Diverse polymicrobial communities—including bacteria, archaea, viruses, yeasts, and protists are ubiquitously associated with aquatic organisms, colonizing niches such as the gastrointestinal tract, skin, gills, and muscle tissues (Li et al., 2022). Their composition and abundance are shaped by environmental factors and host-specific traits like genetics, developmental stage, sex, and diet. Despite this variability, a core gut microbiota often persists across conspecifics, reflecting adaptation to host-specific selective pressures (Diwan et al., 2021). These microbial communities are essential for maintaining physiological homeostasis, supporting nutrient assimilation, immune function, and defense against pathogens. The development of the digestive system and immune modulation are closely tied to the presence of these microbes (Li et al., 2022; Merrifield and Rodiles, 2015). Recent research, including single-cell analyses, highlights the molecular complexity of host microbe interactions and their critical roles in health and disease outcomes (Sharma and Thaiss, 2020).

The study understanding of the complicated internal workings of organisms has been considerably improved by breakthroughs in single-cell analytical tools, particularly those that examine genes, RNA messages, and the spatial organization of cells (Sharma and Thaiss, 2020). While the profound influence of host-microbiota interactions on host development, immunity, metabolism, and associated signalling pathways is now well-established, specific knowledge regarding these interactions in fish and shellfish remains comparatively limited (Sharma and Thaiss, 2020). However, recent research endeavours have begun to elucidate the nature of host-microbiota interactions in the context of various physiological functions within these aquatic organisms. One study investigated these interactions in hybrid fish derived from parental lineages exhibiting contrasting herbivorous and carnivorous dietary adaptations (Pérez et al., 2010). Their findings indicated comparable growth trajectories during early ontogeny and minimal divergence in microbial composition at this initial developmental stage. However, significant alterations in microbiota structure were observed during subsequent developmental phases, coinciding with shifts in dietary regimes. Subsequent analyses revealed a predominance of microbial species associated with metabolic processes and growth in both dietary groups. Furthermore, differentially expressed homologous genes within the intestine, linked to cellular proliferation, immune responses, and metabolic pathways, exhibited correlation with the dominant gut microbiota taxa, suggesting host genes and gut microbes likely work together to help these hybrid fish adapt to their diet (Pérez et al., 2010). Investigations have also focused on the microbial populations within fish digestive systems and their relationships with the mucosal layers (Merrifield and Rodiles, 2015). The research team led by Nerea Arias Jayo also investigated how zebrafish’s gut bacteria changed when the fish ate a diet high in saturated fats with added fish oil. Their work emphasized how important what an animal eats is for the relationship between the animal and the microbes living in its gut (Arias-Jayo et al., 2019). Moreover, research analyzing the gut bacteria of five marine fish species reared together suggested that this intestinal microbial community functions like a second set of genes, influencing various vital physiological processes (Nikouli et al., 2021). The study also reported that a fish gut bacterial community develops in response to both internal factors and external environmental conditions, including diet (Nikouli et al., 2021).

