This data set contains data collected during zebrafish larvae experiments at the Wageningen University as part of Adrià López Nadal PhD Thesis. This study corresponds to the article: “Exposure to Antibiotics Affects Saponin Immersion-Induced Immune Stimulation and Shift in Microbial Composition in Zebrafish Larvae” published in Frontiers in Microbiology the 29th of October 2018