Effect of Different Feeding Habits on Metabolomics Profiles and Microbiota Composition and Functions of Tilapia Gut

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.