Many studies have elucidated the functional roles of gut microbiota and their interactions with fish and shellfish hosts, including their involvement in digestive enzyme production (Ray et al., 2012) and processes like vitamin synthesis, short-chain fatty acid production, biofilm formation, and iron metabolism in freshwater and marine fish (Romero et al., 2014; Tsuchiya et al., 2008; Xing et al., 2013). The study thoroughly investigated the connection between gut microbiota and growth performance in hybrid fish (Li et al., 2022). While fewer studies have assessed phenotypic variations in fish and shellfish in correlation with gut microbiota, “the species composition of the gut microbiota has been analyzed to determine the involvement of microbial genomes in the selection of core microbiota members (Mushegian et al., 2019). Studies have also examined how the relationship between fish and their gut microbes helps manage stress in different types of fish (Cui et al., 2022; Mohanta et al., 2020). In the context of shellfish, particularly penaeid shrimp, the available information regarding host-microbiota interactions is comparatively limited. Thorough investigation has shown that disease-causing microbes exist in different tissues of penaeid shrimp, negatively impacting their health and the output of aquaculture (Chaiyapechara et al., 2021). However, the burgeoning appreciation for the microbiota’s role in bolstering physiological functions has highlighted its contributions to enhanced immunity and healthy growth. Therefore, to effectively use the shrimp gut microbiota for improving overall health and quality, it’s essential to grasp how external and internal elements affect its composition. Moreover, the study explored how the community of microbes present in the gut of black tiger shrimp (Penaeus monodon) changes, and how their gene activity varies when the shrimp are exposed to different salinities (Chaiyapechara et al., 2021). Their findings indicated that shrimp acclimatized to higher salinities exhibited a gut microbiota dominated by the phylum Proteobacteria, followed by Bacteroidetes and Planctomycetes. The most prevalent genus was Vibrio, belonging to the Harveyi species. Furthermore, they reported differential expression of genes associated with stress and immunity at higher salinities, as the abundance of pathogenic Vibrio increases, expression of genes related to the host’s innate immune response also increases. Other studies have also noted comparable effects of salinity on the bacteria in shrimp intestines (Angthong et al., 2020; Fan et al., 2019; Huang et al., 2016; Rungrassamee et al., 2013). This study looked more closely at the part gut bacteria play in keeping shrimp healthy and controlling diseases. It proposed that changing the gut’s microbial balance by giving shrimp beneficial microbes can have a positive impact on their growth and survival rates (Holt et al., 2020). Recognizing the crucial roles of gut microbiota in shrimp health and immunity (Ma et al., 2018; Tarnecki et al., 2017), an alternative approach for preventing diseases and enhancing shrimp well-being involves strategically modifying the gut microbial community to encourage the growth of beneficial bacteria. Given that factors like culture conditions, developmental phases, and health status can alter shrimp gut microbial composition (Angthong et al., 2020; Fan et al., 2019; Huang et al., 2016; Zheng et al., 2017), a well-defined research strategy is essential to understand these intricate relationships. Researcher investigated the relationship between growth performance in P. monodon and gut microbiota composition, transcriptome, and metabolites, reporting a relative surfeit of bacteria such as Brevibacillus and Spongiimonas in the majority of shrimp guts (Uengwetwanit et al., 2020). Researchers have also identified distinct gene activity patterns in the intestines and specific immune-related genes in shrimp showing different growth rates. Recent progress in studying the microbiota and gene expression in shrimp after probiotic feeding has revealed a strong connection between the types of gut bacteria present and the host’s gene activity related to immunity, digestion, and programmed cell death (Duan et al., 2018, 2019b, 2019a). Researchers investigating the gut bacteria of different penaeid shrimp species have emphasized the crucial part played by the relationships between the host and its microbes in elucidating the basic mechanisms that underpin a wide range of bodily functions (Imaizumi et al., 2021; Dai et al., 2018; Zoqratt et al., 2018).

This review synthesizes current knowledge on the complex interactions between host organisms and their gut microbiota in commercially important fish and shellfish species. It critically evaluates the role of gut microbial communities in key physiological processes, with a focus on digestive efficiency, nutrient assimilation, and metabolic regulation. The review first explores the diversity and composition of gut microbiota across freshwater and marine fish, as well as various shellfish species. It then examines the functional contributions of these microbes to host metabolism and analyses the environmental, genetic, and dietary factors that shape microbial diversity and function. Adopting a multidisciplinary perspective, this review highlights the potential of microbiota-driven strategies to enhance aquaculture productivity, support host health, and promote sustainable aquatic food systems ( Figure 1 ).

The complex and dynamic microbiota inhabiting the fish gastrointestinal tract exerts a significant influence (Zhang et al., 2021). A stable state characterized by a harmonious interaction between the host and gut microorganisms is vital for healthy intestinal function (Banerjee and Ray, 2017). In fact, these resident bacterial populations significantly influence numerous physiological processes, such as maintaining equilibrium, growth, nutrient processing, reproduction, and immune responses (Butt and Volkoff, 2019). Acknowledging the significance of gut flora for the health of fish, including their immune system, physical functions, and overall well-being (Yang et al., 2021), and given that an unbalanced gut microbiota is associated with internal instability and disease development (Wang A, et al., 2018), current scientific research is focused on the potential of using prebiotics, probiotics, and symbiotic to alter the gut microbiota as a way to improve fish health (Nguyen et al., 2018).

