Biofilm Shape vs. Flow in Paper Channels

ISEF Category: Microbiology

Subcategory: Bacteriology  ·  Difficulty: Intermediate  ·  Setup: School Lab  ·  Time: 1 to 2 Months

The Hook

Biofilms are not just slime. They are tiny cities that change shape when water moves past them. If the flow changes, the cells may change their building plan. That gives you a real way to test how physics can steer biology.

What Is It?

A biofilm is a group of microbes that stick together and build a shared matrix, which is a sticky protective layer. Think of it like a neighborhood built from glue, not bricks. Some biofilms stay smooth and flat. Others grow wrinkled, ridged, or folded.

In this project, you test whether flow helps decide which form wins. A narrow channel creates stronger shear, which is the sideways force from moving fluid. A wider channel usually creates gentler flow. If B. subtilis makes different colony shapes in those spaces, you can connect the physical environment to microbial architecture.

The paper-fluidic device works like a simple maze for liquid. You use different channel widths to create different flow conditions, then compare how the colonies look over time. The Lattice-Boltzmann simulation helps you estimate the shear pattern before or alongside the experiment, so your biology results have a physics layer too.

Why This Is a Good Topic

This is a strong science fair topic because you can test one clear variable, flow width, and measure a visible outcome, colony architecture. You also connect microbiology, fluid dynamics, and pattern formation, which gives the project depth without needing a giant lab setup. A student can learn how to design controls, compare images over time, and turn visual changes into data. That makes the project both doable and research-like.

Research Questions

• How does channel width affect the balance between wrinkled and smooth B. subtilis colony morphology?
• What is the effect of shear gradient on the rate of biofilm expansion in paper-fluidic channels?
• Does the position in the channel, center versus edge, change the likelihood of wrinkled architecture?
• To what extent does flow direction influence biofilm thickness and surface texture?
• Which channel width produces the strongest change in colony roughness over days 1, 3, and 5?
• What is the effect of simulated shear stress on predicted biofilm patterning in a Lattice-Boltzmann model?

Basic Materials

• Paper-fluidic device materials such as chromatography paper, tape, and a cutter for channel shapes.
• Sterile Petri dishes or sealed growth chambers.
• Nonpathogenic B. subtilis culture from an approved school source.
• Basic growth medium appropriate for the strain and school rules.
• Micropipettes or disposable transfer tools.
• Digital camera or phone with a tripod or fixed stand.
• Ruler or printed scale for image calibration.
• Permanent marker for labeling channels and time points.
• Gloves, lab coat, and disinfectant approved by your lab.

Advanced Materials

• Access to a controlled incubator.
• Fluorescence or stereo microscope for surface texture imaging.
• Confocal microscope for 3D biofilm structure, if available.
• Image analysis targets or calibration slide.
• Flow meter or pressure control setup for validating channel conditions.
• Computer with Python and scientific libraries.
• Simulation software or code for Lattice-Boltzmann modeling.
• Statistical analysis software for mixed-effects or multivariate comparisons.

Software & Tools

• ImageJ: Measures colony area, texture, and roughness from time-lapse images.
• Python: Processes images, runs statistics, and plots morphology versus channel width.
• Fiji: Extends ImageJ with plugins for thresholding, segmentation, and texture analysis.
• COMSOL Multiphysics: Models fluid flow if your school or lab has access to a license.
• OpenLB: Runs Lattice-Boltzmann flow simulations for channel geometry comparisons.

Experiment Steps

1. Define the one geometry variable you will change, then keep every other design feature fixed.
2. Map how each channel width should change local shear before you grow any colonies.
3. Choose image features that represent architecture, such as area, edge roughness, wrinkle count, or texture score.
4. Plan controls that separate flow effects from paper wetness, inoculum size, and nutrient spread.
5. Build an analysis plan that compares days 1, 3, and 5 across the same channel locations.
6. Decide how you will match the simulation output to the biological measurements so the two datasets speak to each other.

Common Pitfalls

• Letting the paper dry unevenly, which creates fake differences in growth that look like flow effects.
• Comparing channels with different inoculum spread, which makes the starting point different before the experiment begins.
• Using photos from changing light or angle, which breaks image-based shape measurements across days.
• Treating every wrinkled colony as the same, which hides size, edge, and texture differences that matter.
• Ignoring edge effects near channel walls, which can make the center and border populations look misleadingly different.

What Makes This Competitive

A stronger version of this project goes beyond simple before-and-after photos. You could quantify texture with image features, compare several channel geometries, and test whether simulation predicts the same trend you see in the biofilm. Strong controls matter too, especially if you separate flow from paper chemistry, moisture, and starting cell density. If your analysis can link shear gradient to a measurable shift in architecture, the project feels much deeper than a pretty growth pattern.

Project Variations

• Use a different safe strain or environmental isolate to compare whether flow sensitivity changes across Bacillus-like colonies.
• Swap paper channels for a thin agar microchannel setup and test whether the same shear pattern still changes morphology.
• Focus on image analytics by comparing texture metrics, edge fractal score, or wrinkle density instead of only colony area.

Learn More

• PubMed: Search for review articles on biofilm formation, Bacillus subtilis colony morphogenesis, and shear stress responses.
• NIH NCBI Bookshelf: Find free background chapters on microbial growth, biofilms, and laboratory methods.
• Annual Review of Microbiology: Read review articles on biofilm structure, regulation, and surface sensing through your school or library access.
• MIT OpenCourseWare: Look for fluid mechanics and transport lessons that help you understand shear and channel flow.
• NOAA National Ocean Service Education: Use basic flow and fluid behavior resources to build intuition for water movement in channels.