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.

National Institute of Health (NIH)
National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)
Center Core Grants (P30)
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Special Emphasis Panel (ZDK1)
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University of Chicago
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McDonald, Daniel; Hyde, Embriette; Debelius, Justine W et al. (2018) American Gut: an Open Platform for Citizen Science Microbiome Research. mSystems 3:
Samanta, Priyanka; Wang, Yitang; Fuladi, Shadi et al. (2018) Molecular determination of claudin-15 organization and channel selectivity. J Gen Physiol 150:949-968
McDonald, Benjamin D; Jabri, Bana; Bendelac, Albert (2018) Diverse developmental pathways of intestinal intraepithelial lymphocytes. Nat Rev Immunol 18:514-525
Martinez-Guryn, Kristina; Hubert, Nathaniel; Frazier, Katya et al. (2018) Small Intestine Microbiota Regulate Host Digestive and Absorptive Adaptive Responses to Dietary Lipids. Cell Host Microbe 23:458-469.e5
Johnson, Carl D; Barlow-Anacker, Amanda J; Pierre, Joseph F et al. (2018) Deletion of choline acetyltransferase in enteric neurons results in postnatal intestinal dysmotility and dysbiosis. FASEB J 32:4744-4752
Pierre, Joseph F; Hinterleitner, Reinhard; Bouziat, Romain et al. (2018) Dietary antioxidant micronutrients alter mucosal inflammatory risk in a murine model of genetic and microbial susceptibility. J Nutr Biochem 54:95-104
Williams Jr, James C; Borofsky, Michael S; Bledsoe, Sharon B et al. (2018) Papillary Ductal Plugging is a Mechanism for Early Stone Retention in Brushite Stone Disease. J Urol 199:186-192
Micic, Dejan; Yarur, Andres; Gonsalves, Alex et al. (2018) Risk Factors for Clostridium difficile Isolation in Inflammatory Bowel Disease: A Prospective Study. Dig Dis Sci 63:1016-1024
Brown, Hailey M; Biering, Scott B; Zhu, Allen et al. (2018) Demarcation of Viral Shelters Results in Destruction by Membranolytic GTPases: Antiviral Function of Autophagy Proteins and Interferon-Inducible GTPases. Bioessays 40:e1700231
Lu, Lei; Claud, Erika C (2018) Intrauterine Inflammation, Epigenetics, and Microbiome Influences on Preterm Infant Health. Curr Pathobiol Rep 6:15-21

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