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Updated: May 3, 2026

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Innovative engineering approaches to model host-microbiome interactions in vitro.

Karen M Mancera Azamar1, Samanvitha Deepthi Sudi1, Zahra Mohammadalizadeh1

  • 1J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL, United States.

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Summary

Engineered in vitro models are advancing microbiome research by integrating human cells and microbes. These platforms offer better control and human relevance for developing targeted microbiome therapies.

Keywords:
BiomaterialsHuman-microbiome interactionsIn vitro modelsMicrobiomeMicrophysiological systemsOrgan-on-chipTissue engineering

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Area of Science:

  • Microbiome research
  • Bioengineering
  • Translational medicine

Background:

  • The human microbiome is crucial for health and disease, with disruptions linked to various pathologies.
  • Targeted microbiome interventions require advanced experimental models to study host-microbe interactions.
  • Existing models have limitations in replicating the complexity of host-microbiome dynamics.

Purpose of the Study:

  • To review emerging engineering approaches for in vitro platforms modeling host-microbiome interactions.
  • To identify challenges and innovative solutions in developing these advanced models.
  • To highlight the potential of these models for microbiome research and therapeutic development.

Main Methods:

  • Scoping review of engineering approaches for in vitro host-microbiome models.
  • Focus on microfluidics, biomaterials, and organoid technologies.
  • Analysis of systems integrating host and microbial components.

Main Results:

  • Advanced microphysiological systems offer improved experimental control, human-specific biology, and reduced costs/ethical concerns.
  • Developed co-culture systems replicate key host-microbiome interface features (e.g., mucosal barriers, gradients).
  • These models provide new insights into epithelial-microbiota crosstalk, immune modulation, and systemic effects.

Conclusions:

  • Engineered in vitro models are crucial for understanding complex host-microbiome interactions.
  • These platforms accelerate the translation of microbiome science into clinical practice.
  • Future opportunities lie in scaling and increasing the complexity and clinical relevance of these models.