Microbiomes play critical roles in maintaining ecosystem health, nutrient cycling, and climate regulation (Lennon et al., 2023). Within aquatic environments, fish, the most diverse group of vertebrates, are host to complex microbial communities that significantly impact their physiology and the health of the surrounding environment (Lorgen-Ritchie et al., 2023). The fish gut microbiome presents an invaluable window into host-microbiota-environment interactions, offering insights with direct implications for aquaculture and conservation. The composition of fish gut microbiota is shaped by a combination of environmental, biological, and behavioral factors, which collectively influence microbial communities across diverse fish species (Nayfach et al., 2021; Bertoncin et al., 2022). These microbiomes are sensitive to environmental conditions, including water temperature, oxygen levels, pH, and salinity, as well as intrinsic factors such as feeding behaviors, life stages, and various anthropogenic influences (Liu et al., 2016; Li et al., 2017a; Du et al., 2019; Zotta et al., 2019; Huang et al., 2020; Mukherjee et al., 2020). The dynamic interplay between fish and their gut microbiota plays a crucial role in shaping fish communities, making this an important area of study for better understanding and managing aquatic biodiversity.

Beyond contributing to essential ecosystem functions, such as nutrient cycling and climate regulation, gut microbiota are also critical for individual health. Alterations in microbial communities can affect phenotypic traits, immune mechanisms, and animal fitness in response to climate change, as physiological functions originate mostly from the gut (Dinan and Cryan, 2016; Mohajeri et al., 2018; Sepulveda and Moeller, 2020). Microbiomes are leveraged to enhance fatty acid production in muscle tissue and improve fish development (Eichmiller et al., 2016; Stephens et al., 2016; Mohajeri et al., 2018; Aldars-García et al., 2021; Asnicar et al., 2021; Chen et al., 2021; Zhang et al., 2022; Yin et al., 2023). The gut microbiome helps protect the intestinal barrier, prevent the overgrowth of opportunistic pathogens, and modulate the host immune system, all of which are crucial for maintaining fish health (Merrifield and Rodiles, 2015; Llewellyn et al., 2016; Nohesara et al., 2023). Conversely, disruption of the microbial balance can result in the proliferation of harmful bacteria, leading to disease outbreaks in aquaculture settings (Talwar et al., 2018; Vargas-albores et al., 2021; Wang et al., 2021). Therefore, understanding and manipulating the fish gut microbiome has become an important strategy for developing sustainable and disease-resistant aquaculture practices.

This review investigates how microbial abundance varies in response to temperature, habitat, and taxonomic differences across major fish groups in global aquaculture. We focus on cyprinids, ictalurids (catfish), salmonids, and cichlids (tilapia), which are economically significant aquaculture species (Lu and Luo, 2020). Additionally, we compare the gut microbiomes of farmed fish, which are raised in controlled environments with standardized diets, with those of wild-caught fish, which interact directly with their natural habitats, to understand how these contrasting conditions influence fish gut microbiomes. This comparative approach will help identify key environmental and dietary factors shaping the gut microbiome and highlight bacterial groups particularly sensitive to these variables. By highlighting these variations and their underlying causes, this review offers valuable insights into the role of the gut microbiome in promoting fish resilience and health under changing environmental conditions. These insights are essential for informing conservation strategies and optimizing sustainable aquaculture practices worldwide.

Gut microbiota composition varies among fish taxa, with hosts from the same taxonomic group generally exhibiting more similar gut microbiota than those from different groups; however, biological factors such as feeding habits can lead to remarkable differences within taxa (Huang et al., 2020). Distinct gut microbiome compositions were observed across different fish groups, with Proteobacteria, Fusobacteria, and Firmicutes being the most prevalent (Figures 1A, B). While Actinobacteria was present in cyprinids, salmonids, cichlids, and zebrafish, it was not reported in the catfish group (Figure 1B). Fish species exhibit distinct feeding behaviors across water layers, which shape their gut microbiome composition. Cyprinids, ictalurids (catfish), salmonids, cichlids, and zebrafish, ranging from bottom dwellers to surface feeders, display microbiota variations based on diet and ecological niches (Ang and Petrell, 1998; Rahman et al., 2008; Ramesh and Kiran, 2016; Thomas and Opeh, 2018). The variation in microbiota phyla highlights the impact of feeding behaviors on gut microbiome diversity (Figures 1B, C), emphasizing ecological adaptation (Sinha and Jones, 1967; Magoulick and Lewis, 2002; Watzin et al., 2008).

Studies also revealed the composition of fish gut microbiomes varies based on habitat characteristics and geomorphology, with factors like salinity and the differences between nearshore littoral and offshore profundal zones significantly influencing microbial diversity (Zotta et al., 2019; Huang et al., 2020; Sylvain et al., 2020; Kim et al., 2021; Shang et al., 2021). Farm-raised fishes in controlled environments show higher microbiome abundance, especially of Firmicutes, Fusobacteria, and Proteobacteria, compared to wild-caught fishes, where Firmicutes and Proteobacteria are most abundant (Figure 1C, Table 1).

