The Host-Microbe Core (HMC) 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 facility. 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, DDRCC 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 HMC is committed to: (1) Providing DDRCC 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 HMC to meet both current and anticipated demands. The HMC not only provides valuable expertise to DDRCC users for experiment planning, troubleshooting and discussion of the results but is also integrated with the other DDRCC cores to augment these capabilities. The HMC together with the Integrated Translational Research (ITR) Core are essential for providing cells, tissues, and patient samples to investigators for establishing experimental models. Likewise, the Enteric Microbiology component of the HMC provides high-quality, customized service for cultivation- dependent and -independent analyses of complex gut microbiomes, and in conjunction with the Computational Analysis and Modeling Resource (CAMR) component of the Administrative Core provides assistance and instruction in the analysis of large datasets. Thus, the HM Core has had tremendous impact in enabling DDRCC members to advance knowledge in the DDRCC's thematic areas that focus on the study of IBD, host- microbe interactions, mucosal immunology and inflammation. Of the 306 DDRCC-acknowledged publications over the past funding cycles, 59 (~20%) cited the HMC as the primary core that they used. Further underscoring the integration of DDRCC Cores, the HMC was also listed as a secondary core for an additional 24 pubs, totaling 83 or 28% of the total publications that helped by the DDRCC over the past funding period.

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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Cockrell, Chase; An, Gary (2017) Sepsis reconsidered: Identifying novel metrics for behavioral landscape characterization with a high-performance computing implementation of an agent-based model. J Theor Biol 430:157-168
Pekow, Joel; Meckel, Katherine; Dougherty, Urszula et al. (2017) miR-193a-3p is a Key Tumor Suppressor in Ulcerative Colitis-Associated Colon Cancer and Promotes Carcinogenesis through Upregulation of IL17RD. Clin Cancer Res 23:5281-5291
Messer, Jeannette S (2017) The cellular autophagy/apoptosis checkpoint during inflammation. Cell Mol Life Sci 74:1281-1296
An, G; Fitzpatrick, B G; Christley, S et al. (2017) Optimization and Control of Agent-Based Models in Biology: A Perspective. Bull Math Biol 79:63-87
Arvans, Donna; Jung, Yong-Chul; Antonopoulos, Dionysios et al. (2017) Oxalobacter formigenes-Derived Bioactive Factors Stimulate Oxalate Transport by Intestinal Epithelial Cells. J Am Soc Nephrol 28:876-887
Nobutani, Kentaro; Miyoshi, Jun; Musch, Mark W et al. (2017) Daikenchuto (TU-100) alters murine hepatic and intestinal drug metabolizing enzymes in an in vivo dietary model: effects of gender and withdrawal. Pharmacol Res Perspect 5:
Messer, J S; Liechty, E R; Vogel, O A et al. (2017) Evolutionary and ecological forces that shape the bacterial communities of the human gut. Mucosal Immunol 10:567-579
Nie, Litong; Shuai, Lin; Zhu, Mingrui et al. (2017) The Landscape of Histone Modifications in a High-Fat Diet-Induced Obese (DIO) Mouse Model. Mol Cell Proteomics 16:1324-1334
Denzin, Lisa K; Khan, Aly A; Virdis, Francesca et al. (2017) Neutralizing Antibody Responses to Viral Infections Are Linked to the Non-classical MHC Class II Gene H2-Ob. Immunity 47:310-322.e7
Alverdy, John C; Luo, James N (2017) The Influence of Host Stress on the Mechanism of Infection: Lost Microbiomes, Emergent Pathobiomes, and the Role of Interkingdom Signaling. Front Microbiol 8:322

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