Microbiome Core

The Duchossois Family Institute optimizes wellness and thriving longevity through
groundbreaking science on the human immune system, genetics, the microbiome and their shared systems.

Eric Pamer, Donald F. Steiner Professor, Departments of Medicine, Microbiology, and Pathology, and Director of the Duchossois Family Institute (DFI) is a board-certified physician in internal medicine and infectious diseases. As director of the DFI, Dr. Pamer’s research focuses on the microbiome’s impact on resistance to a wide range of microbial pathogens. The DFI’s aim is prevention, rather than treatment, of disease through a deeper understanding of the microbiome.

Composition of the microbiome, the complex microbial populations that live on human bodies and especially in the intestine, can enhance disease resistance. Antibiotic use and poor diets, among other things, can cause changes to the microbes that live within us, and those changes can be drivers of a number of diseases including autoimmune diseases, inflammatory diseases, and susceptibility to infection. Dissecting the microbiome and identifying the specific bacterial strains that are associated with health is one of the ways to maintain wellness and prevent disease, instead of treating disease after the fact.

The DFI is developing commensal bacteria that produce substances that are beneficial, so they can be administered to patients in clinical trials. The longer-term goal is for the DFI to be able to facilitate clinical trials that will help reestablish the microbiome in patients where it has been damaged, or to potentially modify the microbiome in patients who may be vulnerable to one disease or another.

The Duchossois Family Institute has established three facilities to further research in the microbiome:

1. Biobank

The biobank of commensal bacterial strains contains over 1,000 strains of bacteria cultured from healthy donors. The strains have been sequenced and their entire genomes are available for academic investigators who want to test the ability of these different strains to provide health benefits or disease resistance.

2. Metagenomics

The Metagenomics Facility provides bacterial 16S ribosomal RNA gene and shotgun metagenomic sequence analyses on intestinal contents and other samples containing complex microbial populations. The facility works with investigators to analyze microbiota sequence data from experimental and clinical samples. More information can be found on the DFI Metagenomics webpage.

3. Metabolomics

The Metabolomics Facility measures, characterizes, and identifies the metabolites produced or modified by the complex populations of microbes that make up the microbiome in order to better understand the role these bugs play in mammalian physiology. It aims to support the understanding of how these molecules function in microbe-microbe and host-microbe interactions/communication and how these processes influence human health and disease. The DFI Metabolomics webpage provides more information.


Supporting the three facilities is the DFI’s team of bioinformaticians. Bioinformaticians in the DFI perform genomic analyses including genome assembly and annotation and work with computation software programs to analyze microbial genome sequences and characterize their metabolite utilization and secretion.