DOI: 10.5061/dryad.m905qfvcp
title: Hydrodynamic confinement of bacteria within intestinal folds

description: 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.
description: # 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
 **Description:** Speed data of E.coli movement through zebrafish gut folds
 used to draw speed figure 2g.The first three columns show the raw
 experimental data. The next three columns are the mean and standard
 deviation of these data, as well as the results of the computational
 simulation. Variables named `exp_*` represent the results of the
 experiment and `sim_*` represent the results of the computational
 simulation. `*_control`,`*_fold`,`*_lumen` denotes the control, fold, and
 lumen groups in Figure 2. `*_ratio` indicates the ratio of velocity. #####
 Variables exp_control:speed data for control group exp_fold:speed data for
 fold group exp_lumen:speed data for lumen group sim_control:speed data for
 nowall group sim_fold:speed data for wall with groove group
 exp_contro_ave:average speed for control group exp_contro_SD:Standard
 deviation of speed in the control group exp_fold_ave:average speed for
 fold group exp_fold_SD:Standard deviation of speed in the fold group
 exp_lumen_ave:average speed for lumen group exp_lumen_SD:Standard
 deviation of speed in the lumen group exp_c-f_ratio:speed ratio of the
 control group to the fold group exp_l-f_ratio:speed ratio of the lumen
 group to the fold group sim_ratio:speed ratio of the control group to the
 fold group for simulation results #### File:
 results\_experiment\figure\_angular\_probability.py **Description:**
 Python code for drawing E.coli speed figure 2g. #### File:
 results\_simulation\results\_vector\_field\data\_vector\_field.xlsx
 **Description:** Orientation φ and the z position of the bacterial body
 data used to draw figure 4. The data in this excel file comes from the
 compilation of all the raw data in the folders of“
 noRepForce,onlyRepForce, RepForce&Hedro”. ##### Variables z0:the z
 position of the bacterial body center phi_ini/pi:initial orientation φ of
 bacterial body phi_fla[pi]:Rotation angle of the flagellum ex:Component of
 the bacterial body orientation vector in the x-axis direction ey:Component
 of the bacterial body orientation vector in the y-axis direction
 ez:Component of the bacterial body orientation vector in the z-axis
 direction phi/pi:orientation φ of bacterial body d_ey/dt:Time-averaged
 bacterial body orientation vector φ dz/dt:Time-averaged bacterial body
 position vector #### File:
 results\_simulation\results\_vector\_field\vector\_field.py
 **Description:** Python code for drawing vector field figure 4. #### File:
 results\_simulation\results\_vector\_field\base\_results.csv
 **Description:** The actual trajectory of basic simulation case #### File
 folders: results\_simulation\results\_vector\_field\noRepForce &
 onlyRepForce & RepForce\&Hedro **Description:** The raw data for
 figure 4. The "noRepForce" folder is the result without
 repulsive forces in Figure 4. The file with the folder name
 “noForce_1.0zini_-0.05phi_0” is the result of the simulation under the
 initial conditions of 1.0z-aixs , -0.05phi and 0 pi flagellar rotation
 angle. The "onlyRepForce" folder is the result only with
 repulsive forces in Figure 4. The file with the folder name
 “noMotor_1.0zini_-0.05phi_0” is the result of the simulation under the
 initial conditions of 1.0z-aixs , -0.05phi and 0 pi flagellar rotation
 angle. The "RepForce&Hedro" folder is the result with
 repulsive and hydrodynamic forces in Figure 4. The file with the folder
 name “1.0zini_-0.05phi_0” is the result of the simulation under the
 initial conditions of 1.0z-aixs , -0.05phi and 0 pi flagellar rotation
 angle. “results.dat” is the raw results file for data_vector_field.xlsx,
 and the variables in these files are the same as in the raw data file
 below. "gap_min.dat" is the result for minimum distance.
