Modeling host-pathogen interactions in the context of the microenvironment: Three-dimensional cell culture comes of age

Jennifer Barrila, Aurélie Crabbé, Jiseon Yang, Karla Franco, Seth D. Nydam, Rebecca J. Forsyth, Richard R. Davis, Sandhya Gangaraju, C. Mark Ott, Carolyn B. Coyne, Mina J. Bissell, Cheryl Nickerson

Research output: Contribution to journalArticlepeer-review

95 Scopus citations


Tissues and organs provide the structural and biochemical landscapes upon which microbial pathogens and commensals function to regulate health and disease. While flat two-dimensional (2-D) monolayers composed of a single cell type have provided important insight into understanding host-pathogen interactions and infectious disease mechanisms, these reductionist models lack many essential features present in the native host microenvironment that are known to regulate infection, including three-dimensional (3-D) architecture, multicellular complexity, commensal microbiota, gas exchange and nutrient gradients, and physiologically relevant biomechanical forces (e.g., fluid shear, stretch, compression). A major challenge in tissue engineering for infectious disease research is recreating this dynamic 3-D microenvironment (biological, chemical, and physical/mechanical) to more accurately model the initiation and progression of host-pathogen interactions in the laboratory. Here we review selected 3-D models of human intestinal mucosa, which represent a major portal of entry for infectious pathogens and an important niche for commensal microbiota. We highlight seminal studies that have used these models to interrogate host-pathogen interactions and infectious disease mechanisms, and we present this literature in the appropriate historical context. Models discussed include 3-D organotypic cultures engineered in the rotating wall vessel (RWV) bioreactor, extracellular matrix (ECM)-embedded/organoid models, and organ-on-a-chip (OAC) models. Collectively, these technologies provide a more physiologically relevant and predictive framework for investigating infectious disease mechanisms and antimicrobial therapies at the intersection of the host, microbe, and their local microenvironments.

Original languageEnglish (US)
Article numbere00282-18
JournalInfection and immunity
Issue number11
StatePublished - Nov 1 2018


  • 3-D
  • 3D
  • Gut-on-a-chip
  • Host-microbe interaction
  • Host-pathogen interactions
  • Mechanotransduction
  • Organ-on-a-chip
  • Organoid
  • RWV
  • Rotating wall vessel

ASJC Scopus subject areas

  • Parasitology
  • Microbiology
  • Immunology
  • Infectious Diseases


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