Organoids pp 183-194 | Cite as

Intestinal Organoids as a Novel Tool to Study Microbes–Epithelium Interactions

  • Giulia NigroEmail author
  • Melissa Hanson
  • Cindy Fevre
  • Marc Lecuit
  • Philippe J. Sansonetti
Part of the Methods in Molecular Biology book series (MIMB, volume 1576)


The gut, particularly the colon, is the host of approximately 1000 bacterial species, the so-called gut microbiota. The relationship between the gut microbiota and the host is symbiotic and mutualistic, influencing many aspects of the biology of the host. This homeostatic balance can be disrupted by enteric pathogens, such as Shigella flexneri or Listeria monocytogenes, which are able to invade the epithelial layer and consequently subvert physiological functions. To study the host–microbe interactions in vitro, the crypt culture model, known as intestinal organoids, is a powerful tool. Intestinal organoids provide a model in which to examine the response of the epithelium, particularly the response of intestinal stem cells, to the presence of bacteria. Furthermore, the organoid model enables the study of pathogens during the early steps of enteric pathogen invasion.

Here, we describe methods that we have established to study the cellular microbiology of symbiosis between the gut microbiota and host intestinal surface and secondly the disruption of host homeostasis due to an enteric pathogen.


Intestinal organoids Host–microbe interactions Listeria monocytogenes Bacterial products Flow cytometry Microinjection 


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© Springer Science+Business Media New York 2016

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Authors and Affiliations

  • Giulia Nigro
    • 1
    Email author
  • Melissa Hanson
    • 2
  • Cindy Fevre
    • 2
  • Marc Lecuit
    • 2
  • Philippe J. Sansonetti
    • 1
  1. 1.Molecular Microbial Pathogenesis Unit, Inserm U1202Institut PasteurParisFrance
  2. 2.Biology of Infection Unit, Inserm U1117Institut PasteurParisFrance

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