The structure, composition, and predicted microbiome functional genes in Pacific white shrimp (Litopenaeus vannamei) grow-out ponds with different survival rates through high-throughput sequencing

Microbiomes inhabiting rearing ponds have been frequently associated with the survival rate of cultured animals. However, specific studies reporting on the structure, composition, and functional genes of bacteria in commercial ponds with different survival rates are still scarce. Thus, using high-throughput sequencing, the present study addressed this gap by investigating microbiomes in commercial ponds with different survival rates of Pacific white shrimp, Litopenaeus vannamei. Water samples were collected from ponds with low survival rates (LSR) and ponds with high survival rates (HSR) and profiled by high-throughput sequencing of the 16S rRNA gene. Then, functional genes of microbiomes were predicted using PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) software. The results showed that ponds with different survival rates had distinct bacterial communities. At the genus level, 20 genera had different relative abundance in the two pond groups (LDA > 3), of which 11 genera were in HSR ponds and nine genera were in LSR ponds. The top five most abundant bacterial genera found in LSR ponds were Vibrio, Kocuria, Tepidiphilus, unidentified_Alphaproteobacteria, and Pseudoalteromonas, while the five most abundant found in the HSR ponds were Candidatus_Aquiluna, unidentified_Acinobacteria, Ilumatobacter, unidentified_Deltaproteobacteria, and Marivita. PICRUSt analysis revealed that nine metabolic pathways were higher in HSR grow-out ponds and associated with carbohydrate metabolism, chlorophyll biosynthesis, lignin degradation, arginine and glucosamine biosynthesis, and vitamin K2 synthesis, while nine metabolic pathways were found to be significantly higher in LSR grow-out ponds including lipid IVA biosynthesis (conserved structure in diverse Gram-negative pathogens), and L-tryptophan degradation activity (proteolytic agents). To the authors’ knowledge, this is the first study to report the diversity, composition, and metabolic activity of microbiomes in commercial shrimp grow-out ponds and their effect on the survival rate of Pacific white shrimp. Overall, these findings suggest that the specific microbiomes in rearing water may be linked to the impact on improved survival of Pacific white shrimp.