Using Organ-on-a-Chip Models To Study the Microbiome in Motion

As recognition of the microbiome's role in health and disease continues to grow, attention is shifting from identifying which microbes are present in an individual's microbiome to understanding how these microbes reshape host biology.

“To understand health and disease, we must understand how microbial species compete for nutrients, exchange metabolites, communicate using signaling molecules, and even use the other species to survive,” said Dr. Amin Valiei, senior lecturer and principal investigator at Monash University, where he leads the Microbial Communities for Health and Sustainability research group.

Microfluidic organ-on-a-chip systems have emerged as a powerful approach for studying the microbiome’s role in disease. The technology is capable of recreating key features of the gut, such as dynamic fluid flow, peristalsis-like motions, circulating immune cells, and microbial co-cultures.

These systems offer a way to study human gut biology in motion, providing insights into conditions including inflammatory bowel disease (IBD) and cancer.

Modeling the gut

Standard models used in research, such as conventional 2D cultures, often struggle to capture the complexity of gut biology, which contains multiple interacting components shaped by physical and chemical forces. Animal models also struggle as they have limited human relevance. Organoids, while human-derived, are limited in their ability to incorporate physiological gut dynamics, and they do not permit analysis of many key features of intestinal function.

“With organoids you can't look at things like fibrosis because you don't have the stromal cells. You can't easily examine immune cell interactions. You don't have an absorptive barrier or a transport barrier, mucus accumulation, the microbiome, all of which are important for studying disease,” Prof. Donald E. Ingber, founding director of the Wyss Institute for Biologically Inspired Engineering at Harvard University, told Technology Networks.

Organ-on-a-chip technologies provide an environment that enables more precise control of biological and physical properties. Depending on the system, these devices can be used to simulate continuous perfusion, physiologically relevant shear stress and peristalsis-like motions, mucus and oxygen gradients, epithelial barriers, and co-culture with immune and microbial cells. This enables the real-time observation of host–microbe and microbe–microbe interactions.

Ingber and colleagues have shown the ability of intestine-on-a-chip systems to maintain extended co-culture of living human intestinal epithelium with stable communities of aerobic and anaerobic human gut microbiota. “We've cultured them for at least 5 days in the intestine chip, and we get over 200 different types of microbial species and strains,” Ingber said.

Many gut microbes require low-oxygen or anaerobic environments, whereas human intestinal cells require oxygen and nutrients. This creates a central challenge for host-microbiome modeling. “That's a major advantage of organ-on-a-chip systems over organoids. Organoids, you have to inject the microbiome into the lumen of a little ball of cells, and about 24 hours later they die. However, because we maintain flow in organ-on-a-chip systems and create hypoxia gradients, it is possible to maintain viability of both the microbiome and the human tissues,” explained Ingber.

Controlled oxygen gradients facilitate the maintenance of aerobic and anaerobic populations alongside living epithelium. This enables the study of healthy vs dysbiotic communities and their effects on epithelial barrier function and inflammation.

Studying inflammatory bowel disease—on a chip

Ingber and colleagues have been using organ-on-a-chip systems to advance IBD research.

IBD affects an estimated 3.8 million people, many of whom cannot be effectively treated. The lack of effective treatment options is mirrored by the absence of human in vitro models that capture the disease's complex features.

To overcome this, Ingber and colleagues collected IBD and healthy tissue biopsies from patients’ colons to create donor-specific organ-on-a-chip models of the colon that replicate major hallmarks of IBD in vitro. They discovered that stromal fibroblasts—cells within the supporting connective tissue of the intestinal epithelial lining—and mechanical forces associated with peristaltic motions are drivers of IBD progression.

“This is very important because most drugs for IBD target immune cells and epithelial cells,” said Ingber. “This poses the question as to whether it would be possible to design drugs that target the stroma instead.”

One of the possibilities created by these IBD-on-a-chip systems is the ability to study human cancer initiation in vitro. IBD patients are at higher risk of developing cancer, though the changes in intestinal cells that drive the earliest stages of this transition are still a mystery.

