Fish gut Microbiota and Microbiome: A Key Factor in Health and Nutrition

Scientific studies reveal the complexity of the fish gut microbiota and microbiome and their importance for health and physiology, highlighting the need for continued research to develop strategies that enhance aquaculture across different fish species.

The gut microbiota and microbiome of fish play a mediating role in nutrient digestion, pathogen resistance, and immune response regulation. Given their impact on the sustainability of aquaculture production systems and the health of marine ecosystems, studying and understanding the fish gut microbiota and microbiome is crucial for advancing more sustainable practices.

Fish Gut Microbiota vs. Fish Gut Microbiome

Although the terms fish gut microbiota and fish gut microbiome are often used interchangeably, they have distinct meanings that should be clarified:

• Fish Gut Microbiota: Refers to the microorganisms residing in the gut, considered individually or as a community. This term emphasizes the species present, their composition, and quantity.
• Fish Gut Microbiome: Encompasses not only the microorganisms (microbiota) but also their functions, metabolic products, and interactions. It is a more holistic approach that considers the microbiota’s contribution to the ecosystem and the host.

Both are essential for the health and physiology of fish. Studying the gut microbiota and microbiome is critical to addressing common aquaculture challenges such as diseases or nutritional imbalances and to better understanding the complex interactions between fish and their environment.

Understanding this distinction is crucial for researchers aiming to optimize fish health or develop innovative nutritional solutions.

Types of Gut Microbiota

Tolas et al., (2025) divided the gastrointestinal microbiota (GM) of teleost fish into two main subgroups: autochthonous microbiota and allochthonous microbiota.

Autochthonous Microbiota

Also known as resident or indigenous microbiota, it is associated with the mucus layer covering the intestinal epithelium. These bacteria may be embedded in intestinal folds or anchored to cells through various mechanisms, such as adhesion molecule production, biofilm formation, or modulation of the gut immune response.

Autochthonous microbiota can survive host defense mechanisms, such as antimicrobial peptides. A portion of this microbiota is established during the early life stages of the fish, with its diversity increasing as the fish grows. It plays a fundamental role in intestinal tissue development and immunity.

Allochthonous Microbiota

Considered transient bacteria present in feces, these microorganisms pass through the gut and exit the fish with fecal matter. Typically, they do not colonize any habitat unless under abnormal conditions.

The allochthonous microbiota is generally quantitatively more dominant than the autochthonous microbiota.

The autochthonous microbiota appears more stable than the allochthonous microbiota. For instance, changes in fishmeal did not affect the autochthonous microbiota of sea bass but caused significant changes in the allochthonous microbiota.

Study of Fish Gut Microbiota and Microbiome

Research on the gut microbiota and microbiome of fish has significantly advanced in recent years, transitioning from culture-based approaches to next-generation sequencing (NGS) techniques and metagenomics. These advancements have enabled a deeper understanding of the diversity, function, and interactions of the microbiome in fish health.

Here are the most relevant current approaches in the scientific literature regarding the gut microbiota and microbiome of fish:

Next-Generation Sequencing (NGS) and Metagenomics

The sequencing of the 16S rRNA gene is widely used to analyze the composition of the microbiota. This technique identifies the different bacteria present in the fish gut, including those that cannot be cultured in the laboratory. Studies based on 16S rRNA have revealed that the fish microbiota is dominated by phyla such as Proteobacteria, Firmicutes, Fusobacteriota, Bacteroidota, and Actinomycetota, though the relative abundance of these phyla varies across species and conditions.

Metagenomics studies the total genetic material of the microbiota, providing insights not only into the species present but also into their metabolic functions and genetic potential. Metagenomics can identify genes related to nutrient metabolism, enzyme production, and immune responses.

Gnotobiotic Models

Gnotobiotic models, such as zebrafish, are used to study host-microbiota interactions under controlled conditions. These models enable the analysis of the impact of specific bacterial species on fish physiology and the establishment of causal relationships. It has been shown that the microbiome modulates nutrition, immunity, and other physiological functions of fish, and that the host can regulate the microbiome through immune and non-immune components.

These models are also employed to investigate the effects of opportunistic pathogens in fish larvae, helping to understand how the microbiota influences disease susceptibility.

