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.