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Hydrogel-based experimental models of the gastrointestinal tract
Mink Sieders1, Pieter Candry2, Sahar El Aidy3,4
1Department of Microbiome Engineering, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, Amsterdam, The Netherlands.
Microbiome
|November 13, 2025
Summary
Hydrogel models offer advanced 3D environments to study the complex gut microbiome, mimicking the gastrointestinal tract for deeper insights into microbial interactions and human health.
Area of Science:
- Microbiome research
- Biomaterials science
- Gastrointestinal physiology
Background:
- The gut microbiome is crucial for human health but difficult to study in detail.
- Traditional in vitro models lack the complexity of the in vivo environment.
- Hydrogel-based models bridge this gap by mimicking physiological conditions.
Purpose of the Study:
- To review the transformative potential of hydrogel matrices in microbiome research.
- To highlight how hydrogels enable the study of microbial behavior and interactions.
- To discuss implications for understanding human health and developing therapeutics.
Main Methods:
- Utilizing hydrogel matrices to create 3D, tunable architectures.
- Replicating key physical and biochemical features of the gastrointestinal tract.
- Enabling cultivation of mucosa-associated microbes and co-culturing with human cells.
Main Results:
- Hydrogels provide porous, mucosa-like environments for microbial study.
- These models allow investigation of spatial organization, nutrient gradients, and communication.
- Hydrogel platforms integrate benefits of in vitro and in vivo models.
Conclusions:
- Hydrogel-based models revolutionize microbiome research by providing physiologically relevant environments.
- They accelerate discoveries in microbial ecosystems and their role in health.
- This approach holds significant promise for developing targeted microbiome therapeutics.

