Co-culture protocols for microbes and organoids

With the arrival of so-called organoids – miniature versions of human organs in a petri dish, the ways in which researchers can model healthy organ function and disease in the lab are rapidly improving. Furthermore, organoids are well-suited to study how bacterial, viral or parasitic pathogens interact with human cells to cause diseases ranging from colorectal cancer to COVID-19. When two or more different organisms, such as organoids and microbes, interact in a dish, this is called a co-culture.

Building organoid co-cultures

Researchers from the group of Hans Clevers developed new approaches to expose organoids to microbes and characterize their interactions in detail. They now share their know-how of co-cultures with the rest of the scientific world in a new publication in Nature Protocols. Together with their colleagues, co-first authors Jens Puschhof and Cayetano Pleguezuelos-Manzano for example describe how to inject microbes into the middle of organoids with miniscule needles, which is an important step in growing co-cultures.

They also illustrate how advanced microscope techniques and other assays can be used to profile the transcriptional and mutagenic effects of pathogens using organoids, which has already delivered groundbreaking studies. Additionally, the researchers discuss expected behaviors of bacterial co-cultures and common issues in the process of establishing and characterizing them, and provide troubleshooting guidance.

New research avenues

The presented protocols to grow human miniature organs and expose them to defined microbes open up various possibilities for further research. For example, microbial communities of ever-increasing complexity can be assembled and co-cultured with human organoids. Furthermore, including immune cells or fibroblasts in microbial organoid co-cultures represents a promising strategy for gaining stepwise understanding of the cancer microenvironment.

Publication

Intestinal organoid co-cultures with microbes. Puschhof J*, Pleguezuelos-Manzano C*, Martinez-Silgado A, Akkerman N, Saftien A, Boot C, de Waal A, Beumer J, Dutta D, Heo I, Clevers H. Nature Protocols, 2021. doi: 10.1038/s41596-021-00589-z