Studies have shown that the Bacteroidetes phylum is important for boosting the natural defences system of fish (Gómez and Balcázar, 2008) and for changing the host immune responses, which helps protect them from diseases (Talwar et al., 2018). Furthermore, the Bacteroidetes phylum exhibits a notable metabolic capability to catabolize complex polysaccharides into simpler monosaccharide units (Xu et al., 2003). The development of fast and affordable high-throughput sequencing has dramatically changed how we measure and describe the makeup of microbial communities. This has greatly improved our understanding of the microbiota and made it possible to thoroughly study the bacteria living in fish guts (Chen et al., 2022). Recent advancements in ichthyic microbiota research have garnered considerable attention, recognizing the microbiota a complex consortium encompassing bacteria, fungi, and viruses (Morshed and Lee, 2023) as a critical determinant of host health and homeostasis. Correspondingly, a growing understanding of the microbiota vital function within the host physiology, representing a significant area of application within holobiont research, which focuses on the prevention and therapeutic intervention of diseases through targeted modulation aimed at restoring dysbiotic microbial communities (Diwan et al., 2023). The phylum Actinobacteria, the most extensive prokaryotic group, predominantly comprises Gram-positive bacterial species exhibiting a diverse array of morphological and developmental characteristics (Bhatti et al., 2017). Notably, comparative analyses have identified Bacteroidetes and Firmicutes as potential biomarkers for assessing lipid metabolism in Cyprinus carpio (Meng et al., 2018). A specific study (Talwar et al., 2018) indicated a positive correlation between the phylum Firmicutes and accelerated growth rates in fish compared to the phylum Bacteroidetes. Geerlings et al., 2021 research suggests that bacteria belonging to the phylum verrucomicrobia play a role in breaking down mucus in fish digestion. Recent scientific discoveries highlight the significant influence of gut microbes on the proper development of reproductive systems and subsequent successful reproduction in fish. When zebrafish (Danio rerio) were given Lactobacillus rhamnosus, a type of bacteria in the Firmicutes phylum, from hatching until they reached sexual maturity, their gut bacteria changed, and they developed faster. This was likely due to enhanced growth and the processes that determine their sex (Avella et al., 2012; Carnevali et al., 2013). Conversely, Bozzi et al., 2021 identified Tenacibaculum dicentrarchi as a pathogenic bacterial strain and observed a distinct microbial profile in the distal gastrointestinal tract (GIT) of diseased fish compared to their healthy counterparts. Early exposure of newly hatched fish larvae to commensal microbiota present in the aquatic environment likely confers a protective advantage against opportunistic pathogenic bacteria such as Aeromonas hydrophila (Brugman et al., 2018).

The intestinal microbial community significantly influences the nutritional physiology and metabolic homeostasis of fish by actively contributing to the breakdown and absorption of food constituents and modulating the host’s metabolic processes ( Figure 2 ).

Fish rely on their gut microbes to enzymatically digest complex parts of their diet. Numerous bacterial species within the fish gut produce digestive enzymes, such as amylases for carbohydrate breakdown, proteases for protein hydrolysis, and lipases for lipid catabolism, which augment or compensate for the host’s own enzymatic capabilities (Ray et al., 2022; Zhang et al., 2024). This microbial enzymatic activity significantly enhances the efficiency of nutrient digestion in the host (Zhang et al., 2024). Furthermore, the gut microbiota stimulates the proliferation and maturation of the intestinal epithelium, thereby increasing the absorptive surface area available for nutrient uptake (Nayak, 2010). Zebrafish research indicates that gut bacteria promote an elevated count and size of lipid droplets within intestinal epithelial cells, indicating improved lipid absorption (Semova et al., 2012). Cheesman et al. (2011) further elucidated that the microbiota, in conjunction with Wnt signalling pathways, promotes intestinal epithelial cell proliferation by stabilizing β-catenin within gut tissues, potentially contributing to enhanced digestive capacity. Inherent metabolic pathways in fish often demonstrate suboptimal efficiency in processing carbohydrates. However, gut-associated microorganisms enhance carbohydrate digestion through the production of relevant enzymes and by potentiating the activity of the host’s digestive enzymes (Zhang et al., 2024). The microbial fermentation of carbohydrates yields short-chain fatty acids (SCFAs), which are subsequently absorbed by the host and utilized as energy substrates (Pardesi et al., 2022; Hao et al., 2017; Petit et al., 2022). Cetobacterium somerae, a dominant bacterial taxon in the gut of many freshwater fish species, has been shown to improve glucose homeostasis via the production of acetate, which exerts its effects through the activation of parasympathetic pathways in zebrafish (Wang J, et al., 2021). Similarly, the administration of Bacillus amyloliquefaciens SS1 in Nile tilapia fed a high-carbohydrate diet resulted in improved metabolic phenotypes, including reduced fasting glucose levels and decreased lipid accumulation, potentially mediated by an increase in acetate-producing bacteria (Petit et al., 2022). A comparative analysis of the gut microbiota in herbivorous and carnivorous fish by Liu et al. (2016) revealed that cellulase and amylase activities were more closely associated with herbivores, whereas trypsin activity correlated with carnivores. It seems the specific makeup of the microbial community adjusts to the host’s diet and actively participates in breaking down and using carbohydrates and proteins.