Host-Microbiota Interaction Studies

Scientific studies focus on the reciprocal interactions between the host and its microbiota. Researchers investigate how host factors, both immune and non-immune, regulate the composition of the gut microbiota. This approach also aims to identify strategies to modulate the microbiota by targeting host factors.

Interactions between diet and microbiota are also explored. Herbivorous fish tend to have a higher abundance of cellulose-degrading bacteria, while carnivorous fish have a greater abundance of other bacterial types. Diet significantly influences the composition and functionality of the microbiota.

Scientists also study how the microbiota affects fish metabolism, immune systems, and disease resistance. For example, certain bacteria have been shown to enhance intestinal immune protein expression and increase pathogen resistance. In this context, tools such as SAMBA can become valuable allies for researchers.

Finally, the influence of the microbiota on the gut-brain axis is being investigated. It has been observed that the microbiome can affect behavior and stress responses in fish.

Environmental Factors

The impact of various environmental factors on microbiome composition, such as salinity, temperature, pH, and changes induced by pollutants, has also been studied. These scientific studies reveal that microbiota adapt to environmental conditions and that abrupt environmental changes can alter their composition and function.

The impact of antibiotics and other chemical compounds on gut microbiota is also a research focus, as these substances can cause dysbiosis and increase pathogen susceptibility.

Comparative Studies

Comparative studies of the gut microbiome are conducted among different fish species, as well as between fish from different environments (marine vs. freshwater) and with different feeding habits (herbivorous vs. carnivorous).

Additionally, comparisons between wild fish and farmed fish are made to better understand the impact of captivity conditions on microbiota composition.

Current approaches to studying the fish gut microbiome include advanced sequencing and metagenomics techniques, gnotobiotic models, host-microbiota interaction studies, aquaculture applications, and a focus on environmental factors. The knowledge gained from these studies is essential for understanding fish health and physiology and for developing more sustainable aquaculture practices.

Factors Shaping the Intestinal Microbiota and Microbiome of Fish

Various intrinsic and extrinsic factors influence the composition and function of the intestinal microbiota and microbiome in fish. Based on scientific literature, these factors can be classified into three main categories: host factors, environmental factors, and dietary factors.

Host Factors

Host Selection

The composition of the intestinal microbiome is not merely a reflection of the environment but is subject to specific selection by the host. Fish of the same species, even when raised in different environments, share a core microbiota, highlighting the importance of host selection. This indicates that the fish’s intestinal environment selects certain bacterial taxa.

Host Genetics

Host genetics play a significant role in shaping the intestinal microbiota. Studies have shown that the microbiota composition varies among different fish species, even when raised in the same environment. Host genes influence the selection of specific microbial species and the construction of the intestinal microbial community.

Developmental Stage

The intestinal microbiota composition can vary significantly across the different life stages of fish. In larval stages, initial colonization of the gut is influenced by the surrounding environment, while host factors become more determinant in later stages. As the host matures, the selection of intestinal microbiota is reinforced over time.

Immune System

The host immune system can influence the composition of the intestinal microbiome. Immune components contribute to microbiome homeostasis and the selection of certain bacterial species. Intestinal immune cells can discriminate between commensal and pathogenic bacteria. Additionally, the fish intestine functions as a multifunctional organ involved in pathogen recognition and regulation of intestinal microbiota composition.

Environmental Factors

Water and Sediments

Water and sediments in aquatic environments are critical sources of microorganisms that colonize the fish gut. The microbiota composition may reflect the microbial communities present in water or sediments. The relative contribution of water and sediments to the intestinal microbiome varies among fish species, depending on their habits. For example, the gut microbiota of benthic fish resembles that of sediments, whereas fish living in the water column exhibit microbiota similar to that of the water.

Salinity

Water salinity is a crucial factor influencing the intestinal microbiota composition in fish. Studies have found that fish exposed to varying salinity levels have different microbiota profiles. Salinity affects the relative abundance of certain bacterial groups in the fish gut.

