Considering the crucial role of the gut microbiome in animal health and nutrition, solutions to shrimp aquaculture challenges, such as improving disease resistance and optimizing growth on lower cost feeds, may lie in manipulation of their microbial symbionts. However, achieving this goal will require a deeper understanding of shrimp microbial communities and how their composition is influenced by diet formulation, environmental conditions, and host factors. In this context, the current study investigated the intestinal bacterial communities of the Pacific whiteleg shrimp (Litopenaeus vannamei
—the most widely aquaculture-farmed shrimp worldwide) reared in indoor aquaculture facilities and outdoor pond systems. While samples showed very consistent intestinal bacterial community profiles within each production system, major differences were uncovered between the two practices. Indeed, bacteria affiliated with Rhodobacteraceae (Proteobacteria) and Actinobacteria were significantly more abundant in indoor samples (84.4% vs. 5.1%; 3.0% vs. 0.06%, respectively), while Vibrionaceae (Proteobacteria), Firmicutes, Fusobacteria and Cyanobacteria were predominant in pond samples (0.03% vs. 44.8%; 0.7% vs. 36.0%; 0.0% vs. 7.9%; 0.001% vs. 1.6%, respectively). Accordingly, the abundance of 11 of the 12 most prominent Operational Taxonomic Units (OTUs) were found to be statistically different between the two production environments. Together, these results indicate that aquaculture practices greatly influence the intestinal bacterial profile of the whiteleg shrimp, and further suggest that bacterial communities of this economically important crustacean could be effectively manipulated using diet composition or environmental conditions.
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