Effects of probiotics, prebiotics, and synbiotics on immune function, disease resistance, digestive health, and stress management in fish culture

Abstract

Aquaculture is a fast-growing farming sector, and fish production aims to meet global nutrient demand. Aquatic organisms are directly exposed to deteriorated ecological environments and die during outbreaks. In the beginning of aquaculture, several synthetic drugs were introduced to protect organisms, and continuous exposure results in antibiotic accumulation in fish and the development of drugresistance among microorganisms. In addition, exposure to these antibiotics affects the environment and affects nontargeted organisms. Probiotics, followed by prebiotics, were introduced in the aquaculture industry, and synbiotic interventions were subsequently proposed. Synbiotics are active combinations of prebiotics and probiotics that are used to improve digestive enzyme activity, antioxidant enzymes, antioxidant chemicals, immunity, growth performance, and feed utilization efficacy in fish. The application of synbiotics improved overall fish growth, stress mitigation and improved yield in aquaculture. Prebiotics, probiotics, and synbiotics are considered alternatives to synthetic drugs. Synbiotics improved gut microbiota, immune response, antioxidant mechanism, and stress mitigation effects. This narrative review focuses on current research advancements to address the research gap between synbiotics and healthy fish production. The variations in standard methodology in feed formulation, dosage of synbiotics, stages of fish, treatment period, route of administraton, selected fish type, and environmental conditions, and effectiveness of synbiotics have contributed to the major complexities of the field. The present study aimed to summarize the current research on the effects of probiotics, prebiotics, and synbiotics on antioxidant molecules, digestive enzymes, and stress mitigation effects in fish, shrimps and oysters. From these results, it can be found that fish have the potential to change their microbial community according to the surrounding environment. Identifying research gaps in this field and understanding the role of synbiotics can improve fisher-friendly strategies to maximize fish growth performance, the immune response, and ecological balance.

Introduction

Aquaculture is one of the leading sectors that addresses the basic need for nutritional demand and causes disease outbreaks in aquatic environments (Pepi and Focardi, 2021; Tavares-Dias, 2021). Traditionally, fish farmers use several synthetic antimicrobial agents (e.g., chloramphenicol, sufamerazine, oxytetracycline dihydrate, and quinolones) and various synthetic chemicals (e.g., copper sulfate, malachite green, potassium permanganate, and formalin) to control bacterial and fungal diseases (Mohamed et al., 2000). Moreover, most of these antimicrobial and chemical agents have been restricted and have negative impacts on marine debris accumulation, immunosuppressant activity, toxins and drug resistance threats. The use of chemicals and antimicrobials leads to the generation of toxic antibiotic residues or chemicals or derivatives emerging from the chemicals. The administration of potassium permanganate and formalin had adverse effects on the gill and altered mucous cells (Ghelichpour et al., 2016; Leal et al., 2018). The unrestricted use of antibiotics in fish farming has led to their increased bioaccumulation in fish (Zhang et al., 2021). In addition, these factors cause various side effects, such as vomiting, diarrhea, and stomach illness. However, the use of these chemicals frequently fails to control disease outbreaks on aquaculture farms (Hoseinifar et al., 2017; Musthafa et al., 2018; Safety, 2011; Yilmaz et al., 2022). In aquatic organisms, the gastrointestinal tract microbial flora performs several functions, and the microbial population in the gut improves digestion, improves immune function, protects against highly pathogenic organisms, and improves gut development (Wang et al., 2018; Twetman and Belstrøm, 2025).

Probiotics for aquaculture management may include a single bacterial strain or a range of beneficial microorganisms, including bacteria and yeast. Lactic acid bacteria such as Lactobacillus sp., Enterococcus sp., and yeast such as Saccharomyces cerevisiae are incorporated into fish diets or directly inoculated into water as unique bacteria or mixtures of more than one individual species on the basis of the requirements of fish farming (Bockus et al., 2021; Soltani et al., 2019; Paray et al., 2021; Hassani et al., 2020). The outcomes of probiotics may include prevention of disease, control of virulence, disease prophylaxis, improvements in food conversion efficiency, and increases in the growth performance of fish via the production of several digestive enzymes and antioxidant enzymes, which support the proliferation of the gut microbial flora, improve antioxidant activity, improve immunity and mitigate abiotic (environmental factors) and biotic stresses (e.g., excessive crowding in intensive farming) (Mohammadi et al., 2021; Mohammadi et al., 2020; Putra et al., 2021). The effective benefits of beneficial probiotics for improving fish health significantly contribute to improved immunity, feed conversion efficiency, growth performance, and water quality (Rakab et al., 2025). The supplemented probiotics can alter both systemic and mucosal immune responses in fish, thereby enhancing fish growth, maintaining the microbial biota within the gut, producing antimicrobial compounds, and biosynthesizing antioxidant enzymes, resulting in the prevention of cell damage, a decrease in oxidative stress, a reduction in inflammation in the gut and an improvement in digestive enzymes (Merrifield and Carnevali, 2014; Sugimura et al., 2011; Merrifield et al., 2010a).

The probiotic bacteria such as Pediococcus, Oenococcus, Leuconostoc, Lactococcus, and Enterococcus are commonly used LAB in aquaculture (Ouwehand et al., 2002). The potential of probiotics in various aquatic organisms and fish such as rainbow trout (Oncorhynchusmykiss), African catfish (Clariasgariepinus), Nile tilapia (Oreochromisniloticus), rohu (Labeorohita), European sea bass (Dicentrarchuslabrax), Red seabream (Pagrus major), and snook (Centropomusundecimalis) (Guzmán-Villanueva et al. 2004; Yanbo and Zirong, 2006; Kari et al., 2022). Probiotic organisms confer significance health benefits to fish via a variety of molecular mechanisms, including hydrolytic enzymes production, improvement in feed conversion ratio and the reduction of disease incidence and enhancement of fish growth (Newaj‐Fyzul et al., 2007; Han et al., 2022), In the aquaculture system, various factors can significantly influence the effectiveness of probiotics, including the probiotic strains, fish, environmental conditions and combinations of probiotics, and mode of administration. Bacteria from the genus Bacillus have the potential to improve species and strain specific benefits to fish than other bacterial strains. Hence appropriate probiotics strains are required to meet specific needs in aquaculture management (Chen and Gao, 2023).

Prebiotics are added with experimental diets mainly in juvenile stage and it improve fish growth, survival and disease resistance via various molecular mechanisms. These include the increased biosynthesis short-chain fatty acids, digestive enzymes, enlarged size of intestinal villi, increased level of enterocytes, improvement of the immune function, modulation of the presence of intestinal microorganisms, and suppressing the growth of pathogenic microorganisms and microbial hemostasis in the gut, and the reduction of triglycerides and cortisol (de Jesus Raposo et al., 2016). Prebiotics has been widely used to improve growth and health benefits in fish. The major prebiotics are FOS (Ortiz et al., 2013), inulin (Li et al., 2023), β-glucans (Wang et al., 2022), GOS (Hahor et al., 2019), MOS (Ren et al., 2020), and XOS (Wang et al., 2022). The prebiotic diets improved fish growth and to improve the economy of commercial farmers and the fish such as carp, catfish, tilapia, and salmonoids have cultivated using prebiotic diets in inland and marine aquaculture practice for the past two decades (FAO, 2022). The supplemented β-glucan improved lysozyme activity, phagocytosis, and bactericidal effect, whereas, inulin improved the biosynthesis of digestive enzymes, immune system, and production of short-chain fatty acids (Akter et al., 2019). MOS improved immune system, survival and growth rate in fish and inhibit the generation of pathogenic bacteria such as Vibrio spp. and Aeromonas spp (Amillano-Cisneros et al., 2023). In aquaculture industry, the demand of prebiotics supplements increasing continuously for few decades. The prebiotic market reached 1.35 million tons in 2024 and the demand increasing continuously (Rajan et al., 2021).

Prebotics are any substrate, compound, nutrient, long-chain sugar that effectively serves as food for nonpathogenic bacteria in the host gut (Mountzouris, 2022). Unlike probiotics, prebiotics are highly stable under extreme environmental conditions. The important sources of prebiotics are microalgae, seaweed, vegetables, plants and animal dairy products (Van Doan et al., 2020). The application of prebiotics can prevent the adherence of pathogenic organisms to the epithelial cells of the fish gut, remove harmful bacteria from the gut, control inflammation and act as modulators of the host immune system directly and indirectly (Gephart et al., 2020). Aquaculture production is carried out near coastal regions or inland, and any impact on aquaculture directly affects the ecosystem and consumer health. In recent years, the aquaculture sector has faced several challenges, most of which are associated with disease maintenance. Aquatic organisms are vulnerable to ecological threats and disease outbreaks. Inorganic synthetic drugs are used to treat disease (Mohammadi et al., 2021). Prebiotics also improve the health status of fish, promote the growth of the gut microbial flora, and increase the enzyme activity of probiotic bacteria. There are few examples of prebiotics, including mannan oligosaccharide (MOS), inulin, β-glucan, fructooligosaccharides (FOS) and galactooligosaccharide (GOS) (Yilmaz et al., 2022). These prebiotics have the potential to improve fish growth, digestive enzyme activity, the proliferation of microbes within the gut, antioxidant enzymes, and immunity. Hence, prebiotics can help improve aquaculture production and waste management and reduce abiotic stress. Moreover, each gut microbiota is selective, and the growth-promoting activity of prebiotics in the gut is species specific. For example, the prebiotic GOS promoted the growth of Bifidobacterium sp., whereas FOS was found to improve the growth of Lactobacillus sp. This is due mainly to the fermentation potential of bacteria by specific enzymes (Yilmaz et al., 2022).

Synbiotics are combinations of prebiotics and probiotics that achieve synergistic activity to improve health-promoting activity in fish. In aquaculture, the application of probiotics aims to improve the probiotic activity and colonization in the gut by improving essential nutrients and the optimum environment through the use of prebiotics (Goh et al., 2022). Synbiotics improved the size of intestinal villi and improved digestive enzyme activity. Apart from digestive enzymes production, synbiotics improved antioxidant enzymes. These enzymes protect the host toward oxidative stress, reducing the generation of ROS and protecting the fish against pathogenic microorganisms. The SOD produced by bacteria involved in the decomposition of reactive O₂, whereas CAT convert H₂O₂ into O₂ and H₂O (Bœuf and Payan, 2001). The supplemented synbiotics contributed immunostimulatory activities, and they improved the generation of NOS. However, the mechanism of synbiotics on fish remain unclear and critical information still missing (Holt et al., 2021). Synbiotics show significant effects than prebiotics or probiotics supplement alone for aquatic animals and fish. Synbiotics promote the growth of beneficial microbes in the gut and stimulate the metabolism of LAB, which significantly improve the growth and host health (Dawood et al., 2018; Maftei, 2019). The supplemented β-glucan and Klebsiella sp. E26 in Litopenaeusvannamei regulate gut microbial population, immune activation, and energy production, thereby effectively improving the growth and survival rate of fish (Chang et al., 2025). Likewise, the dietary supplementation of L. delbrueckii (1 × 10⁷ CFU/g) with Asparagus officinalis L. root (5 g/kg) improved feed utilization, feed conversion, digestive enzyme activity and growth in rainbow trout and improved antioxidant activity to mitigate crowding stress (Yousefi et al., 2024). The combination of more than on probiotic bacterial strains, for example Bacillus sp. PM8318 and Bacillus sp. KRF-7 with β-gluco-oligosaccharide significantly improved the growth of fish growth, digestive enzyme production and improved the size of intestinal villi, thus enhance nutrient absorption. In addition to these effects, the supplemented synbiotics improved microbial colonization in the gut. However, the synergistic effect of probiotics and prebiotics remains unclear (Cadangin et al., 2024). The exact effect of synbiotics may vary depending on the type of fish species, the stage of fish, the mode of administration, the environmental condition, dosage and length of treatment (Wen et al., 2026). The supplemented pre, pro, and synbiotics could improve intestinal morphology, leading to more efficient gut functions (Alvanou et al., 2023). An overview of the use of probiotics, prebiotics, and synbiotics in aquaculture species is presented in Figure 1.

