Hydrodynamic confinement of bacteria within intestinal folds

The gut microbiota significantly influences host health by impacting metabolism, immune function, and development. Understanding bacterial behaviors in intestinal folds is crucial due to its role in biofilm formation, which protects bacteria from immune responses and antibiotics and is associated with colorectal cancer. In this study, we observed behaviors of Escherichia coli bacteria in intestinal folds of zebrafish larvae (Danio rerio). It is found that E. coli swim in the intestinal folds for extended periods and is confined in a groove on the wall. In order to clarify the mechanism of the confinement, we further performed numerical simulation using a boundary element method. Our simulations demonstrate that bacterial movement in the groove is constrained by hydrodynamic and steric forces. The groove configuration significantly influences bacterial confinement, with bacteria in a deep groove escaping more easily in the presence of background flow. Based on the aggregation rate of E. coli in intestinal folds of zebrafish larva, it is indicated that the groove trapping significantly reduces the cell flux away from the wall. These findings enhance our understanding of bacterial accumulation and biofilm formation in the gut, with implications for other environments with geometric constraint.