The gut microbiota (GM) represents a dynamic microbial community whose collective set of genes encodes a vast array of functions. These microbes play a major role in many physiological processes within the host and are essential for health and well-being. Ongoing research suggests that the GM is not only involved in gut physiology but may also have significant effects on many other aspects of health and disease. However, many researchers are unaware of the impact the GM can have on their animal models, which can hinder reproducibility. Here, we demonstrate the ability of the GM to influence a broad array of behavioral phenotypes in both mice and zebrafish. First, we show that isogenic mice with divergent GM exhibit different, sex-specific neurobehavioral phenotypes. Specifically, male mice with a less diverse GM spent significantly more time in the open arms of an elevated plus maze and displayed less time immobile during a forced swim test. Opposing effects were observed in female mice, wherein a more diverse GM resulted in reduced anxiety- and depression-related behavior. Moreover, we demonstrate that the GM mitigates anxiety-related behavior and is required for characteristic stress responses in zebrafish larvae. Germ-free zebrafish larvae displayed significantly less thigmotactic behavior and exhibited a blunted response to an osmotic stress test compared to conventionally raised larvae. Lastly, we show that alterations of the GM via Lactobacillus plantarum supplementation can reduce anxiety-related behavior and protect from stress-induced dysbiosis in adult zebrafish. These findings underscore how changes in GM that can occur during model development may contribute to phenotypic differences of various animal models. Identifying and maintaining a consistent GM will not only facilitate in providing a robust phenotype for particular animal models but also aid in generating reproducible results between experiments.