Executive Committee Members

morris-alisonAlison Morris, MD, MS

Director, Center for Medicine and the Microbiome
Professor of Medicine and Immunology

Dr. Morris’s research initially investigated the causes of chronic lung diseases in HIV-infected individuals. These studies led her to work in the microbiome, and she now investigates the role of the microbiome in both the lung and the gut. Current projects include the role of the microbiome in pulmonary hypertension, evolution and impact of the lung and gut microbiome in the ICU, and the microbiome in transplantation.

More about Dr. Morris
morrisa@upmc.edu

cooper-vaughnVaughn Cooper, PhD

Associate Director, Center for Medicine and the Microbiome
Associate Professor of Microbiology and Molecular Genetics

Dr. Cooper’s research explores how bacteria adapt to new environments and/or cause disease, with a primary focus placed on biofilm-associated infections and antimicrobial resistance. He conducts highthroughput genomic analysis of evolved populations and longitudinal studies of infectious isolates to define the genetic causes of adaptation. Additional interests of Dr. Cooper include the evolutionary dynamics in structured communities, such as biofilms or solid tumors; the microbial origins of multicellularity; why genome regions evolve at different rates; and the use of experimental evolution as a powerful teaching tool for high school students.

More about Dr. Cooper
vaughn.cooper@pitt.edu

Barbara Methé, PhD

Director, Center for Medicine and the Microbiome
Visiting Professor of Medicine

Dr. Methé has extensive experience in genomics, metagenomics, microbial ecology and physiology and handling large data sets from high throughput functional genomic methodologies including gene expression studies. She has participated in numerous annotation and comparative genome analyses of diverse prokaryotes such as Shewanella oneidensis, Desulfovibrio vulgaris, Methylococcus capsulatus, and Dehalococcoides ethenogenes. Dr. Methé led studies on which metagenomic approaches to apply in investigations of the links between the human microbiome and psoriasis, as well as the sequencing and use of microarray technology to analyze gene expression of the piezophile, Colwellia sp. MT41 and a comparative and functional genomics project to uncover virulence factors in fourteen serovars of Ureaplasma parvum and U. urealyticum.

More about Dr. Methé
metheba@upmc.edu

morowitz_michael_143687Michael Morowitz, MD

Associate Director, Center for Medicine and the Microbiome
Associate Professor of Surgery, Attending Surgeon, Children’s Hospital of Pittsburgh of UPMC

Dr. Morowitz is a general and thoracic pediatric surgeon with a research interest in the microbiome of critically ill surgical patients. For many years, his laboratory has studied changes in the microbiome at multiple body sites of newborn premature infants with and without necrotizing enterocolitis. More recently, he has extended this work to study the microbiome at multiple body sites in critically ill pediatric and adult trauma patients, with a particular interest in the relationship between nutrition, the microbiome, and outcomes in the ICU.

More about Dr. Morowitz
michael.morowitz@chp.edu

duerr-richardRichard Duerr, MD

Inflammatory Bowel Disease Genetic Research Chair
Professor of Medicine, Human Genetics, and Clinical and Translational Science
Co-Director and Scientific Director, UPMC Inflammatory Bowel Disease Center

Richard H. Duerr, MD, holds the Inflammatory Bowel Disease Genetic Research Chair and is Professor of Medicine, Human Genetics, and Clinical and Translational Science at the University of Pittsburgh. He is the Co-Director and Scientific Director of the University of Pittsburgh Medical Center Inflammatory Bowel Disease Center.

Dr. Duerr has been involved in research related to inflammatory bowel disease throughout his career. He leads one of six genetic research centers that comprise the NIH/NIDDK Inflammatory Bowel Disease Genetics Consortium. His research program has had uninterrupted funding from the NIH, CCFA, and other foundations since 1995. He was recently appointed Associate Chief Scientist, Translational Research on the Leadership Team of the Crohn’s & Colitis Foundation of America (CCFA) IBD Plexus research and information exchange platform that will engage academic and industry researchers, IBD patients, and clinicians and other healthcare providers in a partnership to accelerate the science of IBD.

More about Dr. Duerr
duerr@pitt.edu

hand-timTimothy Hand, PhD

Assistant Professor, Department of Pediatrics
Assistant Professor, Department of Immunology

We now understand that humans exist as a combination of host cells and a vast consortium of bacteria, viruses and fungi, called the microbiota, that overwhelm the host both in terms of cell number and genetic information. The adaptive immune system has evolved alongside the microbiota and the cardinal feature of adaptive immunity, immune memory, may be an effort to ‘remember’ previous responses and shape subsequent host – microbial interactions. Maintaining ‘friendly’ relations with the microbiota is a particular problem for the immune system because of the huge number of bacteria present that can be inflammatory depending upon the context within which they are experienced.

Gastrointestinal infection is a particularly dangerous situation because it has the potential to put inflammatory obligate pathogens in the same space with benign members of the microbiota. Our group hopes to identify the factors derived from host genetics, the environment (diet, infection etc.) and the microbiota that shape the activation, differentiation, regulation and survival of T cells in the GI tract. Because adaptive immunity evolved within the context of the microbiota we believe that these mechanisms will be broadly applicable to our understanding of the immune system. Our hope is that this work will help us understand the root causes of diseases that are characterized by a disrupted relationship between the immune system and the microbiota, such as Crohn’s Disease and Environmental Enteropathy.

