Epithelial Transcription Factor Elf3 mediates host immune responses to microbiota and protects against aerocystitis in zebrafish

We identified Elf3 as a conserved microbially responsive transcription factor and generated an elf3 mutant zebrafish allele to test whether it mediates host responses to microbes. We performed bulk RNA-sequencing of elf3 wildtype and mutant larvae reared without (germ-free) or with (conventionalized) the presence of microbes. We found that elf3 does mediate host-microbiota interactions in zebrafish and has an important role in the induction of many immune responsive genes. Overall design: RNA-profiling of elf3 wildtype and mutant 6 days post-fertilization (dpf) zebrafish larvae reared in germ-free (GF) and conventionalized (CV) conditions