​​Through the bidirectional communication along the gut-brain axis (GBA), microbial metabolites interact with the central nervous system (CNS), influencing neuronal development and cellular health. A key factor in CNS health is the blood-brain barrier (BBB), a semipermeable structure that surrounds brain microvasculature. The BBB regulates the movement of molecules and ions between the blood and the brain, helping to maintain a stable brain environment. Novel studies in mice have shown increased blood-brain barrier (BBB) permeability in response to knockdowns in the microbiome, supporting the BBB as a communication mechanism in the GBA. In this study, zebrafish were treated with an antibiotic cocktail (ABX) for 6 days to knock down gut microbial colonization. RT-PCR was used to quantify the relative bacterial abundance post ABX treatment and to analyze expression of BBB-related genes in brain tissue. Mfsd2a, a transcytosis regulator, was assessed. It is hypothesized that the expression of these genes will decrease in response to microbial knockdown, which correlates to increased barrier permeability. Bacterial abundance increased by a 1.4-fold change in ABX fish (n = 10-12), while mfsd2a expression had a 1.5-fold increase (n = 10-12, p = 0.05). Though these results are unexpected, we suspect that the ABX treatment administered allowed for the colonization of bacterial species that promoted BBB integrity. Future studies will identify changes in specific bacterial species and analyze a broader range of genes implicated in BBB integrity to understand further how these two systems interact.