The aquaculture industry is experiencing exponential growth and is known to support the livelihoods of around 1 billion individuals globally (Huynh et al., 2018). Aquaculture is reported to account for 46% of the world’s fish supply (Wee et al., 2024). Asia is the primary producer of aquatic animals, and China is the highest producer among countries (Chen and Gao, 2023). Nevertheless, serious health issues, such as diseases, have been created due to the intensive culturing and increased production of aquatic products over the years. In tackling such problems, aquaculture scientists have sought to use chemicals, antibiotics, and other chemotherapeutics that have been criticized due to their adverse effects on the environment. The widespread use of antibiotics and chemotherapeutics in aquaculture health management has led to an increase in antibiotic resistance among pathogenic bacteria at aquaculture sites, which can subsequently contaminate the food chain (Pepi and Focardi, 2021). Therefore, it is imperative to implement alternative methods for managing the health of aquaculture species. Modern aquaculture practices prioritize sustainability, environmental responsibility, and producing safe consumer products (Gall et al., 1995). In aquaculture, beneficial feed additives such as probiotics and prebiotics are utilized to stimulate growth, enhance immunity to combat diseases, and provide alternative antimicrobial solutions (Badguzar et al., 2024).

According to Wee et al. (2024), a prebiotic serves as nourishment for the beneficial bacteria in the host’s digestive tract, whether in the form of a substance, substrate, long-chain sugar, vitamin, or fiber. Furthermore, as stated by Davani-Davari et al. (2019) and Dhanasiri et al. (2023), a prebiotic is a substance that can withstand the harsh acidity of the stomach, is digested by intestinal microorganisms, and aids in enhancing host health by supporting the proliferation of beneficial gut bacteria. Xylooligosaccharides (XOS) have been shown to enhance mineral absorption, reduce glucose and lipid levels, improve antioxidant status, and specifically stimulate the growth of beneficial intestinal microflora. These microflora play various important roles, such as regulating metabolism and preventing illness (Chen et al., 2022). On the other hand, probiotics, which are live microorganisms that provide enormous host benefits when given in the right amount (Fachri et al., 2024), are known to work through multiple pathways to strengthen the intestinal mucosa and enhance gut barrier integrity (Rohani et al., 2022). Moreover, probiotics are essential for sustaining a harmonious microbial environment by favoring helpful bacteria and preventing harmful ones through competitive exclusion (Mishra et al., 2015). Furthermore, they defend against infections by generating antimicrobial metabolites, modifying toxins or pathogen receptors, and activating distinct immune responses to pathogens (Pardo-Esté et al., 2024). For example, the use of isolated probiotics Bacillus amyloliquefaciens AV5 was noted to enhance the growth conditions, antioxidant capacities, microbial composition, and intestinal structure of Nile tilapia (Oreochromis niloticus) (Shija et al., 2025). Researchers discovered that feeding probiotic live yeast to sea bass led to changes in the activities of antioxidant enzymes and gene expression (De et al., 2014). Probiotics have the potential to alter the metabolism of hindgut bacterial ecosystems, leading to an increase in short-chain fatty acids and other organic acids while decreasing the production of ammonia and isovaleric acid. This is likely achieved by improving the breakdown of complex carbohydrates, ultimately enhancing protein breakdown.

Despite the pressing need for research on the significance of prebiotics and probiotics in various fish species, a noticeable gap exists in comprehensive studies within aquaculture. Therefore, further research is needed to investigate the role of prebiotics and probiotics in various fish species, considering their significance in aquaculture. This review aims to systematically analyze the mechanisms of action of probiotics and prebiotics in fish, with a focus on their roles in antioxidant defense and metabolic regulation. To better understand their potential applications, following the discussion on antimicrobial resistance and the need for alternative strategies, the subsequent section examines the role of probiotics in aquaculture.

Carbohydrates play a crucial role as a non-protein energy source for aquatic species, helping to spare proteins and reduce nitrogen emissions into the water (Abasubong et al., 2019). However, unlike mammals, aquatic animals struggle to utilize dietary carbohydrates efficiently. Excessive carbohydrate intake can lead to metabolic stress, disrupt metabolic balance, and pose various health risks for fish, including hyperglycemia, liver damage, and histopathological issues (Siri and Krauss, 2005; Wang et al., 2021).

