Engineering Biomimetic Intestinal Models to Investigate Host-Microbiome Interactions

Biomimetic in vitro models of organ systems can help elucidate complex biomedical processes and structure-function relationships. For example, the human gut is home to a diverse range of cells which enable the gut to carry out its physiological functions. The gut’s function is further enhanced by a diverse and largely uncharacterized microbiome. Currently, there are few systems which have been developed to study the interactions between human tissue and the microbiome. Further, these existing models like organ-on-chips and organoids are limited due to their lack of cell-type diversity and incorrect spatial configuration. In this project, a new biomimetic system which captures the colonic-crypt micro-architecture, the diverse epithelial cell types, and provides easily accessible luminal and basal compartments is used. With these features, the obtained system can be used to investigate colon development by applying precisely controlled gradients of chemical signals and morphogens that replicate in vivo development. In addition, this system provides an avenue for mimicking the behavior of the intestinal epithelia-microbiome interface by allowing anaerobic co-cultures of bacteria that inhabit the gut. This presentation will describe investigations with the bacteria Candidatus Cibiobacter qucibialis (the most common uncharacterized gut microbe) and discuss the optimization of co-culture conditions, including length of co-culture, bacterial growth behavior, and optimal seeding density. The effect of the bacteria on the gut epithelia is characterized using bulk RNA sequencing to determine differential gene expression between gut tissue with and without the bacterial co-culture.