Temperature is another key factor influencing gut microbiome composition across climate zones. Fish from warmer environments often display greater microbial diversity, with temperature playing a crucial role in shaping species-specific responses (Wong and Rawls, 2012; Kokou et al., 2018). For example, yellow-tail kingfish showed higher gut microbiota richness at 26°C than at 20°C (Soriano et al., 2018), while turbot exhibited greater diversity at 20°C (Guerreiro et al., 2016). In rainbow trout, higher temperatures were associated with a reduction in Firmicutes (Huyben et al., 2018), and in salmon, higher temperatures led to a decrease in Acinetobacter and an increase in pathogenic Vibrio (Ley et al., 2008). Such variations underscore important role of temperature in influencing microbiota, particularly in temperature-sensitive fish (Chevalier et al., 2015). Among those climatic zones, fish from the subtropical region displayed the highest microbial diversity, with tropical, temperate, and sub-equatorial regions following diversity levels (Figures 1D, E, Table 1).

The gut microbiome is increasingly recognized as an important indicator of environmental health and the adaptability of fish populations, offering valuable insights for conservation efforts (Soh et al., 2024). Factors such as geographic location, exposure to contaminants, urbanization, and the introduction of invasive species can significantly disrupt the gut microbiome, impacting essential processes like digestion, metabolism, immunity, and overall health (Zhu et al., 2021a; Clough et al., 2023; Lennon et al., 2023; Lorgen-Ritchie et al., 2023). Such disruptions complicate conservation strategies, particularly for endangered species, by altering microbial diversity and reducing adaptability. Shifts in microbial diversity in response to environmental pollutants or habitat changes can provide early warnings of ecological imbalance, facilitating timely conservation interventions (Zhu et al., 2021a).

Invasive species, such as Nile tilapia, illustrate how microbiome diversity can confer competitive advantages. Compared to native fish, invasive tilapia display higher gut microbial alpha diversity, reduced interspecies microbial competition, and enhanced food utilization, supporting niche expansion and local adaptation (Gu et al., 2020). Similarly, bighead carp and silver carp, major aquaculture species in East Asia, have become invasive in North America, where hybridization in the Mississippi River Basin (MRB) has further increased their adaptability (Wang et al., 2020). Studies suggest that hybrids benefit from a diversified gut microbiome, which, along with genomic adaptability, may facilitate invasion by supporting survival and local adaptation (Wang et al., 2020; Zhu et al., 2021b). These findings underscore the critical role of the gut microbiome in driving ecological success and adaptability in invasive species. As environmental pressures intensify, understanding the interactions between host genetics and microbiome diversity will be essential for managing invasive populations and protecting native biodiversity.

Managing gut microbiota in captive breeding programs can improve reintroduction success rates by enhancing the resilience and ecological fitness of released fish in their natural habitats (Zhu et al., 2021a). Microbiome-based interventions, including probiotics and prebiotics, hold considerable promise for enhancing resilience and adaptability in both farmed and wild fish, reducing mortality rates and reinforcing conservation outcomes (Jin Song et al., 2019; Vargas-albores et al., 2021; de Jonge et al., 2022). This approach is essential for species recovery, as a well-balanced gut microbiome strengthens adaptability, immune function, and overall health in reintroduced populations, enabling them to thrive in challenging environments.

Advancing sustainable aquaculture and implementing effective conservation strategies for vulnerable fish populations hinges on a comprehensive understanding of gut microbiome dynamics. Research has shown that gut microbiota plays a fundamental role in host resilience, immune function, and adaptation to environmental changes, all of which are critical for both farmed and wild fish (Fonseca and Fuentes, 2023; Zhu and Wang, 2023). Fish migration and breeding activities are closely associated with variations in gut microbiome composition, as they drive physiological and environmental changes (Llewellyn et al., 2016; Hamilton et al., 2019; Liu et al., 2021). As conservation and aquaculture practices increasingly incorporate microbiome management, this could become a powerful tool for sustaining biodiversity, aiding species recovery, and supporting sustainable aquaculture.

Embracing microbiome-based solutions strengthens the health and adaptability of individual species and contributes to the stability of entire aquatic ecosystems. Such microbiome-focused approaches have the potential to transform conservation practices by enhancing species survival, mitigating the impacts of invasive species, and restoring ecosystem health. By integrating these strategies, conservation efforts can foster resilient and balanced aquatic environments, paving the way for the long-term sustainability of our aquatic ecosystems.

This review provides a global perspective on the gut microbiome of four major aquaculture fish groups: cyprinids, ictalurids (catfish), cichlids (tilapia), and salmonids. It highlighted microbial composition and diversity across geographic regions and contrasting farmed and wild environmental conditions (Figure 1). By focusing on these important species, we identified dominant phyla and critical patterns that consistently appear across studies. Notably, samples from temperate, sub-equatorial, and subtropical zones exhibited the highest microbial diversity, emphasizing the interplay between taxonomic and environmental factors in shaping the microbiome (Figure 1E, Table 1). These findings underscore the adaptive significance of the gut microbiome in supporting essential functions such as digestion, immunity, and overall health, thereby enhancing the resilience and productivity of aquaculture species.

The fish gut microbiome represents a promising frontier for advancements in aquaculture and conservation biology. By harnessing the power of microbiome research, we can develop more sustainable aquaculture practices, enhance the resilience of wild fish populations, and safeguard the delicate balance of aquatic ecosystems. Interdisciplinary approaches and innovative technologies will pave the way for transformative solutions to global challenges in aquaculture sustainability and biodiversity conservation.