Microbiome/ Host Interactions


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Our laboratory has several research projects and tools in order to examine the interactions of the host with the gut microbiome in health and disease

Microbiome and Virome

This branch of research  in the laboratory focuses on microbiome community structure and function in health and disease. We also study the bacteriophage that comprise the Virome have also been shown to significantly impact digestive health and may provide novel routes of interfacing and manipulating with the microbiome for health benefit.


Due to the complex nature of the interactions and pathways studied in the Chang lab using the most novel and advanced laboratory techniques available, it is necessary to invoke the most advanced statistical techniques. Our team engages is constantly training in the latest statistical methodology available in order to correlate variation in host and microbiome gene composition and expression and with any number of other response variables to enable description and discovery of the relationships that underlie human digestive health.

Epigenetics in Colon Cancer and IBD

Recent work has revealed how important epigentics can be in regulating gene expression and moreover, in overall health. Epigenetic variation has been implicated in inter-generational effects that control for obesity and cancer. Recent advances in cutting edge technology have allowed us to sequence the epigenome and elucidate its relationship to various health parameters.


Inflammatory Bowel Disease (IBD) is of global concern as western diets are adopted by much of the world. Pouchitis occurs when a J-pouch, a surgically adapted small intestine anastomotized to function as a rectum for patients who have undergone a colectomy, becomes inflamed as in colitis. In this research project, patients act as their own control as we longitudinally sample patients to analyze tissue-specific gene expression and associated changes in the microbiome with the goal of identifying triggers and preventative measures for IBD.

Gnotobiotic facility

The University of Chicago has a facility in which mice of many different genetic backgrounds are derived as germ-free, having no microbes on or inside of them. These gnotobiotic mice serve as research models that are key in identifying the genes responsible for so many of our disease predispositions and, more importantly, the mechanisms responsible so that we find ways to interfere with progression.