Hydrogel-based experimental models of the gastrointestinal tract

Microbiome (2025) 13:233 Sieders et al. Microbiome https://doi.org/10.1186/s40168-025-02208-5 Open Access REVIEW Hydrogel‑based experimental models of the gastrointestinal tract Mink Sieders1, Pieter Candry2 and Sahar El Aidy1,3* Abstract The gut microbiome plays a pivotal role in human health, yet its complexity has long eluded detailed study under physiologically relevant conditions. Hydrogel-based models are revolutionizing microbiome research by bridging the gap between traditional in vitro systems and the complexity of in vivo environments. These advanced systems replicate key physical and biochemical features of the gastrointestinal tract, offering unprecedented opportunities to study microbial behavior, adaptation, and interactions within three-dimensional, tunable architectures. Unlike suspension cultures, hydrogels provide porous, mucosa-like environments that enable the cultivation of mucosa-associated microbes, co-culturing with human cells, and mimicking healthy and disease-related states. This review explores the transformative potential of hydrogel matrices in unveiling the spatial organization, nutrient gradients, and community communication that define microbial ecosystems. By integrating the benefits of in vitro and in vivo models, hydrogel-based platforms promise to accelerate discoveries in microbiome science, with far-reaching implications for understanding human health and developing targeted therapeutics. Keywords Gut microbiome, Hydrogel, Microbial dynamics, Microbial ecology, 3D culture systems Introduction The gut microbiome exists within a highly dynamic and complex environment. Key factors such as fluctuating pH levels, fluid dynamics, nutrient availability, and intermicrobial interactions collectively shape the diverse ecosystems within the gastrointestinal (GI) tract [1, 2]. These parameters can shift significantly in disease conditions, challenging microbial stability and requiring adaptive strategies from resident microbes. Despite growing interest in the microbiome’s role in health and disease, our understanding of the native biophysical and biochemical *Correspondence: Sahar El Aidy 1 Department of Microbiome Engineering, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, Amsterdam, The Netherlands 2 Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands 3 Amsterdam Microbiome Expert Centre, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, Amsterdam, The Netherlands environments that shape microbial function remains limited. Meta-omics approaches, such as genomics, transcriptomics, and metabolomics, have significantly advanced our understanding of microbial composition and potential function. However, these methods typically overlook the local microenvironments in which microbes reside, including key gradients and mechanical constraints. This omission risks missing key insights into microbial physiology, community dynamics, and disease mechanisms. A growing body of evidence links alterations in the gut microbiome to various diseases, including, among many others, Parkinson’s disease, inflammatory bowel disease, and multiple sclerosis [3–7]. Notably, Parkinson’s disease has been associated with an increased abundance of mucosa-associated bacteria, such as Akkermansia muciniphila, which may interact with host pathways to influence disease progression [3, 8]. However, the behavior of these bacteria within their native environment remains underexplored. © The Author(s) 2025. 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To view a copy of this licence, visit http://creativecommons.org/licenses/by-nc-nd/4.0/. Sieders et al. Microbiome (2025) 13:233 Page 2 of 27 Fig. 1 Hydrogel-based models bridge the gap between in vitro systems and complex GI environments. This schematic compares two features of traditional suspension cultures (right), physiological GI environments (left), and hydrogel-based in vitro models (center). General characteristics of each system are summarized at the bottom, indicating whether features are captured in the respective in vitro approaches. GI = gastrointestinal Created in BioRender. Sieders, M. (2025) https://BioRender.com/5e0872x Microbial interactions with their surrounding environment, particularly in terms of spatial organization, metabolism, and physiology, differ substantially when observed in vitro versus in vivo [9–15]. Localized gradients in pH, oxygen, and nutrients create highly structured niches that strongly influence microbial behavior and evolution [16–20]. Replicating these microenvironments in experimental systems remains a key challenge for microbiome science. This recognition has driven growing interest in hydrogel-based models designed to mimic aspects of the gut biochemical and physical landscape [21, 22]. Hydrogels, cross-linked polymeric networks of polymer compounds that retain water as their primary phase, offer tunable properties such as porosity, swelling behavior, mechanical strength, and surface chemistry [23]. These characteristics have made hydrogel-based scaffolds indispensable in fieldsranging from tissue engineering and drug delivery [24–27] to biosensing [28, 29] and microbiota modulation [30, 31]. Crucially, hydrogels provide a controlled, customizable medium for microbial culture under physiologically relevant conditions. They enable spatial structuring, co-culture, diffusion gradients, and, in some cases, long-term microbial growth. While they cannot yet fully replicate the compositional and rheological complexity of the GI tract, an ongoing challenge for the field, their modularity and biocompatibility make them powerful tools for interrogating microbial adaptation and interaction in defined contexts, bridging the gap between in vitro and in vivo (Fig. 1). This review focuses on hydrogel-based systems designed to study gut-associated microbes in contexts Sieders et al. Microbiome (2025) 13:233 that approximate their native environment. While we highlight (...truncated)