Figure 1

The combination of prebiotics and probiotics can have various advantages, including improved fish growth, disease resistance, increased adherence of probiotics in the gut mucosa, and metabolic activity bacteria associated with gut. The interaction between prebiotics and probiotics has been established (del Valle et al., 2023). Prebiotics serve as energy for probiotic bacteria, improving survival in the gut microbial flora and promoting the growth of beneficial microorganisms. Synbiotics are working together to improve the growth of beneficial bacteria but selectively through the fermentation capacity of prebiotic molecules (Puri et al., 2022). This selective metabolic capacity of microorganisms influences the total balance of the gut bacteria, digestive enzyme activity, and antioxidant enzymes. These interactions between probiotics and prebiotics improve overall gut health and improve fish digestive processes (Wen et al., 2026). Synbiotic research has recently evolved, providing deeper insights into the interesting molecular mechanisms by which probiotics and prebiotics modulate digestive enzyme activities (Setayesh et al., 2025). While various studies have focused on the beneficial effects of prebiotics, probiotics, and synbiotics individually, few studies have been published on the combined effects of prebiotics and probiotics. There is a desperate research gap between the use of prebiotics, probiotics and synbiotics. The present review aims to fill this research gap by analyzing recent research results, analyzing interactions, and determining research areas that require future exploration. Nonetheless, a large research gap persists in symbiotic research, necessitating a narrative review to analyze existing knowledge, determine present limitations, and list out the course for further studies. This review focuses on how prebiotics, probiotics, and synbiotics affect on digestive enzymes, the oxidative response and immune function.

Probiotics

Definition

The World Health Organization (WHO) and United Nation’s Food and Agriculture Organization (FAO) define living microorganisms as those that improve the health benefits of the host species when they are administered in adequate quantities (FAO/WHO 2001). Additionally, living microbial species supplemented with a diet could improve the health benefits to the hosts of aquatic organisms (Adel and Dawood, 2021). These probiotics are yeast or bacteria that improve the beneficial bacterial community in the gastrointestinal tract of fish.

Characteristic features of probiotics

Probiotics improve the host defense system and resistance to foreign substances or harmful microbes. They also synthesize several bioactive molecules, such as proteins, enzymes, organic acids, lipids, and other micro- and macromolecules. Some of these substances enhance binding to probiotics and mimics, therefore increasing the metabolic activity of pathogenic microorganisms in the gastrointestinal tract through a mechanism called surface competition (Kumar et al., 2016). Probiotics play a significant role in improving the immunesystem of fish (Ringø et al., 2020). Initially, probiotics have been introduced to improve the functional properties of poultry, pigs, ruminants, and humans; subsequently, probiotics were applied in aquaculture to manage fish production (Denev et al., 2009; Balasubramanian et al., 2021). In aquaculture, probiotics can be administered to aquatic organisms in two different ways. Probiotics can be inoculated into pond water directly or can be incorporated with fish feed to improve gastrointestinal health, thereby effectively inhibiting the growth of pathogenic microorganisms. The selection of the suitable mode of administration is a key factor in the utilization of probiotics in aquaculture (Tanwar et al., 2014). These probiotics provide health benefits to the host when supplemented with feed or inoculated in water. This is achieved by improving the microbial balance in the surrounding environment or host gut (Rekecki et al., 2009; Zhang et al., 2020). In the aquaculture system, probiotics have various positive effects on immune functions, growth activity, water quality, feed conversion, the regulation of gut microbes, and the inhibition of pathogenic microbes. In modern aquaculture practice, probiotics are widely used to improve host health. In aquaculture, the application of probiotics is a new trend, and their potential in aquatic organisms and ecosystems has not been comprehensively discussed. In aquatic organisms, probiotics are ubiquitous in nature in the gastrointestinal tract. Most of the reported Lactobacillus species are considered beneficial microorganisms that improve gut functions by producing various secondary metabolites, including bacteriocin, lactic acid, and other organic acids (Ayivi et al., 2020; Feng and Wang, 2020). The secondary metabolites excreted by probiotic bacteria protect against virulence factors from pathogenic microorganisms. The secondary metabolites extracted from laboratory cultures of selected probiotic organisms improve disease resistance, mitigate environmental stress, increase feed quality and increase the feed conversion ratio and growth (Khalid et al., 2021). In recent years, several commercial probiotic products have been introduced to improve fish culture, especially shrimp farming, and are administered through the diet (Butt et al., 2021). The secondary metabolites extracted from probiotic microorganisms are beneficial for improving the health of aquatic organisms, especially farmed animals. Probiotic organisms are generally evaluated on the basis of safety criteria, functional and physiological properties, stress resistance (bile salt tolerance and acid tolerance), proliferation rates, survival rates, rapid growth rates, pathogen-inhibiting properties, nonpathogenicity, and nonhemolytic activity, and they should be free from any plasmid-encoded antibiotic resistance genes. Probiotic organisms produce compounds that are antimutagenic, anti-inflammatory, growth promoters, and immunostimulatory molecules. Newly isolated probiotic microorganisms may possess all these beneficial properties to meet demand (Labba et al., 2020; Rajyalakshmi et al., 2021; Rwezawula et al., 2025). Probiotics are administered through a fish diet or as an encapsulated diet with live organisms, e.g., Artemia, or are inoculated directly in water. Probiotic feed may be useful for improving the health benefits of fish, and direct inoculation is highly useful for improving environmental health (Figure 2). The major probiotic organisms, dosages, and effects on fish health management are depicted in Table 1.

Figure 2

Modes of action of probiotic organisms in fish farming

Probiotic feed supplements (e.g., living Bacillus or Lactobacillus spp.) improve digestive enzyme activity, growth-promoting effects, the resistance of pathogenic organisms (e.g., bacteria), and the immune response (Mingmongkolchai and Panbangred, 2018; Ringø, 2020). Probiotic bacteria produce various antibacterial agents that maintain the microecological balance by preventing the growth of virulence pathogens (Gao et al., 2017).In aquaculture, probiotic organisms have shown antiviral activity; moreover, the exact mechanism of action remains unclear. The extracellular enzymes produced by bacteria exhibit antiviral and antifungal activity (Chauhan and Singh, 2019).

Probiotic microorganisms improved host’s gut defense which played a vital role in disease prevention and inflammation treatment in the digestive tract (Modanloo et al., 2017). They have immunomodulatory function in the gut and the lactic acid bacteria stick with host mucosal epithelium of the gut and resist the entry of bacterial pathogens via host epithelium (Sorroza et al., 2012). The digestive enzymes synthesized by probiotic microorganisms significantly improved feed digestibility (Zokaeifar et al., 2012). They produce fatty acid, lactic acids and other organic acids, bacteriocins, lysozyme, siderophores, and antibiotics (Yue et al., 2025). In fish, innate immune response is the first line of defense which protect host from various infectious diseases. It was found that the supplemented probiotics can strength the mucosal barrier of the gut by activating non-specific immune system such as mono-nuclear phagocytes, polymorphonuclear leukocytes and natural killer cells. Previous reports summarized enhanced monocytes (Aly et al., 2008b), leucocytes (Korkea-aho et al., 2012), granulocytes, macrophage, granulocytes, and lymphocytes after probiotic treatment in fish species (Kumar et al., 2008). The dietary supplementation of Lactobacillus rhamnosus at 10⁵ CFU g⁻¹ improved respiratory burst activity in Oncorhynchus mykiss (rainbow trout). The probiotics also exhibited phagocytosis and antibacterial property (Nikoskelainen et al., 2003). These previous investigations revealed that the probiotics have not only pathogen inhibiting activity but also regulating the host immune system. The mode of action of probiotic organisms in fish farming has been established. These include the regulation of various metabolic processes, including, amino acid metabolism, fatty acid metabolism, the production of cofactors or vitamins, the excretion of digestive enzymes, the production of several antagonistic molecules, the improvement of immune functions, stress mitigation, the disruption of quorum-sensing molecular mechanisms, and the detoxification of heavy metals (Linda et al., 2025). In addition to these reported modes of action, bidirectional communication between the brain and gut and the upregulation of low-molecular-weight metabolites have been reported (Ng et al., 2014). The mode of action of probiotics varies with environmental conditions and is strand specific. The colonization potential and survival rate of newly introduced probiotic organisms in the fish intestine directly influence the functional properties of probiotics and remain unpredictable (Hoseinifar et al., 2017a). Probiotic organisms produce various bioactive secondary metabolites that have bactericidal or bacteriostatic effects on virulent organisms, such as proteases, lysozymes, hydrogen peroxide, siderophores, or bacteriocins (Vinoj et al., 2015). The scheme of mechanism of action of probiotic organism in fish form is depicted in Figure 3.

Figure 3

Probiotics for bacterial disease control in aquaculture

Probiotic microorganisms synthesize various inhibitory compounds that exhibit antibacterial activity against bacterial pathogens. Native lactic acid bacteria (LAB) (Lactococcus lactis and Enterococcus faecium) isolated from the intestine of E. coioides (orange-spotted grouper) produce inhibitory molecules such as bacteriocin-like substances, hydrogen peroxide and other secondary metabolites. These inhibitory molecules prevent the proliferation of pathogenic bacteria such as Vibrio metschnikovi, V. harveyi, and Staphylococcus aureus, which are common pathogens in orange-spotted grouper (Carnevali et al., 2014; Loh et al., 2020). The probiotic strain Bacillus amyloliquefaciens M1 produces lipopeptide N3, which has antibacterial activity, including the ability to block ion-conducting channels, rupture and other membrane-active functions (Xu et al., 2014). The probiotic bacterial strain B. pumilus H2 presented anti-Vibrio activity against Vibrio spp. The anti-Vibrio compound was structurally characterized as amicoumacin, and the major anti-Vibrio mechanism was disruption of the bacterial cell membrane (Gao et al., 2017; Kuebutornye et al., 2020). The cell-free supernatant of Bacillus velezensis produces antibacterial compounds that are effective against A. salmonicida (Emam and Dunlap, 2020). The culture supernatant of the probiotic strain Clostridium butyricum consists of various secondary metabolites, including short-chain fatty acids and organic acids, which reduce the pH of the gut and thus reduce the growth of bacteria in the gut of fish (Yin et al., 2021). The probiotics Enterococcus faecium and fermented soybean meal improved the antioxidant activity, and the probiotic-supplemented diet in turbot improved the antimicrobial activity (Li et al., 2020). The addition of probiotic bacteria improved feed utilization efficacy, growth potential, water quality management, and disease prevention in aquaculture species under various abiotic and biotic conditions during fish cultivation (Mohammed et al., 2025).