An excess of glucose is typically converted into glycogen and lipogenesis, which can be targeted to alleviate symptoms of hyperglycemia and hyperlipidemia resulting from a high-carbohydrate diet. Research has shown (Castro et al., 2016) that prolonged consumption of high-carbohydrate meals can increase the enzymatic activities of GS, G6PDH, and FAS in Sparus aurata, leading to increased fat and glycogen production. High-carbohydrate diets can also trigger fish lipid metabolism disorders, characterized by excessive fat accumulation in the liver and abdomen (Luo et al., 2020). This fat buildup can disrupt endocrine system activities, leading to elevated levels of pro-inflammatory cytokines and insulin resistance (Zhang et al., 2024).

Probiotics can potentially influence immunity, physiology, metabolism, and nutrition by modifying the gut microbiota. Research has shown that probiotics can have beneficial effects on metabolic inflammation and obesity resulting from a high-fat/carb diet by altering the gut microbiota and producing SCFAs (Xu et al., 2022c). Studies have indicated that SCFA butyrate can enhance the production of the peptide GLP-1, which plays a crucial role in regulating appetite, food intake, and glucose metabolism by increasing the expression of the insulin gene in intestinal L-cells (Kim et al., 2018; Yadav et al., 2013). Additionally, research has demonstrated that probiotic-treated larvae exhibit increased glp-1 gene expression, potentially due to the metabolic activity of lactic acid bacteria producing SCFAs (Falcinelli et al., 2016). Moreover, as highlighted by Delzenne et al. (2007), propionate has been found to stimulate the production of glucagon-like peptide-1 (GLP-1) in the intestine, leading to enhanced insulin secretion and increased glycogen synthesis in the liver. Furthermore, SCFAs can activate the AMPK/peroxisome proliferator-activated receptor-γ co-activator-1α/peroxisome proliferator-activated receptor α pathway, facilitating the transport of SCFAs to various tissues and promoting lipid oxidation. This process facilitates the proper metabolism and utilization of fat in various organs.

Research has demonstrated that XOS can improve the function of the intestinal barrier by selectively increasing the presence of beneficial microbes like Lactobacillus and Bifidobacterium, boosting the production of SCFAs, and enhancing the levels of tight junction proteins in the gut (Chen et al., 2024). In addition, compared to a high-carbohydrate diet, supplementing with 1.0% XOS resulted in a decrease in lipid accumulation in muscles and the liver, and an increase in glycogen deposition in the liver (Chen et al., 2022). European sea bass given 1% XOS also exhibited heightened glycolytic activity (Guerreiro et al., 2015). Moreover, the administration of MOS was found to reduce insulin resistance and glucose intolerance in mice fed a high-carb diet, potentially through the modulation of gut microbial composition (Wang et al., 2022c). It has been suggested that combining L. plantarum with a high-carb diet can elevate intestinal acetate levels, trigger uranosol synthesis in hepatocytes, and regulate nucleotide metabolism to enhance oxidative stress and reduce liver lipid deposition (Deng et al., 2024). The manipulation of gut microbiota by probiotics and the subsequent production of SCFAs have shown promising effects on various aspects of health and metabolism.

Probiotic and prebiotic supplementation has been shown to enhance fish weight gain by improving appetite, increasing digestive enzyme activity, enhancing intestinal morphology, and boosting metabolism (Midhun et al., 2019). These factors are crucial in improving nutrient absorption and digestion, leading to increased metabolism and accelerated growth (Zhang et al., 2022). Probiotics have the notable capacity to modify the structure and function of plant proteins through fermentation, producing bioactive compounds such as vitamins, antioxidants, and antimicrobial peptides. Additionally, probiotics aid in addressing protein energy deficiency by facilitating the absorption and utilization of proteins. They also influence the metabolic activity of gut microbiota, maintaining a balance between protein synthesis and breakdown (Rasika et al., 2021). Research by Wu et al. (2024) emphasizes the significance of probiotics in regulating the gut microbiota, which, in turn, influences gut bacteria involved in proteolysis. By breaking down complex plant proteins into simpler forms, probiotics promote the digestion and absorption of nutrients in the host body. This metabolic process also yields beneficial compounds, including SCFAs, exopolysaccharides, and vitamins. Furthermore, probiotics can break down plant-based proteins with anti-nutritional factors in feed into smaller peptides and amino acids, thereby enhancing the nutritional value and digestibility of these proteins. For instance, the addition of 1.5% XOS to rice protein meal has been shown to enhance the hepatic activity of Glutamate dehydrogenase, aspartate aminotransferase, and alanine transaminase in Megalobrama amblycephala (Abasubong et al., 2019).