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“Using these organ chips, we could mimic the early stages of carcinogenesis and show that with the same carcinogen, chips from patients with IBD have increased propensity to initiate cancer formation, as indicated by expression of early-stage colorectal cancer markers, as well as chromosome duplications and gene mutations,” Ingber stated. “We also observed that IBD fibroblasts helped to promote this transition. This opens up the possibility to use these chips for mechanistic analysis.”

Although the gut microbiome wasn’t utilized in the study, living gut microbes can be co-cultured in these intestine chips. Therefore, this experimental system could be used to study how gut microbes contribute to the development of the IBD phenotype in the future.

The importance of considering biologically meaningful variation

Another key advantage of organ-on-a-chip systems is the ability to utilize donor-derived cells to capture patient variation.

“Patient-derived epithelial cells, organoids, and microbiota should be used more frequently to study inter-individual heterogeneity rather than simply averaging it out.” — Dr. Amin Valiei.

Ingber and colleagues' work with IBD highlights the importance of considering variables such as sex in research. IBD symptoms are often exacerbated in women, particularly during pregnancy. By introducing a cocktail of pregnancy-associated hormones to female-derived chips, the researchers showed that these hormones enhanced inflammation and dramatically increased fibrosis. This effect was observed in the IBD chips but not the healthy chips.

Capturing biological variation is not only important for insight into the disease, but could also provide enormous value for clinical trial design. Patient-derived microbiota and cells could help identify subgroups more likely to respond to particular therapies.

Complementing organ-on-a-chip with in silico models

Computational models can help complement organ-on-a-chip research.

Organ-on-a-chip platforms can be used to generate high-quality experimental data in microbiome research. The computational models can then analyze this data to help explain mechanisms that are difficult to observe directly and predict how microbial communities might respond to new conditions or therapies. These predictions can be tested experimentally, providing a continuous cycle between modelling and experiment.

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Valiei used the analogy of driving with a GPS to explain the importance of this iterative feedback loop: “The real road trip is the microfluidic experiment, which gives insight into what happens under controlled conditions. The computational model is the GPS, on the other hand, analyzing the route, predicting traffic, and suggesting alternative paths. But if the GPS is working with inaccurate information, it will make wrong predictions.”

“Thus, the reliability of computational models depends on the experimental data utilized for their construction and validation,” he continued.

Towards a more systems-level understanding of disease

By using patient-derived microfluidic organ-on-a-chip models, computer modeling, and multiomics approaches, it's possible to start to build a picture of how one component of a complex system like the microbiome can affect several others. This can give a more realistic picture of how diseases start, progress, and respond to treatment.

“Advanced modeling approaches are helping researchers to understand this ‘microbial orchestra’ played by microbes by considering the whole system, rather than studying each component in isolation.” — Dr. Amin Valiei.

To fully realize the potential of organ-on-a-chip systems for microbiome research, several limitations will need to be overcome.

So far, no chip can fully replicate the full diversity, scale, and long-term flexibility of the human gut. “Challenges include maintaining complex anaerobic communities, choosing physiologically relevant media, incorporating patient-derived cells and mucus, modeling immune, neural, and vascular interactions, preventing drug absorption by the materials, and obtaining reproducible sampling without disturbing the system,” stated Valiei.

Harmonization of chip design and experimental procedures is key to enabling inter-laboratory comparisons, which is often complicated by variations in shape, cell origin, flow, and analytical outcomes between chips. “There is a requirement for common reference materials, reporting standards, and benchmark datasets to allow comparison between laboratories and to ensure the precision, accuracy, and reproducibility of the outcome,” Valiei explained.

The gut’s complexity may never be reducible to a single model, but that is precisely why microfluidic systems are becoming so important. They allow researchers to build complexity deliberately, observe it in real time, and test how one part of the system reshapes the rest.

“In the future, I believe the integration of microfluidics, computational modelling, multiomics, and artificial intelligence will expand our understanding of microbial populations and accelerate the development of better microbiome-based medicines,” concluded Valiei.