Probiotics for controlling viral diseases in aquaculture

Microorganisms such as Vibrio spp., Pseudomonas spp., and Aeromonas spp. exhibit antiviral activities against hematopoietic necrosis virus infection (Hasan and Banerjee, 2020). The probiotic bacterial strain Pseudoalteromonas undina VKM-124 has antiviral activity against neuro-necrosis virus infection and improves the larval survival rate of yellow jack (Carangoides bartholomaei) (Mondal et al., 2022). An in silico approach has been proposed to screen a large number of natural viral protein inhibitors to develop antiviral drugs (Khang et al., 2025).

Immunostimulant properties of probiotics

Probiotic bacteria have immunostimulant activity and modulate immune function in fish. The probiotic microorganisms presented potential health benefits in aquatic organisms. Earlier studies focused on the use of probiotic organisms to improve the digestive functions of fish. Currently, probiotic organisms are used to improve adaptive and innate immunity in fish (Tran et al., 2022). Several probiotic species improve immune functions, especially the immune functions of marine teleosts, according to both laboratory observations and field studies (de Andrade Belo and Charlie-Silva, 2021). The probiotic bacterial species improved nitric oxide synthesis; serum protein, albumin, and lysozyme production; and phagocytic activity via the expression of IL-1b; myeloperoxidase content; superoxide anion and globulin levels; lysozyme activity, and respiratory burst activity (Akbari et al., 2021; Rachmawati et al., 2021). Previous studies have focused on the use of either individual or mixed probiotics to improve the immune functions of fish (Shah et al., 2021). Most of the previous studies focused on the use of live probiotic organisms because live organisms not only induce immunomodulatory functions but also produce various digestive enzymes. However, in recent years, research has focused on the use of heat-inactivated probiotic bacteria to improve immunity in fish. The indigenous probiotic bacterial strain B. pumilus SE5 isolated from E. coioides (brown spotted grouper) improved immune function. In addition, heat-inactivated bacteria improve the microbiota and immune function in the gut (Liu et al., 2021; Yang et al., 2021). Substances such as peptidoglycan, cell wall and lipoteichoic acid supplemented with fish feed, which were isolated from the probiotic bacterium B. pumilus SE5, induced the up-regulation of immune-related genes and microbial populations in the gut in a 60-day experimental trial. peptidoglycan and lipoteichoic acid have shown more pronounced activity than the cell wall and induced innate immunity in fish (Yang et al., 2019). Moreover, the mechanism of immune induction is not clearly understood (Mohammed et al., 2025).

Probiotics in stress management in aquaculture

Stress management is one of the major tasks in aquaculture, and any stress in aquaculture organisms affects fish growth and immunity. Under stress conditions, stunted growth has been reported, and the application of probiotic organisms helps improve the innate immunity of fishes against environmental factors and pathogens (Mohapatra et al., 2013). Probiotic bacterial species improve the production of fish and subsequently reduce stress conditions under semi-intensive and intensive conditions. In zebrafish, supplementation with probiotic species significantly reduces chronic stress conditions. The probiotic Lactobacillus rhamnosus regulates the expression of melatonin receptors and appetite markers. The supplementation of the probiotic Lactobacillus delbrueckii isolated from seabass decreased the stress marker cortisol in the fish tissue during the experimental period. This stress marker has been reported to be involved in reactions to stress (Carnevali et al., 2006). Compared with those in control groups, the stress tolerance of teleost fish in experimental groups improved (El-Saadony et al., 2021). The probiotic bacterial strains presented antioxidative properties, which were protective in the gastrointestinal tract, favored the growth of beneficial microorganisms and mitigated endogenous and exogenous oxidative stress (Castex et al., 2009). Heavy metal toxicity is one of the major stressors affecting the physiology of fish. In common carp, cadmium-induced toxicity is alleviated by the probiotic bacterium Bacillus coagulans SCC-19, which improves nonspecific immune function damaged by cadmium toxicity (Chang et al., 2021). The applied psychobiotics balance the intestinal microbial flora, gut, and brain and nullify stress (Churilov et al., 2025). Sohn et al. (2016) used probiotic bacteria such as Phaeobacter inhibens S4 and Bacillus pumilus RI06–95 to protect bivalve species Mytilus edulis, Argopecten irradians, Ensis directus, and Mercenaria mercenaria. The probiotic mixture improved survival rate of bivalve larvae and direct inoculums in larvae water decreased Vibrio spp. population in water. The supplemented probiotic bacterial species, Lacticaseibacillus plantarum improved the survival of oyster larvae challenged with Vibrio parahaemolyticus. The probiotic bacteria and microalgae showed synergistic activity and improved survival rate (Savin-Amador et al., 2025).

Probiotics for improving digestion

In aquaculture, probiotics were initially used to improve the production of digestive enzymes. Probiotics are significantly associated with fish growth because they maintain gut health, modulate the microbial population in the gut, and improve the function of gut bacteria (Sumon et al., 2018). Probiotic bacteria increase the enzyme activity in the fish gut via various molecular mechanisms. Lactase activity in fish is increased by probiotic bacteria from the genera Bifidobacterium and Lactobacillus, which improve lactose tolerance (Mardani et al., 2018). In addition, some probiotic organisms produce proteolytic enzymes that hydrolyze dietary proteins. These probiotic proteolytic enzymes complement the digestive enzyme activity of the host and improve the hydrolysis of proteins into amino acids (Mirghaed et al., 2018). Probiotic bacteria produce the amylase enzyme, which breaks down carbohydrates into the simplest form of sugars. The supplemented probiotic organisms have the potential to modulate carbohydrate metabolism and aid in the digestion of carbohydrate-rich diets in fish farming. Both the host and the gut microbial flora, especially those from the generaBifidobacterium and Lactobacillus, produce bile salt hydrolase in the digestive system. This enzyme is involved in the digestion and absorption of fats from the fish diet. A symbiotic microorganism, Cetobacterium somerae, has been recognized as a probiotic microbial species, and supplementation with C. somerae improved the gut health of juvenile Ctenopharyngodon idella (grass carp) (Chen et al., 2025).The probiotic (Bacillus subtilis WB60) and prebiotic mixture improved growth performance, enhanced digestive enzymes production, immune response, and feed utilization in Pacific whiteleg shrimp (Litopenaeus vannamei). The supplemented pre and probiotic mixture improved intestinal function and increased immunity when the shrimp was challenged against Vibrio parahaemolyticus (Eissa et al., 2025). Conversely, the dietary supplementation of probiotics (Arthrobacter bussei powder and Haematococcus pluvialis powder) increased nutrient digestibility in Litopenaeus vannamei (Pacefic white shrimp) (Kim et al., 2025).

Probiotics mimic the proliferation of intestinal pathogens, reduce disease outbreaks, and reduce antimicrobial usage

The fish feeding strategy is a major task in aquaculture and is associated with growth. Fish health, adequate fish feeding, and a significant reduction in the ecological impact of fish farms are major parameters affecting environmental sustainability and the ecological impact of the aquaculture sector (Panteli et al., 2021). An efficient feed conversion ratio decreases the generation of aquaculture waste in an environment or reduces the amount of poorly digested feed (Bureau and Hua, 2010). The accumulation of pathogenic microorganisms is one of the reasons for poor digestion in aquatic organisms. The intestinal health of fish is managed by supplementing alternative nutrient sources (Mousavi et al., 2020). In aquatic animals, intestinal health is very important for improving the efficiency of animal diets (Roh et al., 2020). Pathogenic bacterial strains in the intestines of farmed fish can be strongly associated with malfunction of the intestine and decrease the efficacy of FCR (Mavraganis et al., 2020). Intestinal pathogens cause subacute intestinal inflammation in fish, which may affect feed digestion and conversion (Roh et al., 2020). The uncontrolled pathogenic population in the gut mediates routine intestinal functions and results in increased pathological index scores, secondary inflammation, and increased excretion of nutrients without digestion and absorption (Ostaszewska et al., 2010; Øverland et al., 2009). These problems can be eliminated by supplementing with plant protein, and replacing fish protein can improve subacute pathological gut problems. The application of probiotics reduces their usage in aquaculture, improves the gut microbial flora, reduces gut inflammation and subsequently minimizes digestion-related diseases in fish (Yanbo and Zirong, 2006; Modanloo et al., 2017).The probiotic diet improved antioxidant activity and non-specific immunity when a Pacific white shrimp was fed with probiotic bacterial mixture (Arthrobacter bussei and Haematococcus pluvialis) with feed at 10⁸ (ABH) CFU g⁻¹ (Kim et al., 2025).

Gut health is a major factor for aquaculture farming. In recent years, probiotics have been used to enhance the gut health and manage subacute gut pathological issues and have been tested at farmed levels by various researchers (Sealey et al., 2015; Zhang et al., 2019). Improving a balanced diet with the required probiotics is a prerequisite for improving digestibility and metabolism in aquaculture practices (Shafique et al., 2021; Panteli et al., 2021). The addition of probiotics to the diet improved beneficial microbial flora and reduced gut pathological symptoms in farmed fish. The probiotic S. cerevisiae increased the goblet cell density in fish and enhanced growth performance and feed conversion (Islam et al., 2021). Lactic acid bacteria adhere to the mucosal epithelium of the gut in fish and effectively manage the proliferation of bacterial pathogens. Probiotics have also been supplemented directly with water. For example, probiotic bacterial supplementation in a pond of farmed tilapia increased the population of lactic acid bacteria in the pond and fish intestine, increased the expression of immune response markers and resulted in disease resistance against the fish pathogen Aeromonas hydrophila (Kaushik and de Oliva Teles, 1985). The supplement improved the health status of the fish by improving the proliferation of beneficial microorganisms, resulting in competition between host pathogens and probiotics, alterations in the extracellular pH, increased completion between pathogenic bacteria and pathogenic organisms on the mucosal epithelium of the fish and the production of antibiotic-like molecules (Bhatnagar and Mann, 2025). Kim et al. (2025) reported that the dietary supplementation of probiotic bacteria improved growth, enhanced whole-body composition, and nutrient digestibility than control diet in in Pacific white shrimp. In shrimps, the supplemented probiotics improved protease production and improved digestion in experimental animals fed with probiotic diet. The probiotic treatment improved gut microbial flora, promoted growth and production of bioactive molecules such as vitamins, short chain fatty acids, polyamines, and vitamins (Goh et al., 2023).