The intestinal microbiota significantly enhances host energy extraction via multiple pathways, encompassing the modulation of lipid absorption and the transformation of bile acid profiles and the adjustment of genes involved in maintaining energy balance, Guo and colleagues in 2017 showed that zebrafish consuming diets rich in nucleotides displayed lower basal metabolic rates as a result of changes in their gut bacteria, leading to improved energy storage and growth (Guo et al., 2017). Similarly, Zhang studied that Citrobacter bacteria isolated from Nile tilapia intestines enhanced energy extraction in fish consuming a high-fat diet, highlighting the microbiota’s ability to modulate the adverse outcomes associated with suboptimal nutrient intake (Zhang et al., 2020). Furthermore, De La Torre Canny et al., 2021 indicated that Plesiomonas species reduced fat accumulation in zebrafish, suggesting that specific gut microbes can counteract the obesogenic effects of environmental contaminants like tributyltin (TBT). Bile acids, crucial for the digestion and absorption of lipids, undergo microbial transformation in the gut into secondary bile acids that influence glucose and lipid metabolism. In zebrafish, the primary biliary acids, 5α-cyprinol sulfate (5αCS) and taurocholic acid (TCA), undergo biotransformation mediated by the gut microbiota (Wen et al., 2021). Specifically, an identified Acinetobacter species exhibited the capacity for TCA deconjugation, potentially leading to the activation of farnesoid X receptor (FXR) signaling, a key regulatory axis in lipid and energy homeostasis.

Xia et al. (2023) also observed that bile acids enhance intestinal barrier function through both direct mechanisms and microbiota-dependent routes, potentially impacting nutrient assimilation and metabolic processes. The feed conversion ratio (FCR) represents a crucial economic parameter in aquaculture. Gut microbiota contributes to enhanced FCR by improving digestive and metabolic efficiency. Although more extensively investigated in monogastric animals, accumulating evidence from fish also supports this notion. Specific probiotic strains, such as Lactobacillus acidophilus (Singh et al., 2014), Bacillus coagulans (Adeshina et al., 2020), and Acinetobacter (Amoah et al., 2019), have been associated with improved FCR in fish, although the underlying mechanisms remain to be fully elucidated. Dvergedal et al. (2020) identified three operational taxonomic units (OTUs) that exhibited a positive correlation with enhanced feed efficiency and carbon metabolism in Salmo salar. Similarly, Bozzi et al. (2021) reported a positive association between Mycoplasma abundance and both physiological condition and somatic weight in salmon, indicating a beneficial microbial role in growth and energy utilization. Intestinal microbes can modulate host gene expression related to metabolic pathways. For example, studies in Danio rerio have demonstrated microbiota-mediated regulation of genes involved in lipid uptake, fatty acid metabolism, and energy storage (Sheng et al., 2018). In zebrafish, Semova and colleagues demonstrated in 2012 that the gut microbial community enhanced the uptake of lipids and the accumulation of lipid droplets within the intestinal and hepatic tissues. This observation suggests that the microbially mediated influence on host metabolic pathways particularly lipid processing may represent a conserved biological mechanism across vertebrate species.

