Dr. Huffnagle's Lab - Microbiome Research

Dr. Gary Huffnagle's investigative interests lie in the interaction between the microbiome and host immune system. This includes both control of pulmonary and intestinal inflammation and control of infections. His laboratory has utilized an interdisciplinary approach that combines research approaches in pathophysiology, immunology, microbiology, microbial ecology, microbial genomics, and computational biology. Current projects in the lab include studies of host-microbiome interactions at a molecular/cellular level, in mouse models of inflammation and infection, and in human disease.

Meet the Team

U-M Pulmonary & Critical Care Medicine, Dr. Gary Huffnagle
Gary Huffnagle, PhD

Gary Huffnagle, PhD
Professor, Department of Internal Medicine
Professor, Microbiology and Immunology
BS, Microbiology, Pennsylvania State University, University Park, PA
PhD, Immunology, University of Texas Southwestern Med. Ctr., Dallax, TX
Postdoctoral Training, Immunopathology, University of Texas Southwestern Med. Ctr., Dallas, TX

Email: ghuff@umich.edu

U-M Pulmonary & Critical Care Medicine, Dr. Robert Dickson
Robert Dickson, MD

Robert Dickson, MD
Assistant Professor, Department of Internal Medicine
BA, St. John's College, Annapolis, MD
Post Baccalaureate Premedical Program, Goucher College, Baltimore, MD
MD, Duke University School of Medicine, Durham, NC

E-mail: rodickso@umich.edu
Dr. Dickson joined the faculty in July 2014. He received his undergraduate degree in liberal arts from St. John's College, and received his MD from the Duke University School of Medicine. He then completed a residency in Internal Medicine at the University of Washington, followed by a year as Chief Medical Resident at Harborview Medical Center. He completed his fellowship in Pulmonary and Critical Care Medicine at the University of Michigan. He currently studies the role of the lung microbiome in the pathogenesis of acute and chronic lung disease. He uses the techniques of microbial ecology to understand how the bacterial communities of the respiratory tract are altered by lung disease, and how they in turn contribute to respiratory illness. He treats patients in the Pulmonary Clinic at the Taubman Center and in the Critical Care Medical Unit. Dr. Dickson has published several high impact papers in the field, including journals such as Lancet, Lancet Respiratory Medicine, and the American Journal of Respiratory and Critical Care Medicine. He has been an invited speaker in microbiome-focused symposia at the NIH, nationally, and internationally.

Dr. Dickson's research focuses on understanding how microbial communities in the respiratory tract mediate respiratory illness and health. Utilizing culture-independent techniques of microbial identification, he studies how changes in the lung microbiome interact with host factors, clinical interventions and patient outcomes in order to generate and test novel mechanistic hypotheses regarding the pathogenesis of respiratory infections and inflammatory lung disease. He performs integrative translational research, spanning from molecular characterization of respiratory microbiota to animal modeling of acute lung disease to prospective trials of human subjects. Dr. Dickson's clinical research interests include the acute respiratory distress syndrome (ARDS), lung transplantation, and function of the healthy human respiratory tract.

The Microbiome and Critical Illness, December 2015, The Lancet

U-M Pulmonary & Critical Care Medicine, Dr. John Erb-Downward
John Erb-Downward, PhD

John Erb-Downward, PhD
Assistant Research Scientist, Department of Internal Medicine
BS, Biochemistry, Cornell University, Ithaca, NY
PhD, Microbiology and Immunology, University of Michigan, Ann Arbor, MI
Postdoctoral Training, Pulmonary & Critical Care Medicine, University of Michigan, Ann Arbor, MI

Email: jre@umich.edu
My investigative career has focused on the communication between host and microbe, including the microbiome. Some of my initial publications utilized mass spectrometry to identify the ability of pathogenic fungi, Cryptococcus neoformans and Candida albicans, to produce immunomodulatory prostaglandins. These investigations demonstrated that through small molecules, microbes were capable of communicating directly with mammalian host cells in the same language that the host cells use to communicate with each other. This research led me to study computational and bioinformatic methods to investigate microbial communities and their interactions with the host. Over the last decade, I have developed substantial expertise in the analysis and integration of different kinds of large scale data sets ranging from metabolomics, to bacterial 16S profiling and transcriptomics. In addition to computational biology, I have broad expertise ranging from biochemistry and immunology to microbial ecology. I have worked extensively with Dr. Huffnagle in analysis of the microbiome of the lungs and in establishing high throughput pyrosequencing as a platform in our lab at the University of Michigan, as well as establishing the informatics support for these analyses and the host-microbiome interaction analyses. I have written the code for several of the applications that we use for data analysis.

U-M Pulmonary & Critical Care Medicine, Dr. Roderick McDonald
Roderick McDonald, PhD

Roderick McDonald, PhD
Research Associate, Department of Internal Medicine/Lab Manager
PhD, Animal Physiology, University of Ottawa, Ottawa, ON, Canada
BS, Biology, University of Ottawa, Ottawa, ON, Canada

Email: rmcdonal@umich.edu

U-M Pulmonary & Critical Care Medicine, Nicole Falkowski
Nicole Falkowski, MS, BS

Nicole Falkowski, MS, BS
Research Associate, Department of Internal Medicine/Lab Manager
BS, Biology, Alma College, Alma, MI
MS, Biology, University of Michigan, Ann Arbor, MI

Email: nrobson@umich.edu

U-M Pulmonary & Critical Care Medicine, Ellen Hunter
Ellen Hunter, BS

Ellen Hunter, BS
Research Assistant
Phone: 734-936-9368

Email: ellhunt@umich.edu

U-M Pulmonary & Critical Care Medicine, Dr. Brittan Starr Scales
Brittan Starr Scales, PhD, MPH, BS

Brittan Starr Scales, PhD, MPH, BS
Research Fellow, Department of Internal Medicine
Lecturer, Molecular, Cellular and Developmental Biology
BS, Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA
MPH, Infectious Diseases and Vaccinology, University of California, Berkeley, CA
PhD, Microbiology and Immunology

Email: britstar@umich.edu
My research in the Huffnagle lab merges wet bench molecular methods with in silco bioinformatics tools to answer questions about how bacteria interact with the human host to cause disease. I have focused on a group of bacteria, Pseudomonas fluorescens, that is typically found in environmental habitats (ie. water, plants, soil) but our group has found in numerous types of diseased lung specimens. I hypothesize that these bacteria have molecularly adapted to the inflamed lung environment. My research combines mouse models of disease, in vitro biochemical assays, next-generation sequencing, and comparative genomics to directly characterize the phenotypic and genetic differences between human-adapted and environmentally-adapted isolates of Pseudomonas fluorescens.

U-M Pulmonary & Critical Care Medicine, Dr. Dustin Farr
Dustin Farr, BS

Dustin Farr, BS
Masters Student, School of Public Health, Epidemiology
BS, Clinical Laboratory Science, Michigan State University, Lansing, MI

Email farrd@umich.edu

Relevant Literature

Contact Us

Laboratory Contact Information:
1150 W. Medical Center Drive, 6240 MSRB III
Ann Arbor, MI 48109-5642
Phone: 734-936-7934
Fax: 734-764-2655

Campus Mail Information:
Division of Pulmonary & Critical Care Medicine
University of Michigan
1150 W. Medical Center Drive
6301 MSRB III, SPC 5642
Ann Arbor, MI 48109-5642
Phone: 734-936-7934
Fax: 734-764-2655