Review articleModeling infectious diseases and host-microbe interactions in gastrointestinal organoids

•Organoids are now used widely to study infection biology, interaction with the microbiota and associated diseases such as IBD.•Organoids contain differentiated host cells crucial for interaction with microorganisms.•Organoids provide host cells for microorganisms which were previously difficult to culture.•Simplified 2D layers and engineered tissues complete the spectrum of new model systems.

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.