A multi-omics approach reveals the changes in the gut microbiome and metabolism of large yellow croaker (Larimichthys crocea) by dietary supplementation with Bacillus

Abstract

The intestine serves as the primary site for nutrient absorption in animals. Research in gut biology is increasingly focused on understanding its correlation with the microbiome, specifically by employing probiotics in diets to enhance gut health and stimulate animal growth. In this study, we isolated two Bacillus species (Bacillus halophilus and Lysinibacillus sphaericus) from the intestinal tract of a large yellow croaker and investigated their roles as dietary supplements, assessing their impact on intestinal microbial composition and their efficacy in large yellow croaker growth and immunity. These functions are intrinsically linked to the growth and immune response of large yellow croaker. Our investigation included a comprehensive analysis of various omics results derived from intestinal content samples, encompassing 16S rRNA sequencing and non-targeted metabolomics. These analyses were combined with assessments of differences in immune functionalities observed in the liver and head kidney, aiming to understand the interaction between the two Bacillus species, intestinal microorganisms, and host metabolism. Our findings demonstrated several significant outcomes: (1) Supplementation with two Bacillus species induced considerable alterations in the intestinal microbiome, particularly in the suppression of Vibrionaceae among juvenile large yellow croaker. (2) The influence of pathogenic bacteria such as Vibrio on intestinal health is not solely associated with their characteristics but also closely linked to their relative abundance in the intestine. (3) Distinct dietary groups further influenced changes in the metabolome profile by impacting the intestinal microbiota structure in juvenile large yellow croaker, thereby influencing various metabolites such as amino acids, terpenes, bile acids, and steroids. (4) Differences in the composition of intestinal microbiota among different feed types significantly affected individual antioxidant functionalities, impacting the morphology and immune capabilities of immune organs like the liver. Exploring intricate host-microbiome interactions using multi-omics approaches can provide a better assessment of probiotics' functional potential. Our results revealed that Lysinibacillus sphaericus enhanced intestinal development, increased antioxidant enzyme activity, and facilitated the growth of large yellow croaker.