In conclusion, incorporating probiotics and prebiotics into fish nutrition has significantly enhanced nutrient absorption and overall growth. Figure 5 illustrates the mechanism of probiotics and prebiotics in a plant-based protein diet.

The relationship between an organism’s antioxidant defense and physiological state is crucial, as higher levels and efficiency of antioxidant defense offer numerous advantages to the host. Fish have evolved sophisticated antioxidant defense mechanisms involving primary enzymes such as superoxide dismutase (SOD), catalase (CAT), and glutathione peroxidase (GSH-Px), alongside non-enzymatic antioxidants like glutathione, thioredoxin (Trx), and vitamins C and E (Shija et al., 2025; Słowińska et al., 2013; Hoseinifar et al., 2020). Thioredoxin (Trx) is one of the primary intracellular redox systems, and as such, it plays a crucial role in regulating reactive oxygen species (ROS) accumulation (Pacitti et al., 2014). Several studies have demonstrated that probiotics, such as S. cerevisiae and L. bulgaricus, significantly elevate SOD, CAT, and GSH-Px activities in Mugil capito (Shehata et al., 2024). Conversely, supplementation with Aspergillus oryzae enhances antioxidant enzymes and reduces stress markers in Nile tilapia during hypoxic conditions (Dawood et al., 2020a).

The research conducted by Yi et al. (2018) demonstrated a noticeable increase in GSH-Px activity in Carassius auratus when they were fed diets containing Bacillus velezensis JW. Ringø et al. (2022) found that dietary MOS and XOS had a notable impact on antioxidant levels, resulting in a significant decrease in MDA and a significant increase in CAT, GSH-PX, and SOD. The ability of chitosan to eliminate free radicals from the body’s cells gives it its strong antioxidant potential, helping to prevent oxidative damage. This is achieved through the chelation of metal ions and the provision of hydrogen or electron pairs (Yen et al., 2008). Jia et al. (2017) observed a notable increase in SOD and CAT activities in crabs treated with FOS, accompanied by decreased MDA activity. The utilization of XOS and GOS has been shown to enhance the enzymatic activity of GSH-Px and promote the synthesis of glutathione-related enzymes in fish (Xu et al., 2022c). The research suggests that prebiotics play a crucial role in enhancing the immune system through antioxidant pathways. An overview of the effects of various probiotics and prebiotics on antioxidant enzyme activities in different fish species is provided in Table 5 .

The increasing global demand for aquatic food has led to a significant rise in the use of antibiotics within the aquaculture industry. To enhance productivity, these antibiotics are utilized to promote the growth and health of fish stocks. Over the past few decades, the global use of antibiotics in aquaculture has increased significantly. In 2017, worldwide antibiotic consumption reached 93 million tons (Tiseo et al., 2020), and projections indicate that this figure could exceed 236 million tons by 2030, with aquaculture contributing approximately 5.7% of that total (Schar et al., 2020). A concerning aspect of this trend is that many antibiotics are applied directly to coastal habitats, often without effective measures to control their spread. In 2017 alone, over 10 million tons of antibiotic compounds were consumed in aquaculture, with an anticipated increase of 33% by 2030. The distribution of antibiotic use in aquaculture was notably concentrated, with China accounting for 58%, India for 11%, Indonesia for 9%, and Vietnam for 5% of global consumption (Schar et al., 2020). As the aquaculture sector continues to expand over the next decade, the risk of antibiotic resistance is expected to rise, posing a significant threat to ecological biodiversity and the proper functioning of ecosystems. Antibiotics are among the most prevalent chemical pollutants that enter the environment and subsequently infiltrate the food chain (Albarano et al., 2024). Antibiotics can lead to an imbalance in intestinal flora, which may adversely affect fish health, particularly in intensive rearing conditions characterized by high stocking densities that facilitate the spread of infectious diseases (Cox, 2016; Carlson et al., 2017). Studies have shown that the preventive use of antibiotics can reduce the symbiotic bacteria in aquatic animals, ultimately affecting host immunity (Schmidt et al., 2017; Milijašević at al., 2024). For instance, research on the fry of Oncorhynchus mykiss and Cyprinus carpio demonstrated that florfenicol suppressed their immunological responses (Mallik, 2023). Additionally, studies using zebrafish models have shown that antibiotics such as oxytetracycline and sulfamethoxazole can negatively affect gastrointestinal health when administered over extended periods, even at legally permissible dosages. These antibiotics may induce inflammation or disrupt gut flora (Jia, 2023). According to Manage (2018), the use of antibiotics for growth promotion can contribute to the development of antimicrobial-resistant bacteria in aquatic ecosystems. Furthermore, the accumulation of residues in fish tissues may stem from the subtherapeutic use of antibiotics. This practice can lead to the proliferation of antibiotic-resistant bacteria, which may subsequently be transferred to humans through environmental pathways or by consuming contaminated fish. Such transmission poses a significant risk, potentially resulting in diseases that are challenging to treat (Yuan et al., 2023). Moreover, antibiotic residues can persist in the environment and fish, raising critical concerns about their long-term toxicity, potential allergic reactions, and broader implications for human health (Albarano et al., 2024). Figure 6 below summarizes the benefits and drawbacks of antibiotic use, particularly when overprescribed.

