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. ..., , # Hydrodynamic Confinement of Bacteria within Intestinal Folds

DOI: 10.5061/dryad.m905qfvcp

The computational part was dimensionless using the characteristic length a, the characteristic torque T, and the viscosity μ, where a is the radius of the bacterial cell body and T is the thrust torque required for flagellar rotation.

## Description of the data and file structure

### Files and variables

#### File: results\_experiment\data\_figure\_angular.xlsx

**Description:** Trajectory data of E. coli movement through zebrafish gut folds used to draw angular distributions.

##### Variables

id:the index for different E. coli movement trajectory.
angular:the orientation angle of bacteria.
distance:the bacterial swimming distance for start to end.
speed:the bacterial speed.

#### File: results\_experiment\figure\_angular\_probability.py

**Description:** Python code for drawing E.coli angular probability figure 1f.

#### File: results\_experiment\data\_for\_figure\_speed.xlsx

**Descriptio...,