Design and Fabrication of a Compartmentalized 3D Printed Device to Study Microbial Interactions

Overview

The human gut microbiome is made up of many different microbial species that live together and influence our health in both positive and negative ways. However, we still don't fully understand how these microbes interact with one another—some may support each other’s growth, while others may compete or interfere. Thanks to recent breakthroughs by the QUT Centre for Microbiome Research and the Australian Human Microbiome Biobank, researchers can now grow individual microbes from the human gut in the lab.

To study how these microbes interact, there is a need for custom-engineered devices that can grow each microbial strain separately, while still allowing them to communicate through the diffusion of molecules like metabolites and proteins. This project aims to design and build a multiplexed 3D printed co-culture device that meets this need.

The key innovation lies in using 3D printing to create semi-permeable membranes directly within the device. Instead of assembling membranes by hand (which is slow and labor-intensive), this method uses a 3D printed rigid lattice to suspend a soft hydrogel using surface tension forces. This creates a membrane-like interface that allows small molecules to pass through while keeping microbial cultures physically separated.

Research engagement

• To design a 3D printed culture device with multiple compartments for co-culturing gut microbes.
• To develop a membrane interface using a lattice-suspended hydrogel without manual assembly.
• To test how well different designs allow diffusion of molecules similar to those secreted by microbes.

Research activities

• Design and model co-culture devices with different lattice geometries suitable for hydrogel suspension.
• 3D print and prototype the devices using lab-scale printers and assess the printing resolution and structural fidelity.
• Characterize diffusion across the hydrogel membrane using molecules of various sizes (e.g., dyes or model proteins) to simulate microbial signaling.
• Collaborate with microbiome researchers at QUT to refine the device for real-world microbial culture applications.

Research skills

• 3D design and printing — use computer-aided design (CAD) software to model a multi-chamber device, then bring it to life using a 3D printer and assess the quality of the printed parts.
• Experimental planning and data analysis — plan experiments carefully, collect reliable data, and use basic statistical methods to draw conclusions and improve the device design.
• Build-test-improve cycle — experience the real-world engineering process of designing a prototype, identifying what works and what doesn't, and making improvements based on evidence.
• Teamwork in a research setting — collaborate with scientists from a different field (microbiology) to understand what the device needs to do and how to meet those requirements.
• Reading and using scientific literature — search for and read relevant research papers to understand how similar devices have been built and tested, and apply those ideas to the project.

Outcomes

• Practical experience in 3D design and additive manufacturing.
• Understanding of microbiome engineering and microbial co-culture systems.
• Skills in experimental design, prototyping, and quantitative analysis of diffusion and permeability.
• Exposure to interdisciplinary collaboration with microbiology researchers.

Skills and experience

No specific prior experience in microbiology or bioprinting is required. The ideal candidate will have:

• Essential: Experience with CAD software (e.g., Fusion 360, SolidWorks, FreeCAD, or equivalent) and an interest in fabrication or prototyping.
• Personal attributes: Curiosity, attention to detail, and willingness to work iteratively on a design-build-test cycle in a collaborative research environment.

Start date

2 November, 2026

End date

19 February, 2027

Location

Block Q, Kelvin Grove campus,

Keywords

• 3D printing

Contact

Prof. Yi-Chin Toh

0731386170

yichin.toh@qut.edu.au