16S rRNA gene sequencing to study the metabolites and gut microbial communities in tilapia eating different diets (artemia nauplii in the carnivorous diet; plant‐based pelleted feed [PBP] in the herbivorous diet; and a mixture of these two in the omnivorous diet). A total of 225 Nile tilapia (Oreochromis niloticus) were cultured in nine 1500 L outdoor tanks, with three replicate tanks per diet and 25 fish per tank. β‐diversity analysis revealed that there was no significant difference in microbial structure between the three diets. However, significant differences were detected in gut metabolites. The abundance of the core bacteria in tilapia intestine (genus Cetobacterium) increased significantly when an omnivorous diet was fed. Cetobacterium abundance was significantly correlated to some differential metabolites including glucose and amino acids, and significantly correlated to pathways of carbohydrate and amino acids metabolism, identified by metagenome analysis. Metagenomic binning produced seven Cetobacterium MAGs with the completeness >50% and contamination <10%, in which genes related to the above metabolites and metabolism pathways were identified. All seven MAGs contained CAZymes that could act on distinct carbohydrates, providing highly diversified capabilities to this genus to cope with both animal and plant glycans. These tilapia fed with an omnivorous diet also showed increased growth. The differential intestinal metabolites aspartate, isoleucine, ornithine, proline, nicotinate, and NAD+ could be related to the increased growth. Our results expanded the understanding of how tilapia have adapted to an omnivorous diet and may provide knowledge for improving aquaculture management. [ABSTRACT FROM AUTHOR]

Simple Summary: Simple Summary: This study presents the initial findings on how rice cultivation impacts water quality and the microbial community structure in ponds where mandarin fish are being fed an artificial diet. The results indicated that rice cultivation plays a significant role in reducing nutrient salt levels in the water, thus regulating the overall aquatic environment. Furthermore, the cultivation of rice has been found to alter the composition of microbial communities in the water, leading to a decrease in diversity and affecting the abundance of bacteria involved in carbon, nitrogen, and phosphorus metabolism. The study identified Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes, and Deinococcus-Thermus as the dominant bacterial phyla in ponds where mandarin fish are being fed an artificial diet. Additionally, it was observed that Proteobacteria showed a particular preference for proliferation in the aquatic environment with rice cultivation on the water surface. These results provide a valuable foundation for the potential application of aquaculture practices involving mandarin fish fed an artificial diet and rice floating beds. The culture of mandarin fish using artificial feed has been gaining increasing attention in China. Ensuring good water quality in the ponds is crucial for successful aquaculture. Recently, the trial of pond-based rice floating beds (PRFBs) in aquaculture ponds has shown promising results. This research assessed the impact of PRFBs on the microbial community structure and overall quality of the aquaculture pond, thereby enhancing our understanding of its functions. The results revealed that the PRFB group exhibited lower levels of NH4+-N, NO2−-N, NO3−-N, TN, TP, and Alk in pond water compared to the control group. The microbial diversity indices in the PRFB group showed a declining trend, while these indices were increasing in the control group. At the phylum level, there was a considerable increase in Proteobacteria abundance in the PRFB group throughout the culture period, suggesting that PRFBs may promote the proliferation of Proteobacteria. In the PRFB group, there was a remarkable decrease in bacterial populations related to carbon, nitrogen, and phosphorus metabolism, including genera Rhodobacter, Rhizorhapis, Dinghuibacter, Candidatus Aquiluna, and Chryseomicrobium as well as the CL500_29_marine_group. Overall, the research findings will provide a basis for the application of aquaculture of mandarin fish fed an artificial diet and rice floating beds. [ABSTRACT FROM AUTHOR]