The intestinal microbiota of fish is predominantly composed of prokaryotic microorganisms, with research historically focused on bacteria. In contrast, the role of microeukaryotic organisms in the fish gut remains largely unexplored. This review synthesizes current knowledge on the diversity, ecology, and potential functions of intestinal microeukaryotes, particularly fungi and protozoans, in teleost fish. Fungi, especially Ascomycota and Basidiomycota phyla members, are consistently identified across species and may contribute to digestion, immune modulation, and microbial homeostasis. Protists, though often viewed as pathogens, also exhibit potential commensal or immunoregulatory roles, including the modulation of bacterial communities through grazing. Other eukaryotic taxa, including metazoan parasites, microalgae, and zooplankton, are commonly found as transient or diet-derived members of the gut ecosystem. While many of these organisms remain poorly characterized, emerging evidence suggests they may play essential roles in host physiology and microbial balance. The review highlights the need for improved detection methodologies, functional studies using gnotobiotic and in vitro models, and multi-kingdom approaches to uncover fish gut microeukaryotes’ ecological and biotechnological potential.

Research on gut microbiota has primarily focused on bacteria, though eukaryotic microorganisms also play important roles in their host. In fish, the suitability of fecal sampling methods for studying these gut microorganisms remains unclear. This study aimed to evaluate two fecal sampling methods, intestinal scraping and aquarium-bottom sampling, on the diversity and composition of gut microeukaryotes in Nile tilapia (Oreochromis niloticus), highlighting the importance of methodological choices in microeukaryotic studies. Results showed that intestinal scraping provides a more accurate representation of the stable, resident community, avoiding potential bias and emphasizing the critical importance of methodological choices in microeukaryotic research.

The microbiota–gut–brain axis (MGBA) is a dynamic bidirectional communication network that integrates microbial, neural, endocrine, and immune signals to regulate host physiology and behavior. This review synthesizes current evidence on the molecular mechanisms by which gut microbiota modulate brain function through endocrine signaling (hypothalamic–pituitary–adrenal axis and sex hormones), neurotransmitter synthesis (serotonin, dopamine, GABA), microbial metabolites (short‐chain fatty acids, indoles, secondary bile acids), and neural pathways involving the enteric and autonomic nervous systems. It also highlights the role of cytokines and immune responses in maintaining intestinal and neurological homeostasis. Emerging findings underscore the ability of specific bacterial taxa and metabolites to influence neurodevelopment, behavior, and disease pathogenesis, including mood disorders, neurodegeneration, and autism spectrum disorders. However, the physiological relevance of many microbe‐derived signals in humans remains poorly defined. Much of the current mechanistic evidence supporting these interactions derives from animal models, underscoring the need for carefully designed human studies to establish physiological relevance and translational validity. Clarifying dose thresholds, tissue‐specific receptor responses, and bidirectional feedback loops is essential for advancing therapeutic applications. This review supports an integrative systems biology approach to understanding the MGBA, emphasizing the need for translational studies to validate preclinical findings in human physiological contexts.

Nile tilapia (Oreochromis niloticus) is a major aquaculture species worldwide, yet bacterial infections remain a critical constraint to production sustainability. Although pathogen-associated dysbiosis has been widely described, most studies have focused exclusively on bacterial communities, overlooking the multi-kingdom nature of the intestinal microbiota. This study evaluated the impact of experimental Providencia vermicola infection on both prokaryotic and microeukaryotic intestinal communities under controlled conditions. Using 16S (V3–V4) and 18S (V9) rRNA amplicon sequencing, we compared healthy and infected fish and assessed taxonomic, structural, and predicted functional changes. Infection was associated with significant compositional shifts, including increased relative abundances of Bacteroidota and Proteobacteria and decreased relative abundances of Fusobacteriota and Patescibacteria. Concomitantly, microeukaryotic groups such as Protalveolata, Nematozoa, and Phragmoplastophyta were significantly reduced. Functional prediction revealed metabolic pathway reconfiguration consistent with infection-associated ecological disturbance. Together, these results suggest that the pathogen challenge is associated with coordinated changes in the intestinal microbiota as an integrated system across multiple microbial kingdoms rather than as isolated bacterial shifts. This study supports ecosystem-level interpretations of dysbiosis and highlights the importance of incorporating cross-domain analyses into health assessment strategies in aquaculture species.

The fish gut microbiota includes bacterial and microeukaryotic microorganisms that contribute to host nutrition, immune regulation, and intestinal homeostasis. However, the simultaneous responses of both microbial fractions to bacterial infection remain poorly explored in aquaculture species. This study evaluated intestinal microbiota differences associated with experimental Staphylococcus haemolyticus infection in Nile tilapia (Oreochromis niloticus). Juvenile female tilapia were randomly assigned to either a non-infected control group or a group experimentally infected with S. haemolyticus. Intestinal contents were collected seven days post-challenge, and microbial communities were characterized by amplicon sequencing targeting the V3–V4 region of the 16S rRNA gene and the V9 region of the 18S rRNA gene. In the bacterial fraction, infected fish showed higher relative abundances of Proteobacteria and Firmicutes and lower relative abundances of Fusobacteriota, Patescibacteria, and Actinobacteriota. At the genus level, infected fish showed higher relative abundances of Staphylococcus, Mycobacterium, and other potentially opportunistic bacteria, along with lower relative abundances of Cetobacterium and Romboutsia. In the microeukaryotic fraction, infected fish showed higher relative abundances of Ciliophora and Ascomycota and a lower relative abundance of Nematozoa. Shannon and Simpson alpha diversity indices were significantly higher in infected fish in both microbial fractions. PICRUSt2-predicted MetaCyc profiles differed between treatments. Control fish showed higher predicted abundances of pathways related to fermentation and vitamin and cofactor metabolism, whereas infected fish showed higher predicted abundances of pathways related to bacterial cell wall metabolism, arginine and polyamine biosynthesis, lipid metabolism, and microbial adaptation. Overall, experimental S. haemolyticus infection was associated with taxon-specific differences in intestinal bacterial and microeukaryotic communities and in predicted bacterial functional potential.