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

Abstract

Gut microbial products direct growth, differentiation and development in the animal host. Disruptions to host-microbe interactions have profound health consequences, that include onset of chronic inflammatory illnesses. However, we lack system-wide understanding of cell-specific responses to the microbiome. We profiled transcriptional activity in individual cells from the intestine, and associated tissue, of zebrafish larvae that we raised in the presence, or absence, of a microbiome. We uncovered extensive cellular heterogeneity in the conventional zebrafish intestinal epithelium, including previously undescribed cell types with known mammalian homologs. By comparing conventional to germ-free profiles, we mapped microbial impacts on transcriptional activity in each cell population. We revealed intricate degrees of cellular specificity in host responses to the microbiome, that included regulatory effects on patterning, metabolic and immune activity. For example, we showed that removal of microbes hindered transduction of vascular endothelial growth factor-dependent signals in the developing vasculature, resulting in impaired intestinal vascularization. Our work provides a high-resolution atlas of intestinal cellular composition in the developing fish gut and details the effects of the microbiome on each cell type.

Global Host Responses to the Microbiota at Single Cell Resolution in Gnotobiotic Zebrafish

“…2A&B). Comparing our lists of enriched transcripts in digestive tract clusters with previous microarray (Rawls, Samuel and Gordon, 2004) and single cell RNAseq (Willms et al ., 2022) analysis of dissected CVZ and GF larval zebrafish digestive tracts revealed good concordance between these datasets (STable. 2&3; SFig.…”

c-MAF maintains the transcriptional program of enterocyte zonation and the balance of absorptive/intestinal secretory cell types

“…S3d ). Among zebrafish intestinal populations, mafa was strongly produced by enterocytes 3 and 4, involved in lipid and carbohydrate absorption (Willms et al, 2021), while secretory or progenitor cells were negative. Of interest, lysosome-rich enterocytes involved in protein catabolism had the highest levels of mafa ( Fig.…”

“…Kallisto pseudo-alignment results were imported into R (v. 3.5.3) and pre-processed the same way as for the c-MAF KO and WT samples described above with tximport and biomaRt and normalized with DESeq2. c-MAF expression in human and zebrafish intestinal epithelial cells was analysed using Single cell portal analysis tool (https://singlecell.broadinstitute.org/single_cell) and prepublication dataset of human duodenum and ileum (https://singlecell.broadinstitute.org/single_cell/study/SCP817/comparison-of-ace2-and tmprss2-expression-in-human-duodenal-and-ileal-tissue-and-organoid-derived-epithelialcells#study-summary) and dataset of intestine from zebrafish cultured under conventional conditions (GSE161855, Willms et al, 2021).…”

Single-cell transcriptomic profiling of healthy and fibrotic adult zebrafish liver reveals conserved cell identities and stellate cell activation phenotypes with human liver

“…This protocol was adapted from Willms et al, 2020 (83). Marker genes (p-value < 0.05) for each cluster were analyzed in GOrilla (Gene Ontology enrichment anaLysis and visuaLizAtion tool) to determine significantly enriched GO processes (84).…”