The mismanagement of antibiotics in aquaculture poses a grave concern with widespread impacts (Hemamalini et al., 2022). This practice has led to producers routinely administering antibiotics within aquaculture systems, creating a cycle of dependency. Unfortunately, the excessive use of antibiotics has triggered antimicrobial resistance in bacteria from aquaculture settings (Monteiro et al., 2016). As microorganisms evolve, they become immune to the effects of antibiotics that were originally effective against them, leading to antimicrobial resistance (Dcosta et al., 2011; Foster, 2017). The introduction of streptomycin, chloramphenicol, and tetracycline in the late 1940s also led to documented cases of bacterial resistance (Thuy et al., 2011). The continued and widespread use of antimicrobials in aquaculture systems creates a breeding ground for antimicrobial-resistant bacteria, as they face constant selective pressure (Gao et al., 2012). The World Health Organization (WHO) has pointed out the alarming threat of antibiotic resistance to global public health and the safety of aquatic food sources (Hong et al., 2018). Administering antimicrobials via water or medicated feed exacerbates the issue (Zainab et al., 2020). Most antibiotics are poorly absorbed by fish, leading to their release into the environment through waste. This issue is exacerbated because fish farm wastewater, containing runoff water, feces, and uneaten feed, is often discharged directly into natural aquatic environments (Henriksson et al., 2018). Therefore, a large number of bacteria are exposed to antibiotics within aquaculture production systems, such as tanks and ponds, creating ideal conditions for the evolution of antimicrobial resistance (Xu et al., 2017). The exchange of plasmids containing resistance traits and the merging of resistant bacterial populations with various bacterial communities are also part of antimicrobial resistance (Mathers et al., 2015). Resistance genes can spread between bacterial populations through the exchange of plasmids, enabling the formation of multidrug-resistant communities. Despite the increasing popularity of probiotics and prebiotics in aquaculture, a significant lack of understanding persists regarding their overall effectiveness and environmental benefits. Most of the current literature focuses on the effects of probiotics on specific species or environments, resulting in a limited understanding of their overall applicability in diverse aquaculture systems.

In addition to conducting comprehensive scientific research, selecting the appropriate probiotics relies on various technological considerations. Some of these considerations pertain to logistical challenges. Producing and distributing probiotics in tightly controlled laboratory environments poses unique challenges, as does ensuring their effectiveness on a large industrial scale (Todorov et al., 2024). Before incorporating these beneficial microbes into aquaculture practices, it is crucial to consider the key characteristics of probiotics, including their hydrophobicity, acid tolerance, and sensitivity to antibiotics. Probiotics are most effective when used as a preventative measure rather than a cure for illnesses. They are easily incorporated into low-water-level or stationary systems such as tanks and circulatory systems. However, in larger bodies of water, such as lakes used for cage cultures, probiotics may not be as effective. To prevent contamination, it is important to add probiotics immediately after sterilizing the water in the culture system, regardless of its size (Vulla, 2024). Probiotics have gained popularity as an eco-friendly alternative to antibiotics due to their ability to enhance host growth and immunity. The purpose of this study was to identify and isolate novel Bacillus species from the gut of hybrid groupers (Epinephelus fuscoguttatus♀ × Epinephelus lanceolatus♂) that may be used as probiotics, as reports indicate that commercially available probiotics are ineffective because the majority come from non-fish sources (Amoah et al., 2024). Refusing other medications or chemicals for illness prevention or treatment is essential once probiotics are introduced into the system. This is because these substances may not be selective and could potentially destroy the beneficial bacteria (Lieke et al., 2020).

