Probiotics administration in aquafeed is known to increase feed consumption and absorption due to their capacity to release a wide range of digestive enzymes and nutrients which can participate in digestion process and feed utilization, along with the absorption of diet components led to an increase in host's health and well‐being. Furthermore, probiotics improve gut maturation, prevention of intestinal disorders, pre‐digestion of anti‐nutrient factors found in the feed ingredients, gut microbiota, disease resistance against pathogens, and metabolism. The beneficial immune effects of probiotics are well established in finfish. However, in comparison, similar studies are less abundant in the shellfish. In this review, the discussions will mainly focus on studies reported the last two years. In recent studies, native probiotic bacteria were isolated and fed back to their hosts. Although beneficial effects were demonstrated, some studies showed adverse effects when treated with a high concentration. This adverse effect may be due to the imbalance of the gut microbiota caused by the replenished commensal probiotics. The probiotic effects revealed greatest effect on the shrimp digestive system particularly in the larval and early post‐larval stages, and probiotics stimulate the production of endogenous enzymes in shrimp and contribute with improved the enzyme activities in the gut, as well as disease resistance.

The present paper presents an overview of the effects of gut microbiota and probiotics on lipid-, carbohydrate-, protein- and amino acid metabolism in fish and shrimp. In probiotic fish studies, the zebrafish (Danio rerio) model is the most frequently used, and probiotic administration reveals the effect on glucose homeostasis, anti-lipidemic effects and increasing short-chain fatty acids, and increased expressions of genes related to carbohydrate metabolism and innate immunity, along with down-regulation of oxidative stress-related genes. Further, improved length of the intestinal villi and expression of nutrient transporters in fish owing to probiotics exposure have been documented. The present review will present an appraisal of the effect of intestinal microbiota and probiotic administration on the metabolism of nutrients and metabolites related to stress and immunity in diverse fish- and shrimp species. Furthermore, to give the reader satisfactory information on the topics discussed, some information from endothermic animals is also presented.