1. Microbiome Initiatives and Resources
at the University of Chicago
Available for download at
tech.uchicago.edu/areas

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. 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. 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. 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. 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. 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. 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. 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. 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. 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