Probiotics for improving the water quality of farmed fish

Probiotics improve water quality and fish growth in freshwater forms, reduce environmentally related issues and prevent water pollution (Rurangwa and Verdegem, 2015). Probiotics have been administered to fish via different methods to increase the growth performance, physiology, and immune response of various fishes (Elsabagh et al., 2018; Sunitha and Padmavathi, 2013; Deng et al., 2022; Putra et al., 2016; Merrifield et al., 2010b). Probiotic supplements improve nutrient absorption and improve digestive processes and have been reported in several fish species (Zibiene and Zibas, 2019; El-Kady et al., 2022). The supplemented probiotics improved fish health without affecting the surrounding environment; i.e., water quality and probiotic treatment were commercially viable. Improving feed conversion efficiency is a major factor in the aquaculture sector, and improving feed conversion improves yield and increases profit. It has been previously reported that probiotic organisms have the potential to convert available organic matter into carbon dioxide in aquaculture systems, thus significantly reducing the accumulation of particulate organic carbon during cultivation. This mechanism of action improves water quality in the environment by maintaining a balance between phytoplankton production and eutrophication in the surrounding environment (El-Kady et al., 2022). Moreover, the supplementation of probiotics through the diet is one of the key routes of probiotic administration, and some issues, including problems associated with the immaturity of the digestive tract and early life stages of development, have been reported with the application of an animal diet. Presently, the supplementation of probiotics through water is considered a useful method for the uniform distribution of probiotics in the environment and is useful for fishes of all stages, from fingerlings to large fish, resulting in the maximum incorporation of probiotic organisms (Jahangiri and Esteban, 2018). Probiotic bacteria have improved the development of fish in early stages; hence, they have been used to improve productivity. In Chirostoma humboldtianum (shortfin silverside) larvae, the probiotics L. johnsonii and Bifidobacterium animalis subsp. lactis strain BB-12 improved larval growth and viability when the animals were fed a bioencapsulated probiotic diet. Similarly, the optimum probiotic dosage (B. circulans and B. licheniformis) improved the growth of common carp larvae when probiotics were directly added to rearing tanks (Jafaryan et al., 2011). In the early stage of fish development, the administration of probiotics through water was the major successful route of probiotic administration, and the use of enriched live feed may also provide additional advantages (Vázquez-Silva et al., 2017). Probiotic feed supplements improve health benefits and digestion (Merrifield et al., 2010), and the administration of probiotics through water can also improve the health benefits of farmed fish and improve their water quality (Thurlow et al., 2019; Sharma and Thakur, 2018). The denitrifying probiotic bacteria supplemented via a pellet diet, an encapsulated diet or fish pond water can convert available NH4--N and N compounds to nitrites and nitrates. Probiotic bacteria improve water quality in several ways. In aquaculture ponds, probiotic bacteria utilize both inorganic and organic carbon sources for growth, play a major role in the breakdown of available organic matter in pond water, and utilize dissolved organic matter and improve water quality (Gong et al., 2021). It has been reported that certain probiotic bacteria in freshwater systems reduce toxic NH₃ and P (Mohammadi et al., 2021; Mohammadi et al., 2020a; Putra et al., 2021; Bisht et al., 2025).The intestinal microbial flora obtained from the freshwater prawn (Macrobrachium rosenbergii) was sprayed in tanks which increased water quality, lysozyme activity, acid phosphatase production, plasma superoxide dismutase production, and intestinal trypsin activity (Qiu et al., 2023).The probiotic Bacillus spores supplemented pond water showed decreased ammonia content, improved dissolved oxygen, maintain pH level, improved the proliferation of bacterial spores and reduced pathogenic bacteria count in the pond water (Hassan et al., 2022). In Crassostrea virginica (eastern oyster) culture, the supplemented probiotic bacterium, Phaeobacter inhibens S4 improved health benefits, including promoting growth, limiting the proliferation of pathogenic bacteria such as Pseudomonas, and Alteromonas (Takyi et al., 2024). The probioitic mixture (Bacillus subtilis, Saccharomyces cerevisiae, and Lactobacillus plantarum) improved aquaculture environment. The supplemented probiotics increased digestive enzymes activity, improved water nutrient-degrading bacteria, reduced pathogenic bacteria in the gut, and supported sustainable aquaculture in shrimp (Litopenaeus vannamei) farming (Patricia, 2025).

Probiotics mitigate heavy metal stress in aquaculture

In the natural environment, heavy metals such as lead (Pb), cadmium (Cd), chromium (Cr), silver (Ag), mercury (Hg), zinc (Zn), cobalt (Co), copper (Cu), and iron (Fe) have been detected in water, soil, and the atmosphere (Merola et al., 2021; Jyoti et al., 2022; Shahjahan et al., 2022). These heavy metals induce toxicity to aquatic organisms and pose serious threats to crops, food quality, and environmental quality. Moreover, heavy metal toxicity is also associated with anthropogenic effects in the natural environment (Zaynab et al., 2022). Heavy metals are discharged from heavy metal industries, mining industries, and electroplating industries and are mixed with natural water bodies (Stefanescu, 2015; Sonone et al., 2020). Heavy metal contamination in water bodies results heavy metals accumulation in fish tissue, which then enter the human body via the food web (Fatima et al., 2020). Since they pose a severe threat to organisms, their complete elimination is important for improving the survival rate of fish in aquaculture environments (Moiseenko and Gashkina, 2020). Among all heavy metal removal methods, microbial degradation of heavy metals is simple and cost-effective, and this method does not require cellular energy, such as biosorption (Wróbel et al., 2023). Biosorption is a metabolism-independent process where contaminants or other heavy metals are removed passively from water by binding to the cell wall of bacteria. The major biosorption mechanisms include, surface complexation, ion exchange, electrostatic force, and physical adsorption involving various functional groups like hydroxyl, carboxyl, and phosphate groups. For example, lactic acid bacteria such as Bifidobacterium angulatum and Lactobacillus acidophilus are highly effective at removing heavy metals such as Pb, Cd, and As. The anionic functional groups of the microbial cell wall membrane interact with cationic heavy metals through electrostatic interactions (Elsanhoty et al., 2016). Exopolysaccharide-producing bacteria reduce the bioavailability of heavy metals. Probiotic microorganisms accumulate heavy metals via a process called bioaccumulation, which occurs within bacteria through energy-dependent processes. This mechanism involves the synthesis of several heavy meal-binding proteins, including metallothionein. For example, metallothionein-producing Bacillus cereus has been characterized, and it can accumulate Pb and produce metallothionein (Murthy et al., 2011). Bacteria convert free metals into highly insoluble complexes, thereby minimizing their bioavailability. Bacteria use reductive and oxidative metabolic processes to mediate the precipitation of toxic heavy metals (Abdel-Rahim et al., 2025). Bacteria such as Micrococcus spp. sequester Cd, Fe, Pb, and Zn via the calcite precipitation method (Gomaa, 2018). The probiotic bacterial strains utilize heavy metals as dietary supplements, and heavy metal-tolerant bacteria in the intestine control heavy metal accumulation in fish and aquatic organisms (Fakhar et al., 2022).In Litopenaeus vannamei culture, the inoculated probiotic bacterium, Bacillus subtilis IS02 in rearing water improved stress tolerance and immune function of larvae. The inoculated probiotic strains reduced Vibrio counts in the water and changes of nitrate content and over expression of prophenoloxidase genes (Mirbakhsh et al., 2021).

Prebiotics

Prebiotics are nutrients or substrates, fibers, or long-chain sugars that serve as food for nonpathogenic organisms in the host gastrointestinal tract (Mountzouris, 2022). It is also a substance that can be utilized by the gut microbial flora, is stable in the acidic environment of the host, and can improve the growth and immunity of the host (Davani-Davari et al., 2019). Prebiotics are generally foods that cannot be assimilated or digested directly by the host (e.g., fish). Prebiotic substances act as modulators in the host immune system, functioning as receptors in gut epithelial cells and controlling inflammation in the gut, thereby improving digestion (Mohammadi et al., 2021; Al-Sheraji et al., 2013). The role of prebiotics in aquaculture is illustrated in Figure 4 and Table 2.

Figure 4

Prebiotics improve microorganisms in the gastrointestinal tract, metabolic activity, and enzyme biosynthesis and balance host immune system function and gastrointestinal microorganisms, thus maintaining host health and immune function (Gómez and Balcázar, 2008; Bindels et al., 2015; Guerreiro et al., 2018). The long-chain complex carbohydrate serves as energy for nonpathogenic organisms within the fish gut. Prebiotics are derived mainly from plants or plant-based products, whereas mushrooms and certain prebiotics are extracted from animal sources (Balakrishnan et al., 2021; Mohammadi et al., 2020b). Prebiotics are widely distributed in fruits (Al-Sheraji et al., 2013), vegetables (Ahmadifar et al., 2019), seaweeds, beans, animal milk and microalgae (Rashidian et al., 2020; Elumalai et al., 2021; Van Doan et al., 2020). The modes of action of probiotic organisms in fish gut health and stress mitigation effect is presented in Figure 5.

Figure 5

Prebiotics improved feed conversion efficiency and immune function

Prebiotics are beneficial compounds that serve as energy sources for beneficial microorganisms but not for pathogenic microbes (Tran and Li, 2022). Prebiotics have been recommended for use in improving the growth of bacteria in the gut of fish to improve their intestinal health (Rohani et al., 2021). The common prebiotics used in aquaculture are arabinoxylan, β-glucan, fructooligosaccharides (FOSs), galactooligosaccharide (GOS), inulin, mannan oligosaccharide (MOS), and oligosaccharides. These prebiotics improve growth (Li et al., 2019), increase the feed conversion ratio (Shoaei et al., 2015), improve immune function (Li et al., 2021) and increase disease resistance in fish (Li et al., 2019). These earlier reports revealed the beneficial properties of prebiotics in aquaculture. Prebiotics act specifically on beneficial bacteria and improve the health of only targeted bacteria. For example, supplementation with FOS and GOS induces the growth of bacteria from the genera Bifidobacterium and Lactobacillus (Gibson et al., 2017) due to the presence of specific enzymes. The dietary administration of inulin improved intestinal microbial flora in farmed shrimp. The dietary supplements improved growth, antioxidant potential and immune function and intestinal microbial balance in Litopenaeus vannamei. The supplemented prebiotic increased hepatopancreas superoxide dismutase, amylase, acid phophatase, and phenol oxidase activity than control groups (Zhou et al., 2020).

