Innovative engineering approaches to model host-microbiome interactions in vitro

Abstract

The human microbiome plays a critical role in health and disease. Disruptions in microbiota composition or function have been implicated not only as markers but also as drivers of diverse pathologies, creating opportunities for targeted microbiome interventions. Advancing these therapies requires experimental models that can unravel the complex, bidirectional interactions between human tissue and microbial communities. This scoping review examines emerging engineering approaches to design in vitro platforms that successfully integrate host and microbial components to model these interactions. Compared to traditional in vitro and in vivo approaches, these advanced microphysiological systems offer greater experimental control, human-specific biology, and reduced cost and ethical concerns. Here, we identify key challenges in the creation of these in vitro models and innovative solutions to address them by leveraging microfluidics, biomaterials, and organoid technologies, among others. These strategies have enabled the development of co-culture systems that replicate critical features of host-microbiome interfaces, including mucosal barriers, oxygen and pH gradients, mechanical stimuli, and host cell diversity. We also describe how these physiologically relevant models are uncovering new insights into epithelial-microbiota crosstalk, immune modulation by commensal microbes, and systemic effects of microbiota and their metabolites across multiple body sites. We conclude by discussing opportunities to expand these systems in scale, complexity, and clinical relevance. As these models continue to evolve, they hold the potential to transform our ability to mechanistically probe microbiome interactions, personalize therapeutic strategies, and accelerate the translation of microbiome science into clinical practice.