The intestinal microbiota of crustaceans, notably shrimp, is fundamental to their nutritional physiology, metabolic homeostasis, immune system function, and capacity to withstand environmental perturbations. Considering the limited capacity of shrimp to digest complex food components such as carbohydrates, proteins, and fats, the gut microbiota plays a vital role in completing these metabolic processes. The dynamic nature of this microbial community’s structure and function allows for rapid adjustments in response to dietary changes, environmental factors, and stressors, with downstream effects on host health and productivity. Shrimp is critically dependent on their gut microbiota for the assimilation of complex feed components. The intestinal microbiota metabolizes unabsorbed nutrients and generates diverse metabolites that positively influence the host digestive processes and general health (Qiao et al., 2017). These micro-organisms express enzymes including proteases, lipases, and amylases that contribute to the catabolism of proteins, lipids, and carbohydrates, respectively. Distinct anatomical sections of the shrimp gastrointestinal tract exhibit specialized microbial metabolic roles. The foregut microbiota is predominantly involved in the biotransformation of amino acids and carbohydrates. The community of microorganisms residing in the insect midgut is crucial for processing fats, polyketide compounds, and terpenoids. The hindgut microbiota is more engaged in vitamin biosynthesis, energy production, and cofactor metabolism (Garibay-Valdez et al., 2021).

The evident functional diversification highlights the adaptive specialization of the gut microbiota, driven by the spatial heterogeneity and nutrient gradients along the host’s digestive tract. Dietary carbohydrates function not only as a principal energy substrate for shrimp but also as crucial substrates supporting the metabolic activities of the gut microbial community. Through fermentative pathways, these microorganisms metabolize carbohydrates, yielding short-chain fatty acids (SCFAs) and other biologically active compounds. The inclusion of various carbohydrates, such as glucose, sucrose, xylooligosaccharides, and starch, in the dietary formulations for shrimp has been shown to positively influence the composition and resilience of their gut microbial communities. This modulation of the intestinal microbiota is associated with enhanced gut health and improved overall growth performance in shrimp aquaculture (Chen et al., 2021; Gyan et al., 2022). Furthermore, modulation of the carbon-to-nitrogen (C/N) ratio in feed has been shown to optimize the gut microbial architecture, increasing microbial efficiency in nutrient catabolism and anabolism, thereby enhancing shrimp productivity (Guo et al., 2020). An optimized C/N ratio fosters the proliferation of beneficial bacterial taxa and supports a conducive environment for microbial fermentation and energy acquisition. Gut microbiota-mediated protein and lipid metabolism is critical for maximizing feed utilization efficiency in shrimp. Modifications in the dietary protein composition or ratio induce shifts in the gut microbial community towards species exhibiting enhanced proteolytic capabilities, consequently improving the digestion and assimilation of amino acids (Gyan et al., 2022).

The nature of dietary lipid sources, such as soybean oil, tallow, or linseed oil, exerts a considerable impact on the structural assembly of the intestinal microbial community. These alterations in microbial composition modulate lipid metabolic pathways and correlate with observed differences in immunological responses and growth performance (Zhang et al., 2014). Furthermore, specific microbial taxa contribute to the biotransformation of bile acids, indirectly facilitating the processes of lipid emulsification and subsequent absorption. The community of microorganisms residing in the shrimp’s gut is essential for regulating its immune system. A balanced and diverse microbial ecosystem can confer protection against pathogenic organisms through mechanisms including competitive exclusion, the enhancement of mucosal immunity, and the production of antimicrobial compounds. Following infection with White Spot Syndrome Virus (WSSV), shrimp demonstrate shifts in their core gut microbial profile. These microbial dysbiosis events are frequently associated with an increased production of antiviral metabolites of microbial origin, which contribute to the maintenance of immune homeostasis and provide defence against the disease (Zhang and Sun, 2022).

The increasing acknowledgement of probiotic supplementation as a more environmentally sustainable and safe approach compared to antibiotic administration in shrimp aquaculture for disease control is significant. Probiotic bacteria, including genera such as Lactobacillus and Bacillus, have demonstrated positive influences on shrimp growth metrics, immune competence, and survivability. These beneficial effects are mediated through the promotion of advantageous microbial communities and the attenuation of pathogenic organism burdens (Holt et al., 2020). Environmental variables, with a particular emphasis on salinity, significantly impact the compositional architecture of the shrimp gastrointestinal microbiota. Research on Penaeus monodon indicated that shrimp exposed to an initial acclimatization at 20 ppt salinity, followed by transfer to environments of 10 ppt and 30 ppt, exhibited modifications in microbial community structure. Specifically, the relative abundance of Vibrio species established sensitivity to salinity shifts (Chaiyapechara et al., 2012). While Vibrio populations increased in correlation with elevated salinity levels, the relative abundance of other genera, remained relatively constant, indicating a degree of stability within the core microbiota.