Prebiotics and fish digestive health

The use of prebiotics in intensive farms has increased exponentially in recent years. Prebiotics promote the growth of fish and improve the functional properties of beneficial organisms in the gastro intestinal tract, thus improving the health of organisms (Xu et al., 2022). The roles of prebiotics in the digestive health of fish and their mechanism of action, sources, and uses in aquaculture have been established. Balanced nutrient sources such as proteins, carbohydrates, fats, minerals and vitamins are essential for fish health. Prebiotics play a significant role in improving the absorption of nutrients in the gut by improving the proliferation of nonpathogenic microorganisms that promote the digestion process and breakdown of highly complex food sources (Geraylou et al., 2013). Prebiotic polysaccharides stimulate the growth of microbial flora in the fish gut (Song et al., 2014). The polysaccharides extracted from Astragalus exhibited potential activity and improved digestive enzyme activity in O. niloticus (Yu et al., 2022). Similarly, a fructooligosaccharide-supplemented diet improved the gut morphology of white sea bream (Diplodus sargus) and digestive enzyme activity (Guerreiro et al., 2016). Likewise, prebiotics such as galactose-oligosaccharide and b-glucan improved digestive enzyme activity in Channa striata (Munir et al., 2018). In addition, supplementation with small chain fructooligosaccharides, xylooligosaccharides, and galactose oligosaccharides improved digestive enzyme production in Diplodus sargus (Guerreiro et al., 2016). Stress is one of significant factors that negatively affect fish growth and immune function. Prebiotics are helpful in stabilizing the intestinal microbial flora and supporting the production of several bioactive secondary metabolites that mitigate stress (Xu et al., 2022). The supplemented prebiotic molecules selectively stimulate fish and help maintain the healthy environment in the gut. In addition, prebiotics act as substrates for nonpathogenic microorganisms to outcompete pathogenic organisms by means of competitive exclusion, which supports beneficial microbes for resources and attachment (Xu et al., 2022). The addition of prebiotics to the diet improved the feed conversion efficiency, growth rate, and overall health status. Prebiotics effectively control and prevent fish diseases, either bacterial or viral diseases, by improving the immunity and prevent the proliferation of viruses or bacteria. In addition, prebiotics improve nutrient utilization, reduce environmental pollution, and assist in sustainable environmental management (Xu et al., 2022). The effects of prebiotics can vary among commercial fish species, highlighting the importance of optimizing the effective dosage. Moreover, the determination of an effective dosage and preparation of prebiotic diets in fish feed is highly complex, as it varies on the basis of several factors, such as environmental conditions, fish species and age (Xu et al., 2022). Probiotic bacteria from the genus Bifidobacterium and Lactobacillus produce short-chain fatty acids (SCFAs) are organic acids and composed of less than six-carbon atoms (Chen et al., 2017). Among these, butyrate (C4), propionate (C3), and acetate (C2) were the major SCFAs. Butyrate and propionate contribute more than 20% of total SCFAs, while acetate contributes about 60% of SCFAs. The other acids, including valerate, lactate isomers, iso-valerate, and isobutyrate contribute very lower comparable with major acids (Topping, 1996). Propionate, acetate, and butyrate are produced by anaerobic fermentation by bacterial sources in the intestine and smaller amounts of certain fatty acids. They serve as energy for intestinal cells, regulate immune function, and maintain intestinal barrier (Albaladejo-Riad et al., 2024). Short-chain fatty acids binding with G protein-coupled receptors in intestinal cells (Miyamoto et al., 2016) and antioxidant defenses and anti-inflammatory response activated (Nawaz et al., 2018). Liu et al. (2020) reported that prebiotics supply energy to enterocytes and are involved in gastrointestinal homeostasis in shrimp. The dietary supplementation of arabinoxylan-oligosaccharide (AXOS) and inulin exhibited synergistic activity in Litopenaeus vannamei culture and improved gut microbiota population, feed conversion efficacy and growth performance (Li et al., 2021). Fructooligosaccharides improved gut microbial flora, digestive enzyme production, and enteric bacterial community differed significantly than control group after 35-days experimental trial in Litopaneous vennamei (Mustafa et al., 2020).

Prebiotics improved the immune response in fish

Prebiotics are generally highly complex carbohydrates that provide energy to the gut bacterial flora and improve the immune function of fish (Mohammadi et al., 2022b). These immune response-stimulating prebiotics are termed immunosaccharides. These immunosaccharides are considered alternatives to antibiotics in aquaculture (Hoseinifar et al., 2020). The administered prebiotics act in two different ways, either to improve microbial growth or activate the innate immune system of fish (Song et al., 2014). Moreover, prebiotics act specifically on the fish gut; hence, prebiotic mixtures have been recommended to ensure fish health and improve the immune system (Kumar et al., 2022). The combinations of β-1,3 + 1,6–glucans (Guzmán-Villanueva et al., 2014), β-glucan + MOS (Lokesh et al., 2012), FOS + GOS + MOS +GGM (Zhou et al., 2010), and chitooligosaccharides + hydrolyzed shrimp shell chitin (Qin et al., 2014) are considered effective prebiotic mixtures. In Cyprinus carpio (common carp), the prebiotic composition of GOS + FOS + inulin improved the immune response (Hoseinifar et al., 2017). Similarly, in Litopenaeus vannamei (white shrimp), the combination of MOS + inulin increased immunity (Li et al., 2018). These earlier reports revealed the potential of more than one prebiotic in aquaculture production. β-glucan is widely applied to improve aquaculture production for both freshwater and marine fishes (Meena et al., 2013). However, β-glucan has been combined with MOS and GOS to improve immune function in Oreochromis niloticus (Nile tilapia) (Abu-Elala et al., 2018), gilad sea bream (S. aurata) (Guzmán-Villanueva et al., 2014), Chinese mitten crab (Eriocheir sinensis) (Lu et al., 2019), Atlantic cod (Gadus morhua) (Lokesh et al., 2012), snakehead (Channa striata) (Munir et al., 2016), and shabout (Tor grypus) (Mohammadian et al., 2021). Furthermore, β-glucan alone or in combination with other prebiotic treatments improved immune marker levels in fish (Ching et al., 2021). The dietary supplementation of arabinoxylan-oligosaccharide (AXOS) and inulin improved the proliferation of beneficial bacterial species such as Bacillus, Bacteriovorax, Pseudomonas, and Lactobacillus and improved the up-regulation of immune-related genes in shrimps (L. vannamei) infected with Vibrio alginolyticus or white spot syndrome virus (Li et al., 2021). The dietary β-Glucan could improve digestive enzyme activity, antioxidant activity, and nonspecific immunity potentials, and upregulated the expression of osmoregulation genes and nonspecific immune genes and improving carbohydrate metabolism in L. vannamei culture (Qiao et al., 2022).

Role of prebiotics in disease resistance

Prebiotics, or mixtures of MOS and β-glucan, have been utilized as effective immunostimulants to improve the immune function of fish. The combination of β-glucan and MOS increased the disease resistance of common carp (Cyprinus carpio) against Aeromonas hydrophila (Ebrahimi et al., 2012) and Atlantic cod (Gadus morhua) against Vibrio anguillarum (Lokesh et al., 2012), Nile tilapia (Oreochromis niloticus), Nile tilapia (Oreochromis niloticus), Pseudomonas fluorescens (Selim and Reda, 2015), and Pseudomonas fluorescens (Ismail et al., 2019). Each probiotic has its own merits and functional properties. For example, MOS alone has little or no effect on disease resistance in fish; however, β-glucan alone has been reported to be a potent immunostimulant and to improve disease resistance in fish (Gültepe et al., 2012). However, the efficacy of prebiotics may vary depending on the pathogenic organism and host species. For example, the prebiotic mixture (β-glucan and MOS) at 0.8% did not show any protection in Litopenaeus vannamei challenged with Vibrio species (Solidum et al., 2016). Moreover, in a previous study, a probiotic mixture improved the survival rate of Penaeus monodon challenged with WSSV, and the survival rate was 81% (Andrino et al., 2014). In a previous study, Apines-Amar et al. (2014) administered a 0.1–0.4% prebiotic mixture (MOS + peptidoglycan) to Penaeus monodon, and the prebiotic was resistant to WSSV. A prebiotic mixture (β-glucan and MOS) can improve disease resistance in Oreochromis niloticus. Compared with norfloxacin, the supplemented prebiotic mixture improved disease resistance (El-Nobi et al., 2021). The dietary supplementation of arabinoxylan-oligosaccharide (AXOS) and inulin improved the gene expression of cathepsin L, chitinase, and chymotrypsin in L. vannamei (Li et al., 2021). The Pacific oysters (Crassostrea gigas) treated with prebiotics mixture improved immune gene expression in response to V. coralliilyticus pathogenesis. Larvae challenged with V. coralliilyticus improved the gene expression and increased immune signaling proteins and the survival rate of C. gigas larvae (Hesser et al., 2024).

Role of prebiotic or prebiotic mixtures in abiotic stress

Dissolved oxygen, salinity, temperature, pH, photoperiod, and turbidity are the major abiotic factors in aquaculture ecosystems. These abiotic factors significantly influence fish health (Mugwanya et al., 2022). Any changes in abiotic factors trigger abiotic stress. It has been reported that prebiotics have the potential to relieve aquatic species from stress. β-glucan protects Pagrus major (red sea bream) against abiotic stress. In addition, supplementation with FOS decreases C. carpio stress (Hoseinifar et al., 2014). Moreover, specific environmental conditions are required for the activity of prebiotic or prebiotic mixtures. For example, the optimal temperature of a prebiotic mixture (Hoseinifar et al., 2017) improved the immunity of fish and improved gene expression to protect the host. Hybrid juvenile grouper fed prebiotic mixtures (MOS and XOS) presented improved antioxidant activity, growth performance, nonspecific immune function, and stress resistance against ammonia nitrogen in water and prevention of crowding stress. However, the antistress mechanism of XOS differs from that of MOS. After 28 days of treatment, the supplemented MOS effectively improved disease resistance in juvenile grouper challenged with V. harveyi. The increased concentration of FOS in the diet elevated the levels of oxidative stress markers in the freshwater prawn Penaeus semisulcatus (Genc et al., 2007).

Prebiotics improve the bioavailability of nutrients

Algae, yeasts and plants are the vital sources of various functional molecules, including inulin, alginate and several various types of oligosaccharides (Whisner and Castillo, 2018). Structurally, these compounds are soluble dietary fibers or carbohydrates, and microbes can breakdown in the animal body. To improve bioavailability, FOS, IMO, inulin, and MOS have been applied, and significant improvements have been reported in farmed fish (Huynh et al., 2018; Bamigbade et al., 2022).The supplemented prebiotics in the diet have the capacity to improve enzyme activity in the gut, improve growth performance, supply essential nutrients, and improve water quality. In addition to these functional properties, prebiotics improve immune function, assisting host fish in preventing the entry of several pathogenic microorganisms (Dobrogosz et al., 2010). The supplemented yeast culture with crab diet improved survival rate, intestinal microbiota, and reduced heat stress in Chinese crab, Eriocheir sinensis. The other beneficial effects include improvement of antioxidant activity, reducing MDA levels, reduction of oxidative stress, and maintaining gut health (Wang et al., 2025).The dietary inulin supplements improved growth, survival rate, and antioxidant activity in juvenile Litopenaeus vannamei. Furthermore, inulin reduced pathogenic bacteria (Flavobacteria and Vibrio) load and increased Xanthomarina population. The beneficial bacteria induced the production of digestive enzymes and feed conversion ratio (Park et al., 2025).

Role of prebiotics in carbohydrate metabolism

Carbohydrates are major nonprotein energy sources for aquatic organisms. This reduces the requirement of proteins and reduces nitrogen emission into the pond environment (Abasubong et al., 2019). Moreover, fish are less efficient at utilizing carbohydrates from dietary sources than mammals are. The increased consumption of a carbohydrate-containing diet leads to severe metabolic stress and health impacts in fish, including liver damage, hyperglycemia, and histopathological issues (Wang et al., 2021). In fish, an increased carbohydrate content in the fish diet triggers increased accumulation in the abdomen and liver (Luo et al., 2020). This fat accumulation in the liver causes endocrine malfunction, leading to insulin resistance and increased production of proinflammatory cytokines (Zhang et al., 2024a). Aquatic organisms, gut microbial patterns, feeding strategies, feeding behavior, and the type of prebiotics applied play major roles in deciding the potential health of animals (Lokesh et al., 2022). To date, studies on the regulation of carbohydrate metabolism by prebiotics are limited. These studies were restricted to certain commercial fish species. The addition of prebiotics (inulin and MOS) induces the expression of certain genes involved in metabolic activity in the muscle tissues and liver of rainbow trout (Lokesh et al., 2022). The prebiotic xylooligosaccharide (XOS) has been extracted from various raw materials from the nutraceutical industry, especially from agricultural wastes. Recent research revealed that XOS can improve mineral absorption, enhance antioxidant power, decrease lipid and glucose levels, and improve the proliferation of nonpathogenic gastrointestinal microbial flora, revealing in several health improvements, including disease prevention and carbohydrate metabolism (Chen et al., 2022). Common carp fed with diet containing 10 g/kg and 20 g/kg XOS presented decreased ADF, HIS, liver lipid content, and plasma TG, low-density lipoprotein (LDL) and total cholesterol (TC)levels and increased cholesterol concentrations (Abasubong et al., 2018). Earlier, Torrecillas et al. (2015) reported a significant reduction in long-chain monoenoic fatty acids in sea bass fed MOS. However, the prebiotic GOS can modify lipid metabolism in fish by balancing the gut microbial flora (Dhanasiri et al., 2023).

