Diet-derived Microbial Metabolites Modulate Stress-Responsive Gene Expression in Germ-free Zebrafish

The gut microbiome plays a pivotal role in overall host health, yet the extent at which diet-derived microbial metabolites affect neurodevelopment and inflammation remains unclear. Here, we employed the robogut bioreactor system seeded with fecal samples from two healthy pediatric donors to generate microbial communities exposed to four different diets: low fiber Western (LFW), high fiber Western (HFW), Mediterranean (MED), and Yanomami (YAN), as well as three fiber supplements: fruit and vegetable fiber (FVF), cereal fiber (CRF), and resistant starch fiber (RSF). Metabolites produced by these microbial communities were isolated and applied to germ-free zebrafish ( Danio rerio ) embryos to assess their effects on neurodevelopment and inflammatory gene expression under basal and stress-induced conditions. Despite minimal changes in microbial composition across diets and fiber sources, significant differences in short-chain fatty acid concentrations were observed. Metabolite treatments had limited effects on the expression of neural and inflammatory genes under basal conditions. Under stress conditions, metabolites from any diet mitigated stress-induced bdnf expression, suggesting a possible modulatory role of microbial metabolites on stress responses. Overall, these findings highlight the resilience of microbial communities to dietary changes and underscore the importance of microbial metabolite output and its donor-specific nature in influencing host neurodevelopment and immune responses.