The Microbiome

We are developing the next-generation of software tools, experimental technologies, and animal models to deepen our understanding of the role of microbiota in human health.

The microbes that live in and on our bodies––known as our microbiota––affect our health in many ways. Our microbiota mostly influence our intestines, where they are so abundant that they create one of the densest ecosystems on the planet. Our intestines harbor a few hundred species of bacteria. These species remain stably colonized in our intestines for much of our adult lives.

Our goal is to set the stage for a new type of medicine that looks at both our human genomes and the genomes of our microbes. Just as chemotherapy is more effective when it is targeted to a patient's unique cancer, future treatments will be tailored to our personal microbiome––meaning, the right microbes (i.e., next-generation probiotics) can be added or removed from their microbial communities.

Our scientists are particularly interested in how our gut microbes affect inflammatory bowel disease, allergies, and cancer. We are working closely with the Immunology Institute, the Division of Gastroenterology, and other research institutes within the Health System, to create novel therapies and diagnostics that can target our microbes.

We have many resources at our disposal, including the Quantitative Insights Into Microbial Ecology (QIIME) software pipeline––a leading software tool for analyzing high-throughput microbiome data. We are continually making improvements to QIIME, which are available through the Minerva computing cluster. We have developed anaerobic robotics capabilities to isolate and identify microbes of patients in an automated manner. We also have a germ-free facility that houses microbe-free mice in sterile "bubbles." By colonizing germ-free animals with different microbes, we will be able to investigate how particular bacterial strains can cause disease––or be used as a treatment.

Our Published Research

Featured below is some of the work published by our microbiome experts, José Clemente, PhDJeremiah Faith, PhDGang Fang, PhD. 


"Partial Restoration of the microbiota of cesarean-born infants via vaginal microbial transfer." Read the full study

Nature Biotechnology

"Metagenomic binning and association of plasmids with bacterial host genomes using DNA methylation." Read the full study

 Science Advances

"The Microbiome of Uncontacted Amerindians.” Read the full study


"Reconstructing the microbial diversity and function of pre-agricultural tallgrass prairie soils in the United States.” Read the full study

"Gut microbiota from twins discordant for obesity modulate metabolism in mice.“ Read the full study

"The long-term stability of the human gut microbiota.” Read the full study