Temperature

Water temperature is another environmental factor affecting the composition of the intestinal microbiota. Temperature changes can alter the structure and function of the gut microbiota. Temperature influences fish growth and physiology, indirectly affecting their microbiota. Kanika et al., (2025) reported that temperate, sub-equatorial, and subtropical regions exhibit the greatest microbiota diversity. Warmer temperatures are generally associated with higher microbial diversity, although species-specific responses occur. For instance, yellowtail showed greater gut microbiota richness at 26°C than at 20°C, while turbot exhibited higher diversity at 20°C.

Habitat

Kim et al., (2021) concluded that the host habitat is the primary determinant of the fish gut microbiota. Environmental factors, especially salinity and sampling sites, have a greater impact on intestinal microbiome composition than host taxonomy or trophic level. For marine fish in tropical waters, the intestinal microbiota differs from that of the surrounding water, and trophic levels influence microbiota composition (Soh et al., 2024).

Other Environmental Factors

Other environmental factors influencing the intestinal microbiome include water pH, oxygen levels, nutrient availability, and contaminants. Changes in these factors can lead to dysbiosis and affect fish health.

Dietary Factors

Diet

Diet is arguably the most influential factor shaping the gastrointestinal microbiota of fish (Luan et al., 2023; Tolas et al., 2025). Diets rich in proteins, including those incorporating alternative protein sources such as plant and insect meals, can significantly alter microbial communities, affecting the abundance of beneficial bacteria like Cetobacterium (Tolas et al., 2025).

Karlsen et al., (2022) demonstrated that fish feeds have diverse microbiomes that can influence intestinal microbiota composition. Tolas et al. (2025) reported that lipid content also affects microbial metabolism and short-chain fatty acid (SCFA) production—metabolites crucial for host health. Conversely, excessive dietary carbohydrates can disrupt the delicate balance of intestinal microbiota, potentially leading to enteritis.

Dietary Additives

Dietary additives such as probiotics, prebiotics, and antibiotics also modulate the intestinal microbiota composition in fish. Probiotics can enhance immunity and growth, while prebiotics can support the growth of beneficial bacteria. Antibiotics, although effective against pathogens, may disrupt microbial diversity and promote antibiotic resistance.

Interaction Between Factors

It is important to note that these factors do not act in isolation but interact to shape the intestinal microbiota of fish. For example, diet interacts with host genetics and environmental factors such as salinity and temperature to influence microbiome composition.

The configuration of fish intestinal microbiota and microbiome is a complex process influenced by multiple host, environmental, and dietary factors. Understanding how these factors interact is crucial for developing strategies to improve fish health and productivity in aquaculture and for conserving wild species.

Composition of Fish Microbiota

The intestinal microbiome of fish is dominated by bacteria, exhibiting low phylogenetic diversity. According to Talwar et al., (2018), the main phyla are Proteobacteria, Firmicutes, and Bacteroidetes, which together account for up to 90% of the intestinal microbiota. Other represented phyla include Fusobacteria, Actinobacteria, and Verrucomicrobia. However, Egerton et al., (2018) and Luan et al. (2023) found that the most abundant phyla in fish microbiota are Proteobacteria, Bacteroidetes, and Fusobacteria.

Microbial diversity tends to increase as fish diets shift from carnivorous to omnivorous and then to herbivorous (Talwar et al., 2018). Furthermore, Kim et al. (2021) reported that freshwater fish (Firmicutes and Fusobacteria) have greater microbial diversity in their intestines compared to saltwater fish (Proteobacteria). Table 01 presents a comparison of the intestinal microbiota between freshwater and marine fish.

Table 01: Comparison of Intestinal Microbiota in Freshwater and Marine Fish.

Source: Binoy et al., (2025).

According to Kanika et al. (2025), the phyla Firmicutes, Fusobacteria, and Proteobacteria are consistently dominant in the intestinal microbiome of aquaculture fish, including cyprinids, ictalurids (catfish), salmonids, and cichlids (tilapia). Actinobacteria is also present in cyprinids, salmonids, cichlids, and zebrafish but not in catfish. Meanwhile, Li et al. (2024) studied the intestinal microbiota of the grass carp (Ctenopharyngodon idella) and found exclusive relationships among genera belonging to Proteobacteria and Fusobacteria/Firmicutes/Bacteroidetes, suggesting two independent ecological groups within the microbiota. These functional groups differ in their genetic capacity for carbohydrate utilization, virulence factors, and antibiotic resistance.