Alterations in environmental salinity induce shifts in the microbial community structure, which are mirrored at the molecular level. Metatranscriptomic studies show that genes related to stress response and immunity are expressed at varying levels, underscoring the interconnected impact of environmental salinity on the transcriptional profiles of both the host organism and its associated microbiota. However, the precise nature of this interaction whether the shrimp actively regulate these microbial shifts or passively respond to them requires further investigation. Nutrient deprivation, specifically starvation, elicits substantial modifications in the gut microbiota composition and functional attributes. In shrimp experiencing starvation, a downregulation of digestive enzyme activity is observed concurrently with an upregulation of immune response-related genes. Functional pathway analysis reveals a diminished capacity for carbohydrate, protein, lipid, glycan, and enzyme metabolism under conditions of nutrient scarcity (Dai et al., 2020). These physiological alterations heighten the host’s susceptibility to pathogenic invasion, emphasizing the importance of the gut microbiota in maintaining metabolic and immunological homeostasis during periods of stress. Contemporary research has begun to elucidate correlations between the compositional characteristics of the gut microbiota and parameters of shrimp breeding performance. Specific microbial signatures have been linked to enhanced growth rates and weight gain, indicating the potential utility of gut microbial structure as a biomarker for selective breeding initiatives in shrimp aquaculture (Fan & Li, 2019). These findings lend support to the integration of microbiota analysis into aquaculture breeding programs as a strategy to improve sustainability and overall productivity.

Advances in next-generation sequencing (NGS) have greatly enhanced the characterization of fish and shellfish gut microbiota, primarily through targeted amplicon sequencing and shotgun metagenomics (Wensel et al., 2022). While differing in scope and resolution, both approaches have transformed microbiome research in aquaculture.

Amplicon sequencing, typically targeting the 16S rRNA gene for bacteria or ITS regions for fungi, offers cost-effective and scalable profiling of microbial communities (Yang et al., 2025). It has been widely applied to assess how gut microbiota shift across diets, developmental stages, and environmental or health conditions (Perez-Bustamante et al., 2024). Although this strategy cannot directly resolve functional genes or capture non-bacterial taxa, it remains well suited for large-scale ecological comparisons.

Shotgun metagenomics, which sequences total genomic DNA without prior amplification, enables comprehensive profiling of both microbial composition and functional capacity (Yang et al., 2025). This approach achieves strain-level resolution across bacteria, archaea, viruses, and microeukaryotes (Talwar et al., 2018), and allows annotation of metabolic pathways, virulence factors, antimicrobial resistance genes, and mobile elements. Such functional insights are particularly valuable for elucidating microbial contributions to nutrient assimilation, immune modulation, pathogen defense, and stress tolerance in aquaculture species (Khurana et al., 2020). For instance, shotgun studies have linked microbial shifts to dietary efficiency, probiotic action, and disease resistance, thereby informing management strategies that enhance productivity and sustainability.

The choice of method depends on study objectives: amplicon sequencing is ideal for high-throughput surveys of microbial dynamics across treatments or time points (Spilsbury et al., 2022), whereas shotgun metagenomics is preferred for mechanistic analyses of host–microbe interactions and functional profiling (Yang et al., 2025). Increasingly, combined approaches are employed to leverage the breadth of amplicon surveys with the depth of shotgun datasets, providing a more holistic understanding of gut microbial ecology (Sheth et al., 2016).

Looking forward, integration of metagenomics with transcriptomics, metabolomics, and metaproteomic will be critical for linking microbial identity with activity. These multi-omics strategies are beginning to reveal not only community composition but also metabolic function within the gut, creating new opportunities to connect microbiome dynamics with growth performance, disease resistance, and sustainability outcomes in aquaculture.

The structure and variety of microorganisms inhabiting the fish gut are determined by a complex and ever-changing combination of environmental conditions, inherent biological traits, and nutritional inputs. These factors exert specific effects that vary across the life cycle of the fish and in different habitats. An increasing amount of scientific evidence indicates that comprehending these intricate relationships is essential for refining fish farming techniques, as well as for maintaining fish well-being, strengthening their defense mechanisms, and fostering ecological adaptability (Diwan et al., 2023a; Ou et al., 2021) ( Figure 3 ).

