Metagenomic sequencing reveals the intestinal microbial characteristics of Hexagrammos otakii

Abstract:

The intestinal microorganisms in Hexagrammos otakii at different growth stages are analyzed. [Objective] We investigated the changes of intestinal microorganisms in H. otakii and the relationship with the nutrition via metagenomics. [Methods] HiSeq sequencing of the intestinal microbial samples from larvae, juveniles, and young fishes was carried out to analyze the changes in community composition, compare the diversity of microbial community, and explore the interactions between microorganisms and functional relationship in the growth. [Results] The abundance of the dominant Proteobacteria in the intestine of fish decreased, while that of the dominant Firmcutes increased. The dominant genus was Vibrio at larval stage (37.8%), Photobacterium at juvenile stage (77.8%), and Lactococcus at young fish stage (42.5%), suggesting the significant variation of community composition in the growth period. Moreover, the microbial diversity was high at the larval stage and the richness was high at the juvenile stage. Species difference was correlated with the growth. Specifically, at the young fish stage, the differential taxa were Firmcutes, Bacilli, Streptococcaceae, Lactobacillales, Lactococcus and Lactococcus lactis. As for the juvenile stage, the biomarkers were Photobacterium and Photobacterium toroni. At the larval stage, the biomarkers were Phaeobacter inhibens, Colwellia aestuarii, C. polaris, etc. The microbes were mainly involved in the Kyoto encyclopedia of genes and genomes (KEGG) pathway of metabolism and the abundance of this function rose with the growth. To be specific, the intestinal microbiota played an important role in carbohydrate metabolism, amino acid metabolism, nucleoside acid metabolism, energy metabolism, co-factor and vitamin metabolism. Similar results were also presented in terms of protein annotation, which showed that carbohydrate metabolism (3 350) and amino acid metabolism (2 424) dominated the metabolic pathways. The analysis of functional differences demonstrated that microbial functions gradually adapted to the needs of the fish body and environment during the growth. The differential functions were energy metabolism and glucose degradation at the juvenile stage, and the cell growth, death, and apoptosis at the larval stage (mainly in photosynthesis). As for the young fish stage, the major differential function was the biosynthesis of secondary metabolites, followed by carbohydrate metabolism such as glycolysis and gluconeogenesis. [Conclusion] The intestinal microbial structure of H. otakii was significantly different among the larvae, juveniles and young fishes. The functions of the intestinal microbiota changed with the growth and development of the fish. The nutrients for the growth of the fish can be determined based on the differential species and differential functions. This study is expected to improve the breeding efficiency of this fish and lay a theoretical basis for ecological breeding.