More about Dr. Hand
timothy.hand@chp.edu

harrison-leeLee Harrison, MD

Professor of Medicine and Epidemiology

Dr. Harrison’s research focuses on the epidemiology and genomic epidemiology of important vaccine-preventable and drug-resistant bacterial pathogens that are transmitted in the community and causes of hospital-associated infections (HAI’s). He has recently initiated studies to examine the utility of the peri-rectal microbiome to predict both the risk of serious bacterial infection and the transmission of bacterial pathogens in the hospital.

More about Dr. Harrison
lharriso@edc.pitt.edu

okeefeStephen J.D. O’Keefe, MD, MSc, FCRP

Professor of Medicine, Division of Gastroenterology, Hepatology, and Nutrition

Dr. O’Keefe has been Professor of Medicine at the University of Pittsburgh since 2003 and holds an Extraordinary Professorship at the University of Stellenbosch in South African where he is helping develop the Microbiome Institute. His research is translational in the field of nutritional gastroenterology. His current NIH-funded research explores the role diet, colonic microbiota and the metabolome in explaining the profound variations in colon cancer risk in America, Alaska, and Africa.

More about Dr. O’Keefe
sjokeefe@pitt.edu

RAY_PRABIR_PHDPrabir Ray, PhD

Host Immune Response Focus Group Co-Leader, Center for Medicine and the Microbiome
Professor of Medicine and Immunology
Endowed Chair of Lung Immunology

Dr. Ray is interested in immunoregulatory mechanisms of lung inflammation as they relate to disease inception and resolution. Dr. Ray pioneered the development of inducible cell-specific transgenic mice in the early years of his career at Yale (JCI, 1997) and using this system showed an important role for the growth factor KGF in protection from lung epithelial cell death during lung injury (PNAS, 2003). This system also established for the first time an essential role of GATA-3 in driving the Th2 phenotype and allergic airway disease in mice (Immunity, 1999). Currently, his research is focused on host-pathogen interactions in the context of infections of the lung by bacteria and viruses with impact on disease states such as pneumonia and asthma. His key findings in these areas include identification of a central role of the c-kit-PI3 kinase axis in promoting Th17 and Th2 differentiation and development of the asthma phenotype in mice (Nature Medicine, 2008); this study was chosen as a Year in Immunology topic by the New York Academy of Sciences in 2010, the first identification of myeloid-derived suppressor cells (MDSCs) in the lung and their crucial role in resolution of lung inflammation during pneumonia (Mucosal Immunology, 2010, 2013), and the detrimental effect of respiratory syncytial virus (RSV) infection on Treg function and immune tolerance in newborn mice thereby increasing the risk for asthma in later life (Nature Medicine, 2012). In ongoing translational research in the area of infant immunity, his laboratory is investigating interactions between RSV and the host that cause severe bronchiolitis and hospitalization of infants. These studies may lead to new approaches to defend against RSV since no effective vaccine against this virus is currently available. Studies in his lab utilize animal models of disease and human samples, which are analyzed using state-of-the-art immunological, molecular, biochemical, physiological and imaging techniques

More about Dr. Ray
rayp@pitt.edu

Warren C. Ruder, PhD

Assistant Professor, Department of Bioengineering

Dr. Warren Ruder moved his research group to the University of Pittsburgh’s Bioengineering department in January of 2017. Previously, he spent four years as an assistant professor in Virginia Tech’s Biological Systems Engineering department, where he led the Engineered Living Systems Laboratory. His expertise is in synthetic biology, cellular and molecular biomechanics, and lab-on-a-chip systems. Dr. Ruder received his Ph.D. in Biomedical Engineering and his M.S. in Mechanical Engineering from Carnegie Mellon University, and his B.S. in Civil and Environmental Engineering from MIT. From 2003-2005, he was a Health Science Specialist at the Veterans Affairs Boston Healthcare System and Harvard Medical School. From 2005-2009, Dr. Ruder was an inaugural NIH trainee in the Pitt-CMU Biomechanics in Regenerative Medicine program and a Dowd graduate fellow in the groups of Phil LeDuc and Jim Antaki. From 2010-2012, he was a postdoctoral research associate in the group of Jim Collins at Boston University (now at MIT), and Harvard University’s Wyss Institute for Biologically Inspired Engineering.

More about Dr. Ruder
warrenr@pitt.edu

schlomchik-markMark Shlomchik, MD, PhD

UPMC Endowed Professor and Chair, Department of Immunology

Our lab is interested in systemic autoimmune diseases, long-lived B cell immunity, and in immunopathogenesis. We are using transgenic and knockout mouse models to address the questions of how autoreactive B cells arise and what are the role(s) that these cells play in mediating autoimmune disease. We have also used genetic approaches to test the roles of CD11c+ and other myeloid cells in promoting murine lupus and autoreactive B cell activation. We continue to work regulatory role of TLR9 and stimulatory role of TLR7 in lupus, and to define how TLRs function in tissue-specific fashion, including recently defining the role of MyD88. During investigation of NETs in lupus we unexpectedly found a regulatory role for NADPH oxidase, whereas NETs were not required for SLE. Regarding B cell immunity, we have made recent insights into the mechanisms of cellular selection and differentiation in the germinal center, a site of rapid proliferation, mutation, and differentiation into memory cells. Strikingly, we found that BCR signaling was desensitized by elevated phosphatase activity in the GC, which we are actively investigating. We have identified novel subsets of memory B cells in mice and are studying their origins and function. Finally, we are investigating why memory T cells fail to cause graft-vs-host disease using a new TCR transgenic model.

More about Dr. Shlomchik
mshlomch@pitt.edu