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Microbiome Initiatives and Resources

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Microbiome Initiatives and Resources

  1. 1. Microbiome Initiatives and Resources at the University of Chicago Available for download at tech.uchicago.edu/areas
  2. 2. 2 UChicago: Expertise & Resource Network Clinical Expertise: Unique Research Facilities: Computational & Analytical Expertise: • Gnotobiotic Core animal facilities • True microorganism-free conditions • One of select few facilities in the US • State-of-the-art high-throughput sequencing and genotyping facilities • Big data management • New state-of-the-art clinical and research center • Performed fecal/microbiota transplant in youngest patient to date
  3. 3. Areas of Expertise • American Gut Microbiome Project • Home Microbiome Project • Diabetes • GI disease - Chron’s, colitis, IBD, celiac • Food allergies • Autism • Surgery – fixing anastomotic leaks • Earth Microbiome Project • Microbial community systems & ecology • Phylogenetic and evolutionary studies • Soil, crops, and fuels • Coastal and Marine microbial communities • High-throughput sequencing • Computational analytics • Metagenomics • Structural and functional genome annotation • Biological interaction networks • Novel computing for systems biology • Hospital Microbiome Project • Fecal transplants • Access to diverse patient populations with diverse dietary & lifestyle habits 3 Microbiome & Human Health Microbiome & Environmental Ecology Analytics & Data Management Clinical Research & Patient Management
  4. 4. Select Initiatives 4 Earth Microbiome Project: • Led by Jack Gilbert • Analyze 200,000 samples • Reconstruct 500,000 microbial genomes • Generate global Gene Atlas http://www.earthmicrobiome.org/ Hospital Microbiome Project: • Led by Jack Gilbert, John Alverdy, other • Analyze microbial samples from surfaces, air, staff, and patients from the UC new hospital • Characterize bacterial population development in healthcare setting http://hospitalmicrobiome.com/ Home Microbiome Project: • Led by Jack Gilbert • Sponsored by Alfred P. Sloan Foundation • Analyze microbial samples from human environment • Completed analysis of microbial diversity of cell phones and shoes http://www.homemicrobiome.com/
  5. 5. Microbiome & Human Health 5 • Multidisciplinary approaches aimed at studying the intersection of microbiome and human diseases • Research areas cover a diverse spectrum of disease, including GI conditions, obesity, autism, and oncology surgical complications (anastomotic leaks) • Imbalances of gut microbes associated with obesity and cancer • Intestinal homeostasis and digestive diseases (IBD) Eugene B. Chang, MD • HMW-PEG and its derivatives for prevention of anastomotic leaks • Co-leader of Hospital Microbiome Project John C. Alverdy, MD Select Research & Technologies David T. Rubin, MD • New therapies and predictive diagnostics for IBD • Disease genetics and clinical outcomes in patients with IBD • Interim Section Chief, Gastroenterology, Hepatology and Nutrition
  6. 6. Microbiome, Environment, & Allergies 6 • (Meta)genomic and (meta)transcriptomic approaches to characterize microbial communities and ecosystems in environmental samples from soil and oceans. • Environmental factors leading to microbiome changes and disease in humans • Leads multiple microbial ecology initiatives, including Earth, Hospital, and Home Microbiome Projects • Microbially-mediated management of oil spills • Next generation DNA sequencing to characterize microbial communities • Marine microbial communities as markers of marine ecological health Jack Gilbert, PhD • Role of environmental factors and microbiome ecology on food allergies • Comensal microbiome for prevention of food allergen sensitization Cathryn Nagler, PhD Select Research & Initiatives Mitch Sogin, PhD
  7. 7. Marine Microbial Communities 7 • Research at The Marine Biological Laboratory in Woods Hole, MA is part of the UChicago Family • Next generation DNA sequencing to characterize microbial communities • Techniques sensitive to subtle changes in microbial communities in deep sea sponges • Marine microbial communities as markers of environmental stress • Exploring applications in human digestive tract • Microbial communities in water sheds and drinking systems • Microbes as markers of water quality beyond measuring bacterial counts David Mark Welch, PhD Select Research & Initiatives Mitch Sogin, PhD
  8. 8. Analytics & Data Management 8 • Bioinformatics, data mining, cloud computing, and data intensive computing • Studying microbiome and drug metabolism to individualize cancer therapies Robert Grossman, PhD • Second-generation DNA sequencing, shotgun metagenomics, big data management • Formation and development of microbial communities in mammalian GI and environmental systems Dionysios Antonopoulos, PhD Select Research • Utilizing next-gen genomics/transcriptomics technologies and bioinformatics approaches to analyze microbiome communities, build models, and mine data
  9. 9. Clinical Research & Patient Management 9 • Development and role of microbiota during infancy, and effects on health over lifetime Erika Claud, MD • Microbiota transplantation for treatment of inflammatory and infectious diseases of the GI system Stacy Kahn, MD Select Research • Studying the role of microbiome in health and disease. • Studying, evaluating, improving, and performing microbiome transplantation procedures
  10. 10. Other Ongoing Research & Initiatives 10 Daina Ringus, PhD Gut viruses for reprogramming of gut bacteria in disease conditions. Alexander Chervonsky, MD, PhD Studies of microbial-host interactions to prevent autoimmune disease, such as type 1 diabetes. Emily Landon, MD Developing solutions for management of hospital acquired infections. Folker Meyer, PhD Developing new therapeutic strategies for antibiotic resistance. Gary An, MD Modulation of the gut microbiome of patients in the intensive care unit. Cristina Negri, PhD Microbial ecology and water quality. Robert Daum, MD Developing antibiotic potentiator of oxacillin sensitivity.
  11. 11. How to Partner with the University of Chicago 11 To learn more, contact UChicagoTech, the Center for Technology Development & Ventures. We build strong industry partnerships to successfully bring innovation to the marketplace. UChicagoTech can connect you to emerging technologies and field- advancing researchers that may inform and enrich your own innovation efforts. We value your involvement at every stage of the invention pipeline, from idea to tangible asset. For more information, visit us at tech.uchicago.edu or contact anyone below. Divya Varshney, MBA Chief Marketing Officer, UCTech dvarshney@tech.uchicago.edu Matthew Martin, PhD Assistant Director mmartin@tech.uchicago.edu

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