Protein Absorption in the Zebrafish Gut is Regulated by Interactions between Lysosome Rich Enterocytes and the Microbiome

Abstract

Dietary protein absorption is dependent on the activity of lysosome rich enterocytes (LREs), a specialized population of intestinal cells in neonates and zebrafish. The gut microbiome enhances intestinal absorption of certain nutrients, including lipids, but the effects of the microbiome on intestinal protein absorption remained unclear. Using quantitative fluorescent assays and live confocal microscopy, we demonstrated that the gut microbiome reduces the rate of protein uptake and degradation by LREs. Microbes did not affect the number of protein-absorbing LRE cells, but certain strains did reduce expression of LRE endocytic machinery. By employing transgene-assisted cell isolation and single cell RNA-sequencing, we characterized the effects of the gut microbiome on intestinal cells that take up protein. The microbiome upregulates expression of bacteria-sensing machinery and innate immune genes in LREs, and secretory cell types that take up protein also express protein-uptake and degradation machinery characteristic of LREs. Using custom-formulated diets, we evaluated the effects of LRE endocytic activity on the gut microbiome. A low protein diet, coupled with impaired LRE endocytic activity, significantly affects the microbiome community and causes reductions in species richness. Impaired LRE endocytic activity leads to proliferation of bacterial genera that can, in turn, reduce protein uptake activity in LREs. Together, these findings reveal reciprocal interactions between LREs and the gut microbiome that impact protein absorption in the zebrafish gut.