Data from: The aquatic microbiome communicates with the Zebrafish (Danio rerio) embryo through the chorion to influence developmental trajectory

Host-microbiome interactions have a significant influence on fundamental physiological processes including bioenergetics, neurobiology, and xenobiotic responses. However, studies examining host-microbiome interactions are largely limited to post-embryonic developmental stages, highlighting a notable knowledge gap in microbial influences on embryogenesis. This is because the developing embryo, particularly in oviparous organisms, is protected from the surrounding environment by the chorion and typically considered to be sterile. Here, we tested the hypothesis that the aquatic microbiome influences embryonic development in oviparous organisms despite lack of physical contact with microbes, shaping host physiology during and beyond embryogenesis. We utilized zebrafish (Danio rerio) reared germ-free or conventionalized with microbes at 6 and 24 hours post-fertilization to examine transcriptomic and proteomic shifts in embryos at 32 hours post-fertilization and determine physiological responses to a xenobiotic exposure. Our data revealed a significant role of the surrounding aquatic microbial community in regulating embryonic transcript and protein abundance associated with critical developmental processes including energy metabolism and neurodevelopment. Furthermore, we demonstrated the surrounding microbial community drives differential expression of genes involved in xenobiotic metabolism, including cytochrome P4501A (cyp1a). Exposure studies comparing germ-free and conventionalized embryos showed the environmental microbiome affects embryonic mitochondrial function and later-life larval behavioral responses to a CYP1A activating xenobiotic, benzo-a-pyrene. In summary, our findings reveal embryonic developmental processes are an integration of host genetic blueprints and environmental microbial cues, shaping developmental susceptibility to environmental stressors.