Host-Microbe Core (HM)

PROJECT SUMMARY/ABSTRACT
The Host-Microbe (HM) Core is comprised of two components – the Gnotobiotic Component (GBC) and Enteric
Microbiology Component (EMC). They synergize in the isolation, cultivation and analysis of microbiota by
biochemical and sequencing methods with the concomitant analysis of microbes and their communities in vivo
using our state-of-the-art Gnotobiotic Research Animal Facility (GRAF). Recent advances in the analysis of the
commensal microbiota and an increasing appreciation for the role of the microbiota in the vital functions of the
mammalian host have put the studies of host-microbe interactions at the forefront of many areas of the life
sciences. This is especially true for studies of the normal physiology of the gut and pathophysiology of disease
states such as IBD, which has been linked to disruptions in the host-commensal mutualism. The ability to analyze
the composition and structure of the microbiota, as well as its functional properties and ex vivo culturing
conditions, is a base requirement for building a successful research center devoted to studying digestive
diseases. Moreover, to be in the vanguard of these increasingly inter-disciplinary research fields, the University
of Chicago (UChicago) Digestive Diseases Research Core Center (DDRCC) for Interdisciplinary Study of
Inflammatory Intestinal Disorders (C-IID) scientists need access to a reliable mechanism for testing their ideas
in in vivo experiments in animals colonized with defined microbiota – gnotobiotic mice. They are also in need of
germ-free (GF) animals to use as controls for studies of the role of microbes in disease development. As a result,
the HM Core is committed to: (1) providing C-IID researchers with services that reflect their needs, are available
on campus, and are competitively priced compared to commercial services; and (2) further development of the
HM Core to meet both current and anticipated demands. The HM Core not only provides valuable expertise to
C-IID users for experiment planning, troubleshooting and discussion of the results but is also integrated with the
other C-IID cores to augment these capabilities. The HM Core, together with the Integrative Clinical and
Biospecimen (ICB) Core, are essential for providing cells, tissues, and patient samples to investigators for
establishing experimental models. Likewise, the EMC of the HM Core provides high-quality, customized services
for cultivation-dependent and -independent analyses of complex gut microbiomes as well as providing both
assistance and instruction in the analysis of large datasets. Thus, the HM Core has had tremendous impact in
enabling C-IID members to advance knowledge in the C-IID thematic areas that focus on the study of IBD, host-
microbe interactions, mucosal immunology, and inflammation. Of the 322 C-IID acknowledged publications over
the past funding cycles, 92 (28.5%) cited the HM Core as the primary core that they used. This represents a 4%
increase over the previous funding cycle. Underscoring the integration of C-IID Cores, the HM Core was also
listed as a secondary core for an additional 107 publications, totaling 199 or 62% of the total publications that
were supported by the C-IID over the past funding period, a 7% increase over the previous funding cycle.

Grant Number: 5P30DK042086-35
NIH Institute/Center: NIH
Principal Investigator: EUGENE CHANG