Prebiotics and lipid metabolism

Lipid metabolism, which involves a series of metabolic reactions and several enzymes, is associated with this process. Moreover, certain environmental and genetic factors influence lipid metabolic processes. Bile acid (BA) is an important molecule that contributes to the digestion of fat. These BAs are involved in the generation of fatty acids from complex molecules and emulsify fat into fat particles via lipoprotein lipase. Bile acids circulate between the colon and liver, which is termed “bile acid hepatic and enteric circulation” (Lin et al., 2020). Most prebiotics share common physiological properties with dietary fibers, and certain prebiotics are involved in triglyceride metabolism. Thus, prebiotics affect hepatic or serum triglyceride levels in experimental animals (Cho and Kim, 2015). Prebiotics are associated with reduced expression of various key genes, especially genes involved in the consumption of fructan. In the intestine, prebiotics are degraded and produce significant amounts of propionate, acetate and butyrate. Enterocytes breakdown butyrate and the liver receive propionate and acetate through the portal vein (Hijova and Chmelarova, 2007). Acetate enters hepatocytes through the processes of lipogenesis and cholesterogenesis and is activated by cytosolic acetyl-CoA synthetase 2. This metabolic process was implicated in the hypercholesterolemic effects of lactulose (indigestible carbohydrate), which elevates the production of acetate but not propionate. On the other hand, propionate inhibits the protein required for the entry of acetate into the liver (Cho and Kim, 2015).

Synbiotics

Synbiotics are dietary additives that are mixtures of prebiotics and probiotics, and they improve health benefits through synergistic effects. The supplemented fish diet or functional molecules in the diet have positive effects via the following mechanism: synergism, ingredient effects, or potentiation. Synbiotic activity results from the combined effect or the sum of the biological activity of each individual feed supplement. The term potentiation has been interpreted differently by researchers. For example, some researchers use the term potentiation to demonstrate synergistic activity or prebiotics and probiotics/or supplemented mixtures. The term potentiation is also used to describe only the activity of both substances and is applied simultaneously (Dawood et al., 2020; Kuo et al., 2021). Synbiotics are involved in nutrient degradation and improve beneficial bacterial populations, liver health, the production of oxidative enzymes, pathogenic resistance and stress mitigation effects (Figure 6). The beneficial role of synbiotics in aquaculture is shown in Table 3.

Figure 6

Synbiotics improve the digestive enzyme activity and growth of fish

Dietary supplementation with synbiotics improves the digestive enzyme activities of fish. Digestive enzymes improve nutrient degradation, resulting in the improved feed conversion efficiency and weight gain (Ghafarifarsani et al., 2021). The combination of probiotics and monosaccharides with the supplemented diet improved the feed conversion efficiency and immune response in carp. Moreover, few studies have reported on the function of synbiotics in carp (Mugwanya et al., 2022). The addition of synbiotics to a fish diet improved white blood cell counts and lymphocyte counts in carp (Mohammadi et al., 2022a). The combination of prebiotics (FOS) and probiotics (E. faecium) improved the survival rate, and digestive properties of common carp fingerlings (Dehaghani et al., 2015). In addition to the probiotic B. clausii, supplementation with MOS and FOS improved the growth performance and immune stimulatory function of Japanese flounder compared with those of the control group of animals (Hamidoghli et al., 2020). A fish diet supplemented with a probiotic bacterial species (B. subtilis) at 1.35 × 10⁷ CFU g⁻¹ and FOS improved the feed conversion efficiency and specific growth rate of juvenile large yellow croakers (Larimichthys crocea) (Ai et al., 2011).The supplemented synbiotics (Saccharomyces cerevisiae, Bacillus subtilis, mannan, and β-glucan) improved feed utilization, fish growth, maintain intestinal health, and enhanced beneficial bacteria population during experimental trial for 56 days (Yao et al., 2021).The combinations of galactooligosaccharide and different concentrations of Lactobacillus plantarum influenced on superoxide dismutase function, decreased plasma glucose levels, modulate digestive enzyme activity, including lipase, protease, and amylase. The dietary synbiotics enhanced intestinal microbiota, and stress resistance in P. Leptodactylus (Nedaei et al., 2023).The dietary fructooligosaccharide and probiotic (Saccharomyces cerevisiae, Bacillus subtilis, and Lactobacillus acidophilus) mixture increased growth performance, stress resistance and the production of antioxidant enzymes in juvenile Eriocheir sinensis. After eight weeks of experimental trials, increased superoxide dismutase, trypsin, pepsin, and chymotrypsin were observed (Wan et al., 2022).

Synbiotics improve disease resistance and immune function

The combination of prebiotics (galactooligosaccharides) and probiotics (Pediococcus acidilactici) improved the antagonistic activity against S. iniae and the immune response in rainbow trout fingerlings treated continuously for eight weeks (Jamal et al., 2020). In shrimp (Penaeus japonicas), the combination of prebiotics (0.2% isomaltooligosaccharide) and probiotics (Bacillus spp.) protects against V. alginolyticus infection and improves immunity (Prabawati et al., 2022). A fish diet mixed with molasses and Bacillus improved the bacterial population in the gut and improved immunity against pathogens in Pacific white shrimp (Panigrahi et al., 2020). Fish feed prepared with prebiotics (MOS, FOS, and inulin) and probiotics improved the bacterial population in the gut and immunity (Elabd et al., 2022; Lumsangkul et al., 2022; Mugwanya et al., 2022). An amalgamation of prebiotic and probiotic feed supplements is useful for improving the multiplication of beneficial bacteria in the host gut and the survival rate of fish challenged with bacterial pathogens by stimulating immune function (Kapoor et al., 2020). Fish diet supplemented with β-1,3 glucan and fructooligosaccharides increased growth performance, redox status, immune response in Litopenaeus vannamei and showed resistance against Fusarium solani infection. The optimum dosage was 1.5 g kg⁻¹ and treated for 75 days and the symbiotic composition improved disease resistance of L. vannamei and non-specific immunity (Eissa et al., 2023). Likewise, the crab diet with fructooligosaccharide improved growth, immune response and antioxidant activity after 60 days of feeding trials. The crabs treated with synbiotics showed resistance against Aeromonas hydrophila infections and improved survival rate. Synbiotics can stimulate cell-mediated and humoral immunity (Jia et al., 2017).

Regulatory effects of beneficial microbial flora on stress physiology

The microbial population in the gut is classified as either permanent or temporary on the basis of the duration of stay of the bacteria in the gut environment (Shade and Handelsman, 2012). The bacterial population produced via the diet is considered a temporary microbiota, and in most cases, it does not last for a long time, whereas permanent microorganisms live in the host gut longer and play a major role in balancing the microbiota in the gut (Zhang et al., 2016). In fish, the gastrointestinal tract, gills, and skin are the major routes for the entry of microbial species (Bøgwald and Dalmo, 2014); hence, most studies have focused on the determination of bacterial populations in the gut. These microbiome studies have expanded significantly due to the continuous growth of the aquaculture industry and the growing demand for the use of probiotics to maintain microbial homeostasis in the guts of various finfishes and shell fishes (Azizian et al., 2026). Understanding the host species-specific microbiome in the gut and the associated permanent microbiota in the gut coupled with host health is very important and will reveal the role of microbiomes in fish health and the underlying mechanisms (Xiong et al., 2016). The health status of cultivable organisms depends on the presence of a probiotic microbiome in the gut (Zhu et al., 2016). More attention has been given to fin fishes, and no adequate attention has been given to analyzing the microbiome of the invertebrate gut, especially that of crustaceans. Ringø et al. (2020) reported the total microbiome in the fish gut and reported a heavier microbial population in the gut than in the surrounding environment. These earlier findings revealed that the gut microbiome provides a favorable ecological niche for beneficial microorganisms. In addition, the intestinal tract of fish has an increased aerobic bacterial population (10⁸ aerobic bacteria g⁻¹) compared with anaerobic bacteria (10⁵ anaerobic bacteria g⁻¹) (Ringø and Song, 2016). In Atlantic salmon, molecular analysis revealed that the digestive tract consists of diverse bacterial flora, and 60% of the bacteria are Pseudomonas species (Navarrete et al., 2009). Roeselers et al. (2011) used next-generation sequencing analysis and reported the presence of diverse microbial flora in fish from domestic and wild collections. The primary composition of the gastrointestinal tract of the gut solely depends on the type of environment (Eichmiller et al., 2016). Notably, the microbiome composition of freshwater fish is similar to that of marine fish (Sullam et al., 2012). In addition, Aeromonas species are predominant in the gut of freshwater fish, whereas Vibrio spp. are dominant in marine fish (Tarnecki et al., 2017). Moreover, bacteria from various groups, viz., fusobacteria, actinobacteria, and Firmicutes (Li et al., 2017), were reported from the gastrointestinal tract of freshwater fish. In freshwater fish, bacterial species such as Cetobacterium somerae have been reported in the gut, where they produce significant amounts of vitamin B12 and inhibit the proliferation of pathogenic bacteria (Lyons et al., 2017). This particular species requires a special environment for laboratory cultivation and is difficult to culture in the laboratory. A common core microbiome in the gastrointestinal tract of the fish has been reported and has no relationship with host phylogeny or host genetics (Hennersdorf et al., 2016). The core microbiome group of carp species was established earlier because this group is dominant in the aquaculture industry. Bacterial species such as Firmicutes, Proteobacteria, and Fusobacteria are dominant in the guts of carp species; however, the density of each bacterium varies with the host species according to the environmental conditions (Yan et al., 2016). The bacterial species belonging to Cyanobacteria and Bacteroidetes are abundant in Asian carp (Kashinskaya et al., 2015), whereas the Cetobacterium population is predominant in the gut of grass car (Yan et al., 2016). In Atlantic salmon, Firmicutes and Proteobacteria are dominant in the gut in both marine and freshwater environments (Zarkasi et al., 2016; Dehler et al., 2017). These previous reports revealed that bacterial species vary based on the environment, and species-specific variation has been reported. Atlantic salmon have the potential to change their microbial community in the gut according to the environment. In juvenile freshwater salmon, Mycoplasmataceae, Ruminococcaceae, and Pseudomonas are dominant in the gut (Dehler et al., 2017), whereas Weissella and Leuconostoc are dominant bacteria in the gut of adult salmon that survive in cold environments (Gajardo et al., 2016). Moreover, Aliivibrio, Vibrio, and Photobacterium are the dominant bacterial species in the salmon gut in warmer water (Zarkasi et al., 2014). These analyses revealed temperature-specific variation in the same species. In addition, the microbial community in the gut may vary on the basis of the feeding habits of the fish, i.e., omnivores or herbivores (Yan et al., 2016). Owing to the development of commercial shellfish farming, a bacterial population of the shrimp gut has been established to improve aquaculture production. The microbiome of the shrimp P. monodon collected from the polluted environment was more variable than that collected from the less polluted environment. The analysis of the fecal microbiota of the fish collected from the highly polluted water revealed a greater Proteobacteria population (96%) than Firmicutes (0.53%), Fusobacteria (0.96%), and Bacteroidetes (2.3%) and pathogenic bacteria from Pseudoaltermonadales and Vibrionales (Oetama et al., 2016). Wan et al. (2006a) reported that the shrimp gut was dominated by bacterial genera such as Photobacterium, Xanthomonas, Aeromonas, Vibrio, Bacillus, Agrobacterium and bacteria from the Enterobacteriaceae family. In shrimp, Proteobacteria is considered the dominant core bacterial group, and these bacterial species promote shrimp growth. The available opportunistic pathogenic bacteria in the gut of shrimp show varying functional properties based on environmental factors and diet composition. Pathogenic bacteria from various genera, including Flavobacterium, Aeromonas, Shewanella, Escherichia, Vibrio, Rickettsia, and Pseudomonas, have been reported in L. vannamei. These pathogenic bacterial populations are lower in healthy L. vannamei intestines than in infected fish (Zhang et al., 2016; Cardona et al., 2016). The probiotic feed supplements (Enterococcus sp., Pediococcus sp., Lactobacillus sp.) altered the microbial community in the fish gut of rainbow trout (Oncorhynchus mykiss) (Ramos et al., 2013). The microbial population of Oreochromis niloticus was modified by supplementation with probiotic bacteria. A multispecies probiotic diet increased the Firmicutes population in the gut, and the digesta of the experimental fish presented increased Enterococcus, Bacillus, and Pediococcus abundances (Standen et al., 2015). In Yunlong grouper (Epinephelus moara), the probiotic-supplemented diet altered the microbial balance in the gut. The supplemented probiotics improved the Bacillus population and reduced the pathogenic bacterial load (Jin et al., 2024).