The Microbiome in Fish

The intestinal microbiome, considered an “extra organ,” performs essential functions for the host, including gastrointestinal development, vitamin production, nutrient absorption, immune system strengthening, mucosal tolerance, and the production of anticancer and anti-inflammatory compounds (Diwan et al., 2023).

According to Diwan et al. (2023), the concepts of holobiont (the host and its associated microbial community) and hologenome (the sum of the host’s genome and associated microbial genomes) have gained popularity to describe the complex interactions between the host and its microbiome.

The Intestinal Microbiota and Host Health

The intestinal microbiota plays a critical role in the health of the host—in this case, fish—by influencing various aspects of their physiology (Luan et al., 2023). Here are some key elements of these interactions:

Immune System Modulation

The intestinal microbiota is crucial in modulating the host’s immune system. It interacts with epithelial cells lining the intestine, stimulating immune responses and enhancing overall immune function. Xiong et al., (2018) reported that microbiota imbalance (dysbiosis) is associated with diseases and that the intestinal microbiota plays a significant role in intestinal epithelial renewal and maturation, which, in turn, regulates immune responses.

Nutrient Metabolism

The gastrointestinal microbiota significantly contributes to nutrient metabolism and energy utilization. It aids in digesting complex carbohydrates, synthesizing essential vitamins, and regulating nutrient absorption.

Host-Microbe Communication

The gastrointestinal microbiota communicates with the host through various metabolites, including SCFAs (short-chain fatty acids), bile acids, and neurotransmitters (Tolas et al., 2025). These signaling molecules influence a wide range of physiological processes, including appetite regulation, energy metabolism, immune function, and even neural functions.

Dietary Manipulation and Modulation of Fish Gastrointestinal Microbiota

Manipulating the intestinal microbiota of fish is a key strategy to improve their health, growth, and disease resistance, especially in aquaculture. Below are some ways to achieve this based on scientific literature:

Dietary Modification

• Probiotics: Adding probiotics to diets is one of the most common and effective strategies for manipulating intestinal microbiota. Probiotics are live microorganisms that, when administered in adequate amounts, provide health benefits to the host.
  • Pediococcus pentosaceus can enhance pathogen resistance and increase interleukin IL-1β production.
  • Lactobacillus rhamnosus may reduce lipid content by altering intestinal microbiota and the transcription of lipid metabolism-related genes.
  • Other lactic acid bacteria also have beneficial effects.
  • Some probiotics, such as Shewanella putrefaciens, can modulate immunity and intestinal microbiota.
• Prebiotics: Prebiotics are non-digestible substances that promote the growth and activity of beneficial microorganisms in the gut.
  • Fructooligosaccharides (FOS) can influence intestinal microbiota and improve fish gut health.
  • Polysaccharide-based prebiotics can modulate intestinal microbiota.
• Alternative Diets: Diet composition significantly impacts intestinal microbiota.
  • Using alternative ingredients such as insect proteins or plant proteins instead of fishmeal can modify the microbiota.
  • Changes in dietary macronutrients also affect intestinal microbiota.
  • Fermentation of soybean meal can increase lactic acid bacteria in intestinal microbiota.
• Dietary Supplements: Adding specific supplements, such as nucleotides, can promote growth by reducing energy expenditure mediated by intestinal microbiota.

Environmental Modulation

• Salinity: Water salinity influences intestinal microbiota composition.
  • Changes in salinity can alter dominant microbiota species in shrimp.
  • Differences between freshwater and marine fish microbiota suggest that the environment shapes intestinal microbiome composition.
• Temperature: Water temperature is an environmental factor that can affect fish intestinal microbiota.
• Water Quality: Water quality also influences microbiota composition. Water treatments can induce microbial selection, affecting microbiota and pathogen responses.
• Stress: Managing the environment to reduce stress can influence intestinal microbiota. Acclimation to higher salinities, for example, can reduce stress and modify microbiota composition.

Use of Bacteriophages

Bacteriophages, viruses that infect bacteria, can be used to control specific bacterial populations. They may serve as an alternative to antibiotics for controlling pathogens and manipulating intestinal microbiota.

Fecal Microbiota Transplantation (FMT)

Fecal microbiota transplantation (FMT) involves transferring microbiota from a healthy donor to a recipient. This technique can restore microbiota diversity and balance in cases of dysbiosis.