Gut-associated microbial communities in fish and shellfish are now widely regarded as a functional “accessory organ” that exerts significant influence on host physiology, nutrition, and metabolic efficiency. These microbial assemblages differ considerably among freshwater and marine species, as well as across various groups of shellfish, reflecting the combined effects of host traits, ecological roles, and environmental conditions. Through processes such as enzymatic degradation of complex substrates, vitamin biosynthesis, and enhancement of nutrient absorption, the gut microbiota directly contributes to host growth and health. The composition of these microbial communities is not static but dynamically shaped by multiple internal and external drivers, including environmental parameters (temperature, salinity, pH, sediment quality, and geography) and host-related factors (genetics, development, and diet). Collectively, this host microbe environment interaction forms a regulatory network essential for maintaining intestinal balance and overall organismal health. Despite notable advances, the precise cellular, molecular, and metabolic mechanisms that govern these interactions remain insufficiently understood. Future research should focus on unravelling the influence of gut microbiota on host gene expression, immune regulation, and metabolic pathways, using integrative multi-omics and controlled experimental approaches. In addition, the microbial communities of aquatic organisms harbor an untapped reservoir of bioactive molecules with promising applications in pharmaceuticals, nutraceuticals, and sustainable aquaculture practices. A more comprehensive mechanistic understanding will not only optimize health and productivity in aquaculture but also open new frontiers in microbial biotechnology and environmentally responsible cultivation of fish and shellfish.

To significantly propel gut microbiota research forward, foundational experimental methodologies necessitate enhancement. The integration of sophisticated multi-omics analyses offers deeper understanding into the gut microbiota’s role, function, and composition, facilitating the optimization of the intestinal ecosystem for future applications (Ou et al., 2021). Gnotobiotic piscine models, such as zebrafish and stickleback, present valuable systems for these investigations (Zhang et al., 2021). Diverse bioengineering strategies can be employed to cultivate a beneficial microbiota or to remediate dysbiosis in animal models. However, a thorough understanding of the interplay between host disease states and the intestinal microbial community is crucial for effective implementation (Filardo et al., 2024). A synergistic application of various engineering methodologies, targeted at gut microbiota modulation, represents a primary focus for future research endeavours (Nath et al., 2022). Expanding beyond conventional engineering approaches, metabolic engineering strategies hold promises for improved outcomes in gut microbiota modulation (Li et al., 2023). CRISPR-based technologies offer the potential to significantly advance engineering techniques with enhanced precision and efficiency (Careaga, 2024). Beyond single-strain manipulation, the application of synthetic microbial communities (SynComs) provides an emerging strategy. These rationally designed consortia can deliver consistent functions such as nutrient assimilation, pathogen resistance, and stress tolerance, thereby enabling more predictable and stable outcomes in aquaculture systems. Another promising direction is precision aquaculture microbiome engineering, where microbial interventions are tailored to host species, developmental stage, or environmental conditions. Supported by artificial intelligence (AI) and machine learning, such targeted approaches could optimize microbial community dynamics in real time, thereby improving feed conversion efficiency, growth, and disease resilience. In addition, integrating microbiome engineering with climate change resilience strategies represents a crucial future perspective. Microbial communities may buffer fish and shellfish against stressors such as ocean acidification, salinity fluctuations, and rising water temperatures. Designing microbiomes with adaptive traits could thus strengthen the robustness of aquaculture systems under global climate variability.

The development of natural bacteria-derived therapeutics for various human diseases represents a burgeoning field with potential future applications in aquaculture. Further advancements in gut microbiota engineering techniques, coupled with artificial intelligence (AI) and synthetic biology, can drive substantial progress in sustainable aquaculture (Kumar et al., 2022). The establishment of comprehensive protocols and rigorous training programs encompassing advanced strategies and addressing safety considerations is paramount for the successful translation of microbiota engineering to real world applications. Given its capacity to bolster aquaculture sustainability through enhanced productivity, disease resilience, and ecological equilibrium, microbiota engineering emerges as a resilient and forward-looking strategy for advancing sustainable aquaculture practices.