Abstract
Animals defend against infections and other diseases by adaptively responding to the microbiota they encounter. These adaptations are driven by changes in gene expression programs; however, our understanding of the transcription factors regulating host responses to microbiota remains limited. By leveraging gene expression and chromatin accessibility data from zebrafish and mice, we identified the epithelial-specific E74-like ETS transcription factor 3 (Elf3) as a conserved microbially responsive transcription factor. Transcriptomic analysis of gnotobiotic elf3 mutant zebrafish larvae revealed that elf3 is required for a normal host response to microbiota, including induction of immune response genes. Mutation of elf3 led to immune-related pathologies such as inflammation and infection of the swim bladder, granuloma formation, and reduced survival in adulthood. These results establish elf3 as an important mediator of host-microbe interactions in zebrafish.IMPORTANCEAnimals use epithelial barriers to protect themselves from the commensal and pathogenic microorganisms they encounter. These epithelia adapt their function in response to microbial-derived signals, and impairments in these adaptive responses can lead to infection and inflammatory disorders. Improved understanding of the mechanisms underlying host adaptation to microbes can thus be expected to lead to new approaches for promoting health in humans and other animals. Here, we identify the epithelial transcription factor E74-like ETS transcription factor 3 (Elf3) as a mediator of host-microbe interactions in zebrafish. Functional genomic approaches indicated that Elf3 is upregulated by microbiota in both mouse and zebrafish. Using elf3 mutant zebrafish, we find that elf3 mediates induction of host immune responses in larval stages and protects against immune-related pathologies and health deterioration in adults. These results advance our understanding of the transcriptional mechanisms mediating host responses to microbes and provide a new Elf3 deficiency model of epithelial and immune pathology.