GSE182725
RNA-seq analysis of conventionally raised zebrafish larvae compared to germ-free zebrafish larvae and germ-free larvae treated with zebrafish metabolites.
Here, we explore the impact of rearing zebrafish embryos in the absence of microbes on early neural development as well as investigate whether any potential changes can be rescued with treatment of metabolites derived from the zebrafish gut microbiota. RNA was extracted from a pool of five heads for each treatment at long-pec stage (2 days post fertilization) and sequenced at a depth of 80-100 million reads per sample. We identified 361 genes significantly down regulated in GF embryos compared to conventionally raised embryos via RNA-Seq analysis. Of these, 42 were rescued with the treatment of zebrafish gut-derived metabolites to GF embryos. Gene ontology analysis revealed that these genes are involved in prominent neurodevelopmental pathways including transcriptional regulation and Wnt signalling. Overall design: RNA-seq analysis of conventionally raised zebrafish larvae compared to germ-free zebrafish larvae and germ-free larvae treated with zebrafish metabolites.