The metagenomic characterization of bacterial community in aquacultured Shrimp Penaeus monodon

Abstract

Abstract Aquaculture has grown rapidly during the last few decades due to research and developmental activities aiming at various aspects of aquaculture. The use of microorganisms in aquaculture as environmental biomarkers, bioremediators, probiotics, and as a direct food source for the cultured species has expanded further in the last few decades. However, we are still unaware of the various microbial species thriving within the aquaculture systems and their specific roles. Evidence has revealed that the diversity of microorganisms in aquaculture systems is far from being elucidated. Metagenomics is the study of genetic material recovered directly from the environmental sample. It is a culture-independent approach that provides an ample opportunity to discover the unexplored microbial community. The knowledge of bacterial communities in the brackish shrimp farming in Kerala is still insufficient.16S rRNA gene-based high-throughput sequencing revealed distinct and diverse microbial communities in the analyzed sample. Analysis of the results showed a high abundance of Betaproteobacteria, followed by Alphaproteobacteria, Clostridia, Actinobacteria, Gammaproteobacteria and Bacilli in the metagenome retrieved from the gut sample. Unclassified bacteria also contributed a significant portion of the metagenome. Microbes that play essential roles in nutrient cycling and mineralization of organic compounds such as Bacteroidetes, Planctomycetes, Gammaproteobacteria, Firmicutes, Cyanobacteria, and Actinobacteria could also be identified. Due to the strong influence of the gut microbiota on fish health, dominant bacterial species in the gut are strong candidates for probiotics. This study aimed to characterize the gut microbiota of giant tiger shrimp, Penaeus monodon. These findings provide valuable information on the microbial community and contribute to control the diseases in shrimp farms.