Innovative farming approaches that incorporate functional feed additives to promote shrimp growth and health can play a critical role in revitalizing the shrimp industry. This approach not only allows farmers to increase throughput and production, but also minimizes the environmental footprint by reducing the use of chemicals and antibiotics in the field. The increasing importance of gut microbial populations to their host has drawn attention to prebiotics (dietary fiber to promote the growth of beneficial bacteria) and probiotics (beneficial bacteria) as promising functional feed ingredients to maintain gut homeostasis. Understanding microbial dynamics and functional roles in the shrimp microbiome will be critical for the development of such feed ingredients.
Recent advances in next generation sequencing and metabolite detection have led to various -omics-based techniques such as metagenomics (to determine bacterial identity and functional potential), transcriptomics (to determine host responses), and metabolomics (to identify active small molecules) to understand the microbial community and host-gut microbial interactions. Here, next generation sequencing analyses were used to study the gut bacterial communities in wild-caught and farmed P. monodon. Five phyla, Actinobacteria, Fusobacteria, Proteobacteria, Firmicutes and Bacteroidetes, were found in all shrimp from both wild and farm environments. The bacterial profiles showed similar dominant genera in wild-caught and domesticated shrimp, indicating the presence of a resident bacterial population in P. monodon. However, the gut bacterial profiles of wild-caught shrimp showed greater variation than those of farmed shrimp, suggesting that the environments influenced gut microbial composition. To better understand the role of host immunity in gut microbial composition, we used multidisciplinary platforms ( microbiome, transcriptome, and metabolome) to determine the interactions between the gut microbiota and its animal host, P. monodon. RNAi suppression of Toll and IMD signaling pathways, the major immune pathways of P. monodon, was used as a tool to alter host immune gene expression. Suppression of Toll and IMD signaling pathways resulted in differential gene expression in hemocytes, particularly for immune-related genes encoding antimicrobial peptides, heat shock proteins, and pattern recognition proteins. Suppression of the IMD pathway had a greater impact on bacteria, genes, and metabolites in the shrimp gut. Therefore, we proposed a model representing an interaction between gut bacteria and the host immune system, in which IMD is the major immune pathway controlling and balancing commensal colonization.