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Success of the shrimp aquaculture industry requires technological advances that increase production and environmental sustainability. Indoor, superintensive, aquaculture systems are being developed that permit year-round production of farmed shrimp at high densities. These systems are intended to overcome problems of disease susceptibility and of water quality issues from waste products, by operating as essentially closed systems that promote beneficial microbial communities (biofloc). The resulting biofloc can assimilate and detoxify wastes, may provide nutrition for the farmed organisms resulting in improved growth, and may aid in reducing disease initiated from external sources. Nuclear magnetic resonance (NMR)-based metabolomic techniques were used to assess shrimp health during a full growout cycle from the nursery phase through harvest in a minimal-exchange, superintensive, biofloc system. Aberrant shrimp metabolomes were detected from a spike in total ammonia nitrogen in the nursery, from a reduced feeding period that was a consequence of surface scum build-up in the raceway, and from the stocking transition from the nursery to the growout raceway. The biochemical changes in the shrimp that were induced by the stressors were essential for survival and included nitrogen detoxification and energy conservation mechanisms. Inosine and trehalose may be general biomarkers of stress in Litopenaeus vannamei. This study demonstrates one aspect of the practicality of using NMR-based metabolomics to enhance the aquaculture industry by providing physiological insight into common environmental stresses that may limit growth or better explain reduced survival and production.

Reduction or elimination of fish meal and fish oil from aquaculture diets can help to reduce the potential for contamination and dependence of the industry on pelagic fisheries while improving economic competitiveness. However, fish oil provides important omega‐3 (n‐3) fatty acids (FAs) essential to shrimp health and beneficial to humans. This study evaluated an organic, plant‐based diet formulated to replace fish meal and fish oil with plant proteins and docosahexaenoic acid (DHA) produced by algal fermentation. Shrimp cultured in replicate outdoor ponds at 25/m2 were fed either a diet composed of organically produced plant ingredients or a conventional commercial fish‐meal‐based feed. No significant differences were found in production parameters between the conventional fish‐meal‐based diet and the plant‐based diet (production: 4594 and 4592  kg/ha; harvest size: 18.7 and 19.2  g; survival: 93 and 88%; and feed conversion ratio: 1.4 and 1.3, respectively). At harvest, shrimp were analyzed for 147 chemical contaminants and 71 FAs. Contaminant levels were negligible for shrimp raised on both diets. The fish meal and fish oil diet provided significantly higher quantities of eicosapentaenoic acid and DHA than the plant‐based diet, and the shrimp fed the conventional diet reflected this with higher levels of these beneficial FAs in edible tissues. Differences between feeds and shrimp tissues suggest that essential n‐3 FAs may accumulate in shrimp tissues over time or that natural pond productivity may play a role in providing supplemental nutrition. Shrimp raised on the two diets and wild‐caught shrimp are clearly distinguishable by their FA profiles. Compared to alternative protein sources like beef, pork, or chicken, differences in lipid profiles of shrimp raised on either diet may be insignificant because both offer increased human health benefits.

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In this study, we investigated the metabolic effects of four different commercial soy-based protein products on red drum fish (Sciaenops ocellatus) using Nuclear Magnetic Resonance (NMR) spectroscopy-based metabolomics along with unsupervised principal component analysis (PCA) to evaluate metabolic profiles in liver, muscle and plasma tissues. Specifically, during a 12-week feeding trial, juvenile red drum maintained in an indoor recirculating aquaculture system were fed four different commercially available soy formulations, containing the same amount of crude protein, and two reference diets as performance controls: a 60 % soybean meal diet that had been used in a previous trial in our lab and a natural diet. Red drum liver, muscle, and plasma tissues were sampled at multiple time points to provide a more accurate snapshot of specific metabolic states during the grow-out. PCA score plots derived from NMR spectroscopy data sets showed significant differences between fish fed the natural diet and the soy-based diets, both in liver and muscle tissues. While red drum tolerated the inclusion of soy with good feed conversion ratios, a comparison to fish fed the natural diet revealed that the soy-fed fish in this study displayed a distinct metabolic signature characterized by increased protein and lipid catabolism, suggesting an energetic imbalance. Furthermore, among the soy-based formulations, one diet showed a more pronounced catabolic signature.