Intestinal folds accumulate bacteria through physical and biological factors

The gut microbiota is widely acknowledged as a crucial element for maintaining the health of the host. Understanding the mechanisms governing bacterial behavior and distribution within the gut holds significant importance. Bacterial accumulation is particularly noteworthy due to its potential to lead to biofilm formation, but the underlying mechanism remains unclear. Hence, our study focused on investigating Escherichia coli (E. coli) behavior and distribution in zebrafish larval intestines, with a specific emphasis on the gut microenvironment's influence. We observed distinct E. coli movement was restrained within the intestinal folds, resulting in a higher accumulation within these structures. Our in vitro microfluidic experiments confirmed that the physical properties associated with the intestinal wall's geometric shape facilitated preferential E. coli accumulation in the folds. Additionally, a higher density of E. coli was observed on the dorsal side of the intestines. To understand the phenomena, we constructed a continuum model that accounts for the physical factor of decrease in cell flux from the wall to the bulk and the biological factor of directional movement of cells from the ventral to the dorsal side. Through theoretical analysis, we revealed that the overall distribution of E. coli in the intestines resulted from a combination of physical and biological factors. These findings provide valuable insights into how the intestinal microenvironment influences bacterial accumulation.