A Cell Atlas of Microbe-Responsive Processes in the Zebrafish Intestine

To understand intestinal cell-specific responses to host commensal bacteria, we isolated single cells from intestines and associated tissue of zebrafish larvae raised in the presence or absence of a microbiome. We profiled cells with single-cell RNA-seq. Our analysis revealed extensive heterogeneity among cell populations of the fish intestine and associated tissue, and describe distinct microbial responses in each cell type. Overall design: Zebrafish were raised in the presence of absence of a microbiome for 6 days. Intestines and associated tissue was dissected and dissociated to generate a single-cell suspension for sequencing on the 10X Genomics platform.