Microbial Interactions Core

Tom Schmidt, PhD - Director

The overarching goal of the UMCGR Microbial Interactions Core is to catalyze research that will define causal relationships and mechanisms of action that mediate host-microbe interactions in health and disease.

This new core is directed by Dr. Tom Schmidt, an experienced microbiologist who has studied the physiology and ecology of microbes in complex communities.


  • To provide easy access to state-of-the-art facilities to characterize temporal and spatial differences in gut microbiomes.
  • To establish in vitro model systems that reveal mechanistic interactions between oxygen-sensitive microbes and the gut epithelium.
  • To Accelerate research by supplying representative cultivars of beneficial and pathogenic microbes for in vitro and in vivo experiments.

Program Services

The Microbial Interactions Core offers the following program services:

Co-culture of O2-sensitive Microbes with Organoid-derived Human Gut Epithelium under Asymmetric Gas Conditions 

This service provides access to a co-culture facility with an anaerobic chamber for the experiments using an in vitro human model of host-microbe interactions within the gut that uses primary stem-cell derived enteric epithelium.

Repository of Strains from the Gut Microbiome 

This service is designed to accelerate research by preserving, characterizing, and supplying representative cultivars of host-associated microbes.

Access to State-of-the-Art Multi-omics Analyses of Microbial Communities

The Microbial Interactions Core (MIC) will provide consultation with interested UMCGR members to discuss strategies for measuring the composition and function of gut microbiomes, the use of in vitro and in vivo model systems, and experimental designs to test hypotheses about interactions with the gut microbiome.  In addition to assisting with the design microbiome studies, the MIC will provide standardized sampling kits and coordinate distribution of samples to Cores and investigators as needed. Assistance with data analysis by Drs. Gillilland and Colacino will be coordinated via the Administrative Core.