Organoids and organs-on-chips: Insights into human gut-microbe interactions

Jens Puschhof, Cayetano Pleguezuelos-Manzano, Hans Clevers

Research output: Contribution to journal/periodicalBook/Film/Article reviewScientific


The important and diverse roles of the gut microbiota in human health and disease are increasingly recognized. The difficulty of inferring causation from metagenomic microbiome sequencing studies and from mouse-human interspecies differences has prompted the development of sophisticated in vitro models of human gut-microbe interactions. Here, we review recent advances in the co-culture of microbes with intestinal and colonic epithelia, comparing the rapidly developing fields of organoids and organs-on-chips with other standard models. We describe how specific individual processes by which microbes and epithelia interact can be recapitulated in vitro. Using examples of bacterial, viral, and parasitic infections, we highlight the advantages of each culture model and discuss current trends and future possibilities to build more complex co-cultures.

Original languageEnglish
Pages (from-to)867-878
Number of pages12
JournalCell Host & Microbe
Issue number6
Publication statusPublished - 09 Jun 2021


  • Animal Testing Alternatives
  • Animals
  • Coculture Techniques/methods
  • Gastrointestinal Microbiome
  • Host Microbial Interactions
  • Humans
  • Intestinal Mucosa
  • Mice
  • Microbial Interactions
  • Microchip Analytical Procedures/methods
  • Microfluidics/methods
  • Models, Animal
  • Organoids/microbiology
  • Precision Medicine/methods


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