Impact of Aquaculture Practices on Intestinal Bacterial Profiles of Pacific Whiteleg Shrimp Litopenaeus vannamei

Abstract

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.

Investigation of the Potential Effects of Host Genetics and Probiotic Treatment on the Gut Bacterial Community Composition of Aquaculture-raised Pacific Whiteleg Shrimp, Litopenaeus vannamei

“…A total of 2195 OTUs were identified across all samples (Supplementary Table S11), with 707 corresponding to previously described OTUs [32]. OTUs that were common to both SIS and OI genetic lines represented the vast majority (99.3–99.7%) of sequence reads generated in the present study (Figure 1).…”

“…To further investigate the changes in bacterial community composition that had occurred during the trial, the distribution profiles of the most abundant OTUs were analyzed (Table 3). Five of these major OTUs (SD_Shr-00002, SD_Shr-00003, SD_Shr-00004, SD_Shr-00006 and SD_Shr-00010) had previously been described by our group [32], while SD_Shr-00097 (Bacteroidetes-affiliated) and SD_Shr-00098 (Verrucomicrobia-affiliated) were novel OTUs. While SD_Shr-00098 was very closely related to Haloferula rosea (99.4%), the sequence identity of SD_Shr-00097 to its closest valid relative was only 93.2% ( Salinimicrobium catena ) indicating that it likely belonged to a bacterial phylogenic lineage that has yet to be described.…”

“…Both species are known to cause disease in shrimp, with V. alginolyticus thought to be more pathogenic by resulting in failure to thrive and ultimately death of infected hosts, while V. shilonii infection is more likely to cause tissue damage and reduced weight gain [33]. Interestingly, SD_Shr-00004 had previously been identified by our group as prominent in outdoor systems while found in very low abundance in indoor-aquaculture raised shrimp, which had suggested that husbandry practices may play an important role in controlling the abundance of this OTU [32]. However, SD_Shr-00004 was found in much higher abundance in this study.…”

Healthy microbiome: a key to successful and sustainable shrimp aquaculture

“…Differences in aquaculture practices also influence the microbiome composition. Significant variations in the gut microbiome composition of Pacific white shrimp was observed when reared in two different rearing systems, the indoor and outdoor pond-based systems (Landsman et al 2019). In the integrated multitrophic aquaculture (IMTA) system, the gut microbiome of Pacific white shrimp was positively influenced when cultured with Pacific oyster Crassostrea gigas (Omont et al 2020).…”

Editorial for the Special Issue: Gut Microorganisms of Aquatic Animals

“…Moreover, as we get a sharper insight on these associations, symbiotic microbes can reciprocally interact with the aquatic environment even at the ecosystem level [2,3]. The articles published in the special issue “Gut Microorganisms of Aquatic Animals” are a contribution towards the scientific efforts to unravel some of the associations between freshwater [4], ornamental [5] and marine [6,7,8] fish, as well as shrimp [9,10,11] and their microbes. These papers cover multiple issues on aquatic animal–microbe interactions: healthy or diseased fish, the impact of pollution and handling practices on fish gut microbiota, and the effect of probiotics in the gut.…”