Use of Zebrafish to Model Microbiome

George Streisinger and colleagues first introduced zebrafish as a model organism in the early 1980s. Streisinger’s work demonstrated the feasibility of using zebrafish for genetic studies, particularly through large-scale mutagenesis and phenotypic screening. The initial focus was on developmental biology, but by the 1990s, the use of zebrafish expanded to include disease modeling, drug discovery, and studies of human genetic diseases, supported by advances in gene mapping and genome sequencing. Today, zebrafish are widely used in biomedical research and go even further, including their use in the expanding field of host-microbiome interactions. 

Zebrafish as a Model for Microbiome Studies: Scope and Potential

Zebrafish offer several advantages for microbiome research, starting with their high genomic conservation: approximately 70% of human genes have at least one zebrafish homolog, and around 80% of human disease-related genes are conserved in this species.

Their digestive tract presents comparable functional regions to mammals, even though zebrafish lack a stomach and intestinal crypts. The anterior and mid-intestine resemble the mammalian small intestine, participating in nutrient absorption and immune regulation, whereas the posterior segment mirrors the large intestine in its osmoregulatory functions. 

The model’s suitability is reinforced by the availability of germ-free embryos produced using standardized protocols. These embryos are reared under sterile conditions, completely devoid of microorganisms, which enables full experimental control over microbial exposure and host-microbe interactions. Compared to gnotobiotic mice, zebrafish are a cost-effective model suitable for high-throughput screening. 

Early studies showed that up to 200 genes in the zebrafish digestive tract are regulated by microbial colonization. 59 of these showed conserved expression patterns in mice, including genes involved in nutrient metabolism, epithelial proliferation, and innate immunity, highlighting shared host-microbe regulatory mechanisms across vertebrates.

Zebrafish also enable real-time in vivo imaging thanks to their transparency during embryonic and larval stages. Fluorescent transgenic lines allow the visualization of microbial colonization, immune cell recruitment, enteroendocrine activity, and neuronal responses within the same organism. 

Understanding the Gut-Brain Axis Through Zebrafish

The gut-brain axis integrates neural, endocrine, metabolic, and immune pathways to coordinate signals between the gastrointestinal tract and the central nervous system. Enteric neurons express receptors such as TLR-2 and TLR-4, which detect microbial components and modulate neural circuits, while certain bacteria, including Staphylococcus aureus and species of Lactobacillus, can directly activate sensory pathways involved in gut–brain communication. 

The presence of certain microbes in the zebrafish microbiome is essential for the normal development and physiological function of the nervous system. Antibiotic-treated zebrafish show effects on locomotion and anxiety-like behaviour. Altered microbiomes can disrupt zebrafish’s social and explorative behaviour, highlighting the connection between the microbiome and the central nervous system. Changes in gut barrier integrity and intestinal immune activity also shape central responses.

There are many molecular pathways involved in gut-brain communication conserved across vertebrates. Neurotransmitter systems such as serotonin, dopamine, and GABA share key signaling components in zebrafish and humans, and certain neuroendocrine mediators linked to appetite and energy regulation exhibit comparable patterns of expression. These conserved features support the relevance of zebrafish for analyzing the foundational mechanisms that structure the gut-brain axis across species.

Opportunities of Modeling the Human Microbiome in Zebrafish

The zebrafish microbiome differs significantly from human microbial composition. Their guts are dominated by Proteobacteria rather than the Firmicutes and Bacteroidetes, which are prevalent in humans. Nevertheless, germ-free embryos offer the possibility of colonizing zebrafish with human-derived microbiota to expand their translational relevance.  

Recent work has demonstrated that human-relevant bacteria can establish in the zebrafish gut under controlled conditions. Defined microbial communities containing anaerobic species such as Eubacterium limosum and Lactobacillus paracasei were able to colonize 5-day post-fertilization (dpf) larvae via static immersion or microinjection. A subsequent study successfully colonized up to 60 human intestinal phylotypes in germ-free larvae after 48h of incubation, including species of high clinical interest such as Akkermansia muciniphila, Prevotella, Faecalibacterium prausnitzii, and Roseburia.

However, persistent colonization remains limited. Factors such as higher intestinal oxygen levels, the lower density of anaerobes, differences in habitat temperature (26-29 °C vs 35-37 °C), dietary inputs, and the absence of early gut anaerobiosis seen in human neonates constrain microbial persistence. Although colonizing the entire human gut microbiome into zebrafish is difficult, infecting them with some specific bacterial genus also present in zebrafish is feasible. 

Even with these limitations, modeling human gut microbes in zebrafish offers valuable opportunities. Colonization experiments allow controlled investigation of microbial effects on host pathways, including immune activation, metabolism, and epithelial function, in a model where imaging and genetics are straightforward. These studies are already informing how specific bacterial groups behave in a vertebrate intestine and provide insights into the gut-brain axis. 

ZeClinics can conduct your microbiome study 

At ZeClinics, we have performed several projects investigating the role of microbiota for multiple applications. Successful examples of that are the screening of bacteria consortium aimed at promoting neural protection in Parkinson patients, and the identification and validation of bacterial strains improving animal growth, even under low nutrient diets. Both examples demonstrate the relevance and translatability of zebrafish for discovering microbiota-based solutions aimed at improving human and animal health. 

We can do it for you. Contact us!

References

Kiran NS, Yashaswini C, Chatterjee A. Zebrafish: A trending model for gut-brain axis investigation. Aquat Toxicol. 2024 May;270:106902. doi: 10.1016/j.aquatox.2024.106902. 

Lu H, Li P, Huang X, Wang CH, Li M, Xu ZZ. Zebrafish model for human gut microbiome-related studies: advantages and limitations. Medicine in Microecology. 2021;8:100042. doi: 10.1016/j.medmic.2021.100042.

Zhong X, Li J, Lu F, Zhang J, Guo L. Application of zebrafish in the study of the gut microbiome. Animal Model Exp Med. 2022 Dec;5(4):323-336. doi: 10.1002/ame2.12227.

By Miriam Martínez

Miriam is a Human Biologist with a strong background in neuropharmacology and a passion for bridging science and innovation. After earning a master’s degree in the Pharmaceutical and Biotech Industry, she completed her PhD in Biomedicine at Pompeu Fabra University (Barcelona), where her research focused on the behavioral analysis of animal models for neurophenotypical characterization. Following her doctoral studies, Miriam transitioned into the healthcare marketing and communication sector, where she played a key role in developing impactful marketing strategies and educational campaigns for leading pharmaceutical brands. She now leverages her scientific expertise, strategic thinking, and creative communication skills in her current role at ZeClinics.