Quorum Quenching

Quorum quenching is a strategy that disrupts bacterial communication, reducing the ability of pathogens to cause harm. This technique can be useful for manipulating intestinal microbiota by reducing harmful bacteria.

Key Considerations

• Dysbiosis: Avoiding dysbiosis is critical, as an imbalance in microbiota can negatively impact fish health, increasing susceptibility to diseases.
• Antibiotics: Indiscriminate use of antibiotics can cause dysbiosis and promote antimicrobial resistance. Manipulating microbiota is a viable alternative to antibiotics.
• Complex Interactions: Manipulating microbiota is complex and requires a deep understanding of the interactions among the host, microbiota, and environment.
• Indigenous vs. Transient Microbiota: Distinguishing between indigenous (permanent residents) and transient microbiota is important. Manipulation strategies should focus on promoting colonization and maintenance of beneficial bacteria.

Manipulating the intestinal microbiota, and thus the microbiome, is an active and promising research field. Combining dietary, environmental, and other techniques can improve fish health and aquaculture sustainability.

Implications for the Aquaculture Industry

The implications of study findings for the aquaculture industry are significant, covering various key areas to enhance the health, performance, and sustainability of aquaculture practices. Some of the most relevant points include:

Diet Optimization

Studies highlight how diet directly influences the composition of the fish gut microbiota (GM). Fish farmers can design more precise diets, considering not only the nutritional needs of the fish but also how different nutrients and dietary components (e.g., replacing fishmeal with insect meal or using specific oils and fats) affect the microbiota. By manipulating the diet, beneficial microbiota can be promoted to improve digestion, nutrient absorption, and overall fish health.

Strategic Use of Probiotics and Prebiotics

The study supports the use of probiotics and prebiotics to modulate the GM and promote gut health. Supplementation with probiotics such as Pediococcus acidilactici, Lactobacillus, Bacillus, Lactococcus, and Saccharomyces can enhance growth, nutrient metabolism, immune response, and disease resistance in fish. Similarly, including prebiotics such as mannan-oligosaccharides (MOS), β-glucan, and fructo-oligosaccharides (FOS) can encourage the growth of beneficial bacteria and maintain a healthy gut microbiota. It is crucial to tailor the administration of probiotics and prebiotics to each fish species.

Stress Management

Stress factors such as temperature, salinity, heavy metals, and ammonia exposure can alter GM composition and negatively affect fish health. The study suggests implementing better management practices in aquaculture to minimize these stressors and maintain GM stability—for example, improving water quality, avoiding abrupt changes in temperature and salinity, or using stress mitigation strategies for more sensitive species.

Reducing Antibiotic Use

The study demonstrates that antibiotics can cause gut microbiota dysbiosis, leading to increased disease susceptibility and antibiotic resistance. Promoting a healthy microbiota through diet and probiotics/prebiotics can reduce reliance on antibiotics, which is essential for aquaculture sustainability and for reducing overall antimicrobial resistance.

Enhancing Immunity and Disease Resistance

The GM plays a vital role in fish immunity. A balanced microbiota can enhance both innate and adaptive immune responses, making fish more resistant to infections. By manipulating gut microbiota through diet or probiotic use, resistance to common aquaculture diseases can be increased, reducing mortality rates and economic losses.

Monitoring Gut Microbiota

The study highlights that continuous GM monitoring can be a useful tool for assessing fish health and the effectiveness of aquaculture practices. Gut microbiota analysis can reveal the presence of dysbiosis or imbalances, enabling early intervention to correct these issues and prevent production losses.

Conclusion

The gut microbiota of fish is a complex and dynamic ecosystem that plays a fundamental role in fish health and well-being. Understanding the factors shaping gut microbiota and its interactions with the host allows the development of sustainable aquaculture practices that promote fish health, enhance productivity, and minimize environmental impacts.

Furthermore, it is essential to emphasize that the gut microbiome of marine fish is a source of ribosomally synthesized antimicrobial peptides called bacteriocins (Uniacke et al., 2024). These bacteriocins may have broad or narrow activity spectra, enabling the targeting of specific pathogens without harming beneficial bacteria.

References

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