It is well known that healthy gut microbiota is essential to promote host health and well‐being. The intestinal microbiota of endothermic animals as well as fish are classified as autochthonous or indigenous, when they are able to colonize the host's epithelial surface or are associated with the microvilli, or as allochthonous or transient (associated with digesta or are present in the lumen). Furthermore, the gut microbiota of aquatic animals is more fluidic than that of terrestrial vertebrates and is highly sensitive to dietary changes. In fish, it is demonstrated that [a] dietary form (live feeds or pelleted diets), [b] dietary lipid (lipid levels, lipid sources and polyunsaturated fatty acids), [c] protein sources (soybean meal, krill meal and other meal products), [d] functional glycomic ingredients (chitin and cellulose), [e] nutraceuticals (probiotics, prebiotics, synbiotics and immunostimulants), [f] antibiotics, [g] dietary iron and [h] chromic oxide affect the gut microbiota. Furthermore, some information is available on bacterial colonization of the gut enterocyte surface as a result of dietary manipulation which indicates that changes in indigenous microbial populations may have repercussion on secondary host–microbe interactions. The effect of dietary components on the gut microbiota is important to investigate, as the gastrointestinal tract has been suggested as one of the major routes of infection in fish. Possible interactions between dietary components and the protective microbiota colonizing the digestive tract are discussed.

A complex and dynamic community of microorganisms, play important roles within the fish gastrointestinal (GI) tract. Of the bacteria colonizing the GI tract, are lactic acid bacteria (LAB) generally considered as favorable microorganism due to their abilities to stimulating host GI development, digestive function, mucosal tolerance, stimulating immune response, and improved disease resistance. In early finfish studies, were culture-dependent methods used to enumerate bacterial population levels within the GI tract. However, due to limitations by using culture methods, culture-independent techniques have been used during the last decade. These investigations have revealed the presence of Lactobacillus, Lactococcus, Leuconostoc, Enterococcus, Streptococcus, Carnobacterium, Weissella, and Pediococcus as indigenous species. Numerous strains of LAB isolated from finfish are able to produce antibacterial substances toward different potential fish pathogenic bacteria as well as human pathogens. LAB are revealed be the most promising bacterial genera as probiotic in aquaculture. During the decade numerous investigations are performed on evaluation of probiotic properties of different genus and species of LAB. Except limited contradictory reports, most of administered strains displayed beneficial effects on both, growth—and reproductive performance, immune responses and disease resistance of finfish. This eventually led to industrial scale up and introduction LAB-based commercial probiotics. Pathogenic LAB belonging to the genera Streptococcus, Enterococcus, Lactobacillus, Carnobacterium, and Lactococcus have been detected from ascites, kidney, liver, heart, and spleen of several finfish species. These pathogenic bacteria will be addressed in present review which includes their impacts on finfish aquaculture, possible routes for treatment. Finfish share many common structures and functions of the immune system with warm-blooded animals, although apparent differences exist. This similarity in the immune system may result in many shared LAB effects between finfish and land animals. LAB-fed fish show an increase in innate immune activities leading to disease resistances: neutrophil activity, lysozyme secretion, phagocytosis, and production of pro-inflammatory cytokines (IL-1β, IL-6, IL-8, and TNF-α). However, some LAB strains preferentially induces IL-10 instead, a potent anti-inflammatory cytokine. These results indicate that LAB may vary in their immunological effects depending on the species and hosts. So far, the immunological studies using LAB have been focused on their effects on innate immunity. However, these studies need to be further extended by investigating their involvement in the modulation of adaptive immunity. The present review paper focuses on recent findings in the field of isolation and detection of LAB, their administration as probiotic in aquaculture and their interaction with fish immune responses. Furthermore, the mode of action of probiotics on finfish are discussed.

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 aquaculture industry has dramatically developed during the last two decades. However, this development has, in some cases, resulted in environmental degradation, emergence of diseases, and low productivity. The need for improving disease resistance, growth performance, feed efficiency, and safe aquatic production for human consumption has stimulated development and applications of probiotics in aquaculture. Probiotics used in aquaculture include genera of Bacillus, Lactobacillus, Enterococcus, and Carnobacterium, and yeast. However, most of these probiotics are derived from terrestrial sources and not from the environment in which the aquatic animals live or the host animal. The use of “host-associated probiotics” has gained attention, as they offer an alternative strategy within aquaculture, which per se is dependent on the use of terrestrial microorganisms. The benefits of host-associated probiotics include improved growth performance, feed value, enzymatic contribution to digestion, inhibit adherence, and colonization of pathogenic microorganisms in the gastrointestinal tract, increase hematological parameters, and immune response. The present review addressed insight into the application of host-associated probiotics within aquaculture, with special focus on their immunomodulatory and growth enhancing effects. Furthermore, the current review address research gaps and issues that merit further investigations.

Among immunostimulants used in aquaculture, herbal is promising due to their propensities to improve growth performance, fish immunity, and their antimicrobial properties, as they are good alternatives to chemical treatments and antibiotics. As medicinal herbs are eco-friendly, cost effective, have minimal side effects, and they have gained attention in the prevention and treatment of fish diseases. Plant-derived compounds are reported to stimulate fish immunity due to the presence of many bioactive secondary metabolites, and studies comprising gene expression, proteomics, and metabolomics have improved the understanding of the effects that herbal compounds can have on fish immune status. The current review summarizes findings pertaining to the role of plant-derived compounds with immunostimulant properties in fish.