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. 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.