Hydrodynamic confinement of bacteria within intestinal folds
Data files
Apr 04, 2025 version files 122.72 MB
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README.md
9.61 KB
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results_code_RSPB-2024-3068.zip
122.71 MB
Abstract
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.
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.