Modeling infectious diseases and host-microbe interactions in gastrointestinal organoids

Dev Biol. 2016 Dec 15;420(2):262-270. doi: 10.1016/j.ydbio.2016.09.014. Epub 2016 Sep 14.


Advances in stem cell research have allowed the development of 3-dimensional (3D) primary cell cultures termed organoid cultures, as they closely mimic the in vivo organization of different cell lineages. Bridging the gap between 2-dimensional (2D) monotypic cancer cell lines and whole organisms, organoids are now widely applied to model development and disease. Organoids hold immense promise for addressing novel questions in host-microbe interactions, infectious diseases and the resulting inflammatory conditions. Researchers have started to use organoids for modeling infection with pathogens, such as Helicobacter pylori or Salmonella enteritica, gut-microbiota interactions and inflammatory bowel disease. Future studies will broaden the spectrum of microbes used and continue to establish organoids as a standard model for human host-microbial interactions. Moreover, they will increasingly exploit the unique advantages of organoids, for example to address patient-specific responses to microbes.

Keywords: Gastrointestinal disease; Helicobacter; Inflammatory bowel disease; Microbiota; Norovirus; Organoid culture; Rotavirus; Salmonella.

Publication types

  • Review

MeSH terms

  • Animals
  • Gastrointestinal Diseases / microbiology
  • Gastrointestinal Microbiome*
  • Gastrointestinal Tract / growth & development
  • Gastrointestinal Tract / microbiology*
  • Gastrointestinal Tract / physiology
  • Helicobacter pylori / pathogenicity
  • Host-Pathogen Interactions* / physiology
  • Humans
  • Inflammatory Bowel Diseases / microbiology
  • Models, Biological
  • Organ Culture Techniques
  • Organoids / growth & development
  • Organoids / microbiology*
  • Organoids / physiology
  • Receptors, Pattern Recognition / physiology
  • Tissue Engineering


  • Receptors, Pattern Recognition