 Variables in the "gap_min.dat" files t:time gap_ff:minumum gap
 distance between flagellar (disregarded since there is only one flagellum)
 gap_bw minumum gap distance between body and wall gap_fw minumum gap
 distance between flagellar and wall gap_bg minumum gap distance between
 body and groove gap_fgminumum gap distance between flagellar and groovw
 #### File: results\_simulation\*.dat **Description:** Files in *.dat
 format are raw data files. The “h” and “w” in the raw data file name
 indicate the maximum height and width of the bump. For example, the
 1h1w.dat file name is the result when the bump height is 1 and the width
 is 1. "dl" indicates the peak distance of groove,
 "0.013shear_t" indicates that the background shear flow is 0.013
 and cell is trapped,and “0.014shear_e” indicate that the background shear
 flow is 0.014 and the cell is escaped."base" indicates the base
 case, "hf" indicates the flagellar amplitude, "kf" is
 the flagellar wave number and "lf" indecates the flagellar
 length. "Nobump_NoWall_1fla.dat" is the cell free speed result
 for Figure 2f without wall.“zone_shear_data.txt” is the result file for
 plotting Figure 6a. ##### Variables in the raw data files t:time x:the
 location of cell body center on x-axis direction y:the location of cell
 body center on y-axis direction z:the location of cell body center on
 z-axis direction u:Component of the bacterial velocity vector in the
 x-axis direction v:Component of the bacterial velocity vector in the
 y-axis direction w:Component of the bacterial velocity vector in the
 z-axis direction omgx:Component of the bacterial angular velocity vector
 in the x-axis direction omgy:Component of the bacterial angular velocity
 vector in the y-axis direction omgz:Component of the bacterial angular
 velocity vector in the z-axis direction bvh11:Component of the bacterial
 body orientation vector in the x-axis direction bvh12:Component of the
 bacterial body orientation vector in the y-axis direction bvh13:Component
 of the bacterial body orientation vector in the z-axis direction
 bvf11:Component of the bacterial flagellum orientation vector in the
 x-axis direction bvf12:Component of the bacterial flagellum orientation
 vector in the y-axis direction bvf13:Component of the bacterial flagellum
 orientation vector in the z-axis direction ## Code ### File:
 results\_simulation\gnu\_fig2e.txt **Description:** Gnuplot code for
 drawing figure 2e. ### File: results\_simulation\gnu\_fig2f.txt
 **Description:** Gnuplot code for drawing figure 2f. ### File:
 results\_simulation\gnu\_fig3a.txt **Description:** Gnuplot code for
 drawing figure 3a. ### File: results\_simulation\gnu\_fig3b.txt
 **Description:** Gnuplot code for drawing figure 3b. ### File:
 results\_simulation\gnu\_fig3c.txt **Description:** Gnuplot code for
 drawing figure 3c. ### File: results\_simulation\gnu\_fig3d.txt
 **Description:** Gnuplot code for drawing figure 3d. ### File:
 results\_simulation\gnu\_fig3e.txt **Description:** Gnuplot code for
 drawing figure 3e. ### File: results\_simulation\gnu\_fig3f.txt
 **Description:** Gnuplot code for drawing figure 3f. ### File:
 results\_simulation\gnu\_fig3g.txt **Description:** Gnuplot code for
 drawing figure 3g. ### File: results\_simulation\gnu\_figS2a.txt
 **Description:** Gnuplot code for drawing figure S2a. ### File:
 results\_simulation\gnu\_figS2b.txt **Description:** Gnuplot code for
 drawing figure S2b. ### File: results\_simulation\gnu\_figS2c.txt
 **Description:** Gnuplot code for drawing figure S2c. ### File:
 results\_simulation\gnu\_figS2d.txt **Description:** Gnuplot code for
 drawing figure S2d. ### File: results\_simulation\gnu\_figS2e.txt
 **Description:** Gnuplot code for drawing figure S2e. ### File:
 results\_simulation\gnu\_figS2f.txt **Description:** Gnuplot code for
 drawing figure S2f. ### File: results\_simulation\gnu\_figS2e.txt
 **Description:** Gnuplot code for drawing figure S2e. ### File:
 results\_simulation\gnu\_figS2f.txt **Description:** Gnuplot code for
 drawing figure S2f. ### File: results\_simulation\gnu\_fig5.txt
 **Description:** Gnuplot code for each subplot in Figure 5 and Figure S3.
 ### File: results\_simulation\gnu\_fig6a.txt **Description:** Gnuplot code
 for drawing figure 6a. ### File: results\_simulation\gnu\_fig6b.txt
 **Description:** Gnuplot code for drawing figure 6b. ### File:
 results\_simulation\gnu\_fig6c.txt **Description:** Gnuplot code for
 drawing figure 6c. ### File: results\_simulation\gnu\_fig6d.txt
 **Description:** Gnuplot code for drawing figure 6d. ###
 File:results\_simulation\simulation\_code.txt **Description:** CUDA code
 for GPU computation using the boundary element method, with the main
 program and subroutines separated within a single file and properly
 commented. All computational results are executed on the GPU by this
 program with different parameters.