Probiotic organisms synthesize several antibacterial molecules that have bactericidal or bacteriostatic effects on disease-causing organisms, such as proteases, lysozymes, hydrogen peroxide, siderophores, or bacteriocins (Zapata and Lara-Flores, 2013). Certain probiotic microorganisms synthesize organic acid and volatile fatty acids (lactic, butyric, acetic, and propionic acid), significantly reducing the pH of the gastrointestinal lumen and subsequently arresting the growth of opportunistic pathogenic organisms (Ma et al., 2019). In addition, probiotic bacteria produce antibacterial agents, thereby controlling the proliferation of pathogenic organisms directly and maintaining microbial hemostasis in the gut (Gao et al., 2017). The gut mucosal surface of fish interacts with microorganisms and the external aquatic environment. Pathogenic microorganisms invade fish through mucosal surfaces, colonize and produce toxins and cause disease (Li et al., 2019). Thus, pathogenic organisms generally attach to the host mucosal layer to escape from harmful effects and induce infection (Adams, 2010). In this respect, the potential of bacteria to colonize and strongly adhere to the epithelial cell surface and subsequently affect pathogen adhesion is a preferable characteristic for the selection of new probiotics (Merrifield et al., 2010). Probiotic organisms are involved in competition with pathogens for specific binding sites on adhesion receptors in the intestinal mucosa and preventing the attachment of organisms. This mechanism is referred to as “competitive exclusion” and may be a nonspecific means of physicochemical agents, or specific, on the basis of the interactions of surface receptors of microbes and mucosal receptor molecules (Lazado et al., 2011). Thus, quorum quenching can be considered a potential anti-infective strategy to improve fish health. This can be achieved by using degrading enzymes or antagonistic molecules (Roy et al., 2011). This warrants the use of quorum quenching and microorganisms as potential quenchers of quorum signals among pathogenic bacteria and is considered an alternative to antibiotics for controlling the entry of pathogens in the intestine (Kalia, 2013). The marine red alga Delisea pulchra produces quorum quenching molecules, halogenated furanones, which inhibit the growth of Vibrio species in the gut of rainbow trout (Manefield et al., 1999). The major characteristic feature of probiotics is their ability to improve the adaptive or innate immunity of fish, which is desirable for probiotic organisms (Azad et al., 2018). The intestinal mucus layer prevents the entry of pathogens, the available adaptive and innate immune components in the mucosa, the transportation of antibodies by the polymeric Ig receptor and the diverse beneficial microbial flora improve the host’s physiological homeostasis (Simón et al., 2021).

Fish encounter various stressors, including transportation stress, rapid water quality changes, intensive farming with restricted mobility, and changes in feeding patterns. Compared with optimal culture conditions, these stresses reduce fish productivity, digestion, and environmental tolerance (Kesarcodi-Watson et al., 2012). The gut microbiome structure is affected by environmental stress in fish (Bagi et al., 2018). For example, crowding stress affects the gut microbial composition of Megalobrama amblycephala (blunt snout bream), and a positive correlation between the gut microbial flora and metabolites has been reported (Du et al., 2019). The elevated ammonia-nitrogen concentration in the water significantly decreased the microbial population in the gut of Penaeus vannamei (Jiang et al., 2019). The supplementation of probiotic organisms can effectively prevent stressful conditions, improve immune function and thereby reduce the highly harmful effects of several stressors (Taoka et al., 2006b). The generation of ROS in any situation is called oxidative stress, which can disrupt cellular metabolism and subsequently affect cellular components (Jia et al., 2017). In addition to environmental stresses, UV radiation, xenobiotics, hypoxia and other factors cause oxidative stress. The supplementation of probiotic organisms may ameliorate oxidative stress by improving antioxidant activity (Mohapatra et al., 2013). Analysis of cortisol levels in fish tissue reflects stress levels in experimental fish (Sivaraman et al., 2012). In the healthy fish gut, the microbiome population is well balanced, and the amount of pathogens is controlled at the optimum level. Intestinal microbial dysbiosis completely affects immunomodulatory networks, is strongly associated with immune-mediated diseases and gut inflammation (Maynard et al., 2012) and has been proven experimentally in pearl gentian grouper fish (Deng et al., 2020) and sea cucumbers (Zhao et al., 2019). With increasing temperature, the presence of Gemmatimonadetes and Firmicutes declined significantly, whereas the amount of total Bacteroidetes improved effectively in tsinling lenok trout. Under high-temperature stress, adenosine, xanthine, inosine, deoxyguanosine, and guanosine are reduced, and these compounds are essential for the synthesis of genetic materials. Conversely, the amount of D-glucose 6P increased significantly. In addition, high temperature induces structural changes in the gut and subsequently affects barrier function (Fang et al., 2023).

Fishes use molecular oxygen for energy production and metabolism (Hoseinifar et al., 2020). Moreover, this oxygen dependency poses a serious risk of oxidative stress and creates an ‘oxygen paradox’ or ‘aerobic-life paradox’ (Hoseinifar et al., 2020b). In aerobic organisms, oxygen exists in three different forms: an atomic (O), a free biradical or free radical. Reactive oxygen species result from partial oxygen reduction, and hydroxyl radicals (OH), superoxide anions (O₂^-), and hydrogen peroxide (H₂O₂) are the other forms (Halliwell and Gutteridge, 2015). Excess ROS generation leads to lipid peroxidation, cellular damage, DNA alterations and protein modifications (Zhu et al., 2016). Finfish and shellfish exhibit adaptive enzyme mechanisms, including CAT, SOD, and GPx, and antioxidant chemicals, such as vitamin K, vitamin E, vitamin C, amino acids, carotenoids, and peptides (Devi et al., 2019; Hoseinifar et al., 2020b). The enzymatic and nonenzymatic antioxidant systems assist in controlling or repairing oxidative stress in organisms (Parolini et al., 2019). Probiotic microbes produce enzymes such as CAT and SOD, which effectively remove ROS, whereas vitamin E and vitamin C are considered effective reductants or scavengers and maintain antioxidant defense mechanisms in shellfish and finfish (Hoseinifar et al., 2020b). In aerobic organisms, an intricate balance between the generation of ROS and elimination is very important for metabolic functions and for preventing oxidative stress-related damage. Adequate digestion ensures nutrient absorption, which supplies essential biochemicals for antioxidant production. In addition, adequate carbohydrate and lipid digestion are required for the generation of energy, which is required for the production of antioxidant enzymes and biochemicals. Fish are vulnerable to environmental stress, which adversely affects digestion, which contributes to oxidative stress. Antioxidant enzymes mitigate the adverse effects of stress in aquatic organisms (Hoseinifar et al., 2020b). A balanced diet, adequate enzyme production, optimal digestion, an efficient feed conversion ratio, and a robust antioxidant defense mechanism significantly improve overall fish health in both aquaculture and natural settings. Efficient interactions among the digestive enzymes of fish, oxidative stress mediated by environmental and other factors, and antioxidant defense mechanisms are vital for the health management of fish (Yang et al., 2021). The effects of prebiotics, probiotics, and synbiotics on antioxidant defense mechanisms in fish are highly complex and constitute an important area of research. The beneficial organisms in the host or supplemented probiotics modulate the immune response in fish, thus improving antioxidant defense against stress (Amenyogbe et al., 2024). Prebiotics promote beneficial microbial populations in the gut and indirectly contribute to antioxidant mechanisms (Guerreiro et al., 2016). The improved probiotic population and microbial activity improved the production of several bioactive secondary metabolites and organic acids that exhibit antioxidant activities (Hoseinifar et al., 2017a). The anti-inflammatory activity of probiotics subsequently reduces oxidative stress in the host. Probiotics mitigate inflammatory effects, thus contributing to increased antioxidant capacity (Guerreiro et al., 2016). The addition of prebiotics and probiotics improved antioxidant defenses in finfish and shellfish. Most of these prebiotics serve as substrates for probiotics, improving their survival and proliferation in the gastrointestinal tract (Amenyogbe et al., 2024). This effective colonization and proliferation within the gut improved antioxidant health benefits. The synergistic activity of prebiotics and probiotics often results in improved underlying antioxidant mechanisms (Hoseinifar et al., 2020b). Thus, the combination of prebiotics and probiotics improves antioxidant defenses, and this combination is a comprehensive approach in aquaculture practice. Synbiotics exhibit direct and indirect antioxidant activity through microbial hemostasis in the gut and enhance immune function (Ashouri et al., 2020). The utilization of synbiotics offers an alternative avenue for improving fish digestion and managing oxidative stress in aquatic organisms. These probiotic, prebiotic and synbiotic interventions contribute to overall health improvement, reduce the use of antibiotics and improve the ecological balance in aquaculture.