Current research findings show mixed results on the influence of prebiotics in fish farming. The effectiveness of prebiotics is influenced by various factors, including fish species, age, diet, environment, type of prebiotic used, dosage, and duration. Before introducing prebiotics, it’s essential to understand the specific nutritional needs of each type of fish, as improper dosages may cause harm or prove ineffective. Additionally, considering species with similar physiological traits to those that have responded positively to prebiotics in the past may be beneficial. There are scarce regulations governing the use of prebiotics in aquaculture feed, as the current regulations only apply to human consumption and vary between countries (Amillano-Cisneros et al., 2023). Like other costs incurred in aquaculture, probiotics and prebiotics come with associated expenses. Farmers can evaluate the financial viability of incorporating probiotic and prebiotic supplementation into their operations through cost-benefit analyses (CBAs).

As the popularity of probiotic and prebiotic products continues to rise due to their numerous health benefits, conducting a CBA becomes essential for understanding the financial implications of their introduction. However, performing a cost-benefit analysis for probiotics and prebiotics can be complex and requires meticulous attention to detail to yield reliable and accurate results. One of the primary challenges lies in assessing the efficacy of probiotics and prebiotics. While research suggests that these supplements can enhance immunity and promote gut health, their effects can vary significantly depending on the specific strain, dosage, and the medical conditions they aim to address. For a CBA to be effective, it is crucial to establish a clear cause-and-effect relationship between the consumption of probiotics and prebiotics and specific health outcomes. This can be particularly challenging due to individual variability and the presence of confounding factors. Additionally, the diverse range of health issues that probiotics target must be considered when evaluating their economic impact. The prevalence, severity, and financial burden of various conditions ranging from immune-related disorders to digestive problems can differ widely, necessitating comprehensive data and reliable algorithms to accurately estimate potential cost savings and benefits across this broad spectrum. Another significant challenge in estimating the financial advantages of probiotics is recognizing their benefits beyond immediate health effects. Furthermore, the cost component of a CBA encompasses not only the price of probiotic and prebiotic products but also expenses related to marketing, distribution, research, and development. Accurately estimating these costs can be particularly difficult, especially as the probiotic market continues to evolve and expand. The obstacles associated with using probiotics and prebiotics in fish are highlighted in the diagram shown in Figure 7 .

Using probiotics and prebiotics in aquaculture can mitigate the harmful effects of pathogen outbreaks, decreasing economic losses from fish deaths, and reducing the need for antibiotics in controlling bacterial pathogens. This advancement is crucial for promoting the environmental sustainability of the fish farming industry. The health benefits of probiotics, prebiotics, or their combination are widely acknowledged, with strong evidence supporting their effectiveness against pathogenic or drug-resistant organisms. These probiotics and prebiotics offer a potential alternative approach to addressing the growing issue of antimicrobial resistance due to their unique antagonistic mechanisms against target microorganisms. Changing the makeup of gut microbes, boosting the host’s immune system, and improving the efficacy of the epithelial barrier are all essential steps in warding off pathogens by blocking their colonization and survival through exclusion and antimicrobial actions. The effectiveness of biologics as treatments is largely influenced by a combination of factors, including the disease stage, delivery method, and the host’s physiological condition. While probiotics and prebiotics hold great potential in aquaculture, current understanding of their mechanisms, strain-specific effects, and interactions with host metabolism remains limited. Thus, ongoing research and cautious application are essential.

Using probiotics and prebiotics demonstrates potential in minimizing antibiotic dependency. However, to establish them as a reliable treatment option, further well-planned studies are necessary to evaluate their efficacy against multidrug-resistant organisms in real-world disease scenarios. Estimating the true impact of probiotics can be a challenging task. The impact of different strains, dosages, and specific conditions on the efficacy of probiotics for gut health and immunity varies greatly. To conduct an accurate CBA, it is crucial to establish a direct connection between the use of probiotics and the resulting health benefits. Individual characteristics and other variables can influence the outcome and complicate this process. For a more comprehensive understanding of the relationship between lipid metabolism and antioxidants in aquatic species, future studies should focus on key aspects of this relationship. Understanding how hosts maintain a balance of beneficial microbial strains and lipid metabolism is crucial, despite obstacles such as pollution and climate change. Moreover, scientists should investigate the molecular mechanisms underlying the selection and preservation of bacterial types that facilitate specific lipid processing and overall well-being. Applying metabolomics methods to aquatic organisms will play a crucial role in connecting lipid metabolism pathways, microbial composition, and overall well-being. Future studies should investigate molecular mechanisms underlying gut microbiota modulation and lipid metabolism in fish.