Role of probiotics, prebiotics, and synbiotics in mitigating oxidative stress and enhancing antioxidant defense mechanisms in aquaculture species

The probiotic bacteria effectively improved the antioxidant capacity of the fish, disease resistance to bacterial pathogens, and immunity. The role of probiotics, prebiotics and synbiotics in reducing oxidative stress and improving antioxidant mechanisms is complex, and the scheme is presented in Figure 7. The organic acids, bacteriocin and hydrogen peroxide produced by probiotic bacteria exhibited antagonistic activity, which suppressed the growth of virulent bacteria within the gut. The increased food absorption improved digestive enzyme production and enhanced antioxidant enzyme activity. The antioxidant enzymes (SOD, CAT and GPD) and antioxidant chemicals (vitamin E, K, C, amino acids, carotenoids, and peptides) produced by host organisms mitigate environmental and other stresses. Probiotics improve various antioxidant enzymes, including glutathione peroxidase, catalase, and superoxide dismutase, which improve the health of aquatic organisms and reduce oxidative stress (Banerjee and Ray, 2017). Probiotic microorganisms improve the phagocytic activity of leukocytes, modulate the biosynthesis of immunoglobulins, and improve the production of cytokines, thereby improving the immune health of fish (El-Saadony et al., 2021). Probiotic bacteria synthesize various biomolecules, including lysozymes and hydrogen peroxide, in addition to organic acids, bacteriocins, siderophores, antibiotics and digestive enzymes, which improve their antioxidant activity (Bajinka et al., 2020). Aquatic animals rely on a highly complex antioxidant system, including catalase, superoxide dismutase, glutathione peroxidase and several nonenzymatic antioxidant chemicals, such as flavonoids, vitamin E, and vitamin C, to maintain redox homeostasis (Rudenko et al., 2023). Moreover, fish are vulnerable to direct exposure to environmental stressors, and ROS synthesis may be dramatically elevated. This impairment of homeostasis initiates pathological changes, including mitochondrial dysfunction, lipid peroxidation, immune suppression, and the activation of proinflammatory pathways (Dey et al., 2024). In aquatic animals, oxidative stress induces hepatopancreas or liver damage, which decreases the synthesis of metabolic enzymes, increases disease susceptibility and affects the overall growth of fish (Hermenean et al., 2015). Fatty liver disease is common among aquaculture fish species and results in impaired liver function, hepatic lesions and cirrhosis, which affect the overall productivity of aquatic organisms. The major causes are imbalanced fatty acid composition in the diet, high lipid content, and the ingestion of oxidized fats. In fish, the consumption of high-fat diets results in the synthesis of lipids in the liver, but the poor lipid mechanism and transport potential are not adequate, resulting in the accumulation of lipids in the liver (Zhang et al., 2024b). This elevated level induces oxidative stress, and lipid peroxidation results in the generation of ROS, which affect hepatocytes and decrease the synthesis of antioxidant enzymes. In addition, oxidative stress downregulates genes contributing to lipid metabolism, which impairs metabolism and induces fatty liver disease in fish (He et al., 2024). In addition to these factors, environmental factors such as temperature, salinity stress, and UV radiation significantly affect their physiological state. These environmental factors induce oxidative stress in aquatic animals. Hence, to ameliorate these effects, probiotics are introduced through the diet of the fish. It has been hypothesized that the application of probiotics with a fish diet improved diet utilization, increased the assimilation of available antioxidants from the supplemented diet, and that probiotics improved antioxidant potential. The experimental shrimp fed a probiotic diet presented improved antioxidant activity (Castex et al., 2009). The gastrointestinal tract microbial flora and their secondary metabolites improve the host oxidative state by modulating short-chain fatty acids and reactive oxygen species. The antioxidative mechanisms of lactic acid bacteria, including Lactobacillus fructivorans and L. plantarum, involve their antioxidant properties, which reduce cortisol levels and upregulate the HSP70 gene. These probiotics are fed to sea bream, Sparus auratus, via the microencapsulation method through carriers, Brachionus plicatilis, and/or Artemia salina (Liu et al., 2010). Lactobacillus plantarum and Lactobacillus fructivorans supplementation improved cortisol levels under stress conditions (Varela et al., 2010). Prebiotics improved immune function, antioxidant capacity, and microbial communities in the fish intestine. The supplemented prebiotic diets improved the secretion of antimicrobial agents, reduced the gut pH, attenuated virulence, blocked adhesion sites for pathogenic bacteria, blocked toxin receptor sites, and completed nutrient and immune stimulation. Compared with probiotics alone, probiotics and prebiotics improve microbial colonization in the gut and improve microbial effects (Hoseinifar et al., 2020). The probiotic B. cereus improved glutathione peroxidase, catalase, and superoxide dismutase activity and reduced glutathione. The experimental fish Pengze crucian, which was fed heat-inactivated B. cereus, presented a decreased malondialdehyde concentration and significantly improved catalase activity. The increased antioxidant potential was associated with the Nrf2 signaling pathway via the upregulation of the mRNA levels of genes such as glutathione peroxidase, catalase and superoxide dismutase. In addition, heat-inactivated B. cereus suppressed the transcription of proinflammatory cytokines by activating the NrF2 system and inducing the production of interleukin-10 (anti-inflammatory cytokine) (Yang et al., 2020). The combination of probiotics or heat-killed probiotics improved total superoxide dismutase activity and glutamyloxaloacetic transaminase activity in Koi fish, Cyprinus carpiohaematopterus treated with probiotic microorganisms. Heat-killed probiotics increase the height of the intestinal villi (lnaD3) and improve the diversity of microorganisms (Wu et al., 2021). In this context, analysis of oxidative stress and mitigating effects due to the activity of beneficial probiotic microbes is a promising approach in stressful intensive farming. The combination of probiotics, Bacillus licheniformis and butyric acid improved liver antioxidant enzymes in rainbow trout, Oncorhynchus mykiss. The combination of butyric acid and probiotics improved the activity of antioxidant enzymes in experimental animals, thus improving total antioxidant activity (Taherpour et al., 2023). The probiotic Bacillus spp. improved the antioxidant activity of Oreochromis mossabmicus (Gobi et al., 2018) and goldfish (Yi et al., 2018), and lactic acid bacteria such as Pediococcus acidophilus and Lactobacillus plantarum improved the antioxidant activity by reducing the degree of stress caused by environmental stress, reducing the accumulation of ROS, stimulating the immune response, increasing the expression of antioxidant enzymes, increasing intestinal villi, minimizing systemic inflammation, increasing CAT activity, degrading H₂O₂ and upregulating the expression of genes encoding antioxidant enzymes (SOD and CAT) (Hoseini et al., 2023). The supplemented probiotics stimulate the innate immune system and improve competent and lysozyme activity in fish and the production of cytokines. The biosynthesized metabolites, including hydrolytic coenzymes, improved the amylolytic and proteolytic activity of the fish, resulting in an improved feed conversion ratio and improved growth (Nayak, 2010).

Figure 7

Challenges in the application of synbiotics in aquaculture

The application of synbiotics in aquaculture has reduced the use of antibiotics. Probiotic bacteria have been shown to be highly effective at increasing the immunity of the host organism, promoting growth, improving the feed conversion ratio, and increasing resistance to either bacterial or viral infections (Dawood et al., 2019). The viability of probiotic bacteria, their ability to colonize the gastrointestinal tract, and the main challenge of using synbiotics are associated with possible gene resistance acquisition and translocation (Piqué et al., 2019). However, the use of more than one probiotic in fish feed could improve the survival rate of the fish and improve their immunity, growth, and drug resistance (Puvanasundram et al., 2021). The use of prebiotics has several advantages, including the absence of viability problems and decreased susceptibility to environmental factors (Goh et al., 2022). The highly complex mixture of symbiotics has several advantages, including multiple actions against diverse pathogenic species. Moreover, the use of synbiotics in aquaculture is still in its infancy (Sudhakaran et al., 2022). Prebiotics are cost-effective and safe, and these inert biotic agents are derived from plant sources and seaweed. These compounds have several biological functions, including growth-promoting and immunostimulant activities (Carbone and Faggio, 2016). Nevertheless, the optimum dosage may vary among fish, and determination of the optimum concentration is needed for every fish to avoid detrimental effects (Hoseinifar et al., 2011). Compared with prebiotics or probiotics alone, synbiotics are more useful for improving the colonization of bacteria (Goh et al., 2022). This was also true in the case of Nile tilapia (O. niloticus), and improved growth was observed in the fish fed synbiotics compared with those fed prebiotics or probiotics alone (Ghaly et al., 2023). Moreover, further research is required to analyze the possible roles of prebiotics, probiotics and synbiotics in the intestinal health and immune response of fish to various aquatic pathogens, especially drug-resistant strains. The tracing of the mode of action and determination of an effective dosage are also important and have a major impact on their potential (Jahangiri and Esteban, 2018). The use of synbiotics for commercial aquaculture is limited, and most of the former are not aware of the use of synbiotics. In aquaculture, the estimated feed cost is approximately60–80% of the total operational cost, and further use of synbiotics may add additional operational costs to farmers (Subedi and Shrestha, 2020). The application of probiotics in shrimp farming (L. vannamei) has been reported to increase total production costs by 6%. Moreover, the application of probiotics increased the survival rate and reduced the overall production costs by 44% (Peñalosa‐Martinell et al., 2021). The possibility of the use of synbiotics in aquaculture has been revealed by various research groups; however, further evaluation is required to use synbiotics to mimic environmental stress and reduce stress in intensive farming practices or to improve the potential of synbiotics during the reproductive period of fish (Azevedo et al., 2015; Dias et al., 2020).

Conclusions and the future perspective

This review emphasizes the application of probiotics, prebiotics and synbiotics for aquatic organisms. This study analyzed the beneficial effects of various combinations of pro- and prebiotics and mixtures of these two additives as feed additives or via inoculation in water to improve fish production by increasing growth, increasing digestive enzyme production, improving feed conversion efficiency, maintaining gut health, stimulating the immune system, improving drug resistance, and mitigating stress in aquatic organisms. Moreover, reviews on the use of probiotics, prebiotics, and synbiotics other than β-glucan to improve health benefits are limited. A synbiotic or one effective combination can work effectively to improve health benefits. This work focused on recent applications of prebiotics, probiotics, and synbiotics and provided an overview of the benefits of synbiotics over prebiotics and probiotics. The mode of action of tribiotics (prebiotics, probiotics, and synbiotics) is discussed in this review. These biotics improve feed conversion efficiency and gut health, stimulate immune function, increase beneficial microbial combinations and disease resistance, reduce stress and proinflammatory molecules, and upregulate anti-inflammatory compounds. This review highlights the gap between the knowledge of synbiotics and their practical application in aquaculture. Several environmental and nutrient parameters affect fish production, and the use of synbiotics reduces environmental stress and promotes fish production in aquaculture. The use of synbiotics may reduce the application of antibiotics, thus reducing the accumulation of antibiotics or residues in fish muscle and preventing the development of drug-resistant microorganisms. In this context, this review would be useful for farmers to include synbiotics via feed or water to improve fish growth and minimize the environmental impact of aquaculture. Probiotic microorganisms are needed to survive during the manufacturing process and remain viable for a long period of time. Moreover, harsh environmental conditions may reduce the viability of cells. An adequate encapsulation method is useful for improving the viability of probiotic strains. Fish have unique intestinal microbial flora and specific nutritional requirements. Thus, identifying specific groups of probiotic strains in each fish species is challenging. Tailoring the optimal composition of probiotic strains for specific fish species is critical. Determining the optimal dosage of probiotic strain for each fish species is highly complex and may vary with the environment. This is because too few probiotics may be ineffective, while excess probiotics can be wasteful. Understanding the impacts of probiotic microbes on fish growth and the immune response is necessary. Conducting studies to tailor effective prebiotic and probiotic combinations may be useful for improving immune function and mitigating stress. Effective synbiotics can tolerate various environmental conditions, including pH and temperature fluctuations, and poor water quality because these factors can impact the growth performance of probiotics. Tailoring fish-synbiotic interactions to formulate species-specific probiotics and adequate combinations of prebiotics is necessary. The ability of effective probiotic strains to mitigate the effects of stressors in aquaculture environments needs to be completely explored.

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