Gary Huffnagle

Gary Huffnagle, Ph.D.

Nina and Jerry D. Luptak Research Professor
Associate Chair for Undergraduate Studies, MCDB
Professor, Molecular, Cellular and Developmental Biology (MCDB)
Research Professor, Mary H Weiser Food Allergy Center
Professor, Pulmonary & Critical Care Medicine
Professor, Microbiology and Immunology


Gary B. Huffnagle, PhD holds faculty appointments (Professor) in Internal Medicine, Microbiology & Immunology, and Molecular Cellular & Developmental Biology, as well as the Mary H. Weiser Food Allergy Center at the University of Michigan. He also holds the Nina and Jerry D Luptak Professorship in Food Allergy at the University of Michigan.  He received his PhD in immunology from the University of Texas Southwestern Medical School and was elected to the American Academy of Microbiology of the American Society for Microbiology in 2013.  He has been a frequent reviewer for the National Institutes of Health, including standing membership for multiple study sections. He has published over 180 peer-reviewed publications with >9700 citations. He is also the Associate Director of the T32 Multidisciplinary Training Program in Lung Disease training grant, Associate Chair of Undergraduate Studies for the MCDB Department and the Chair of the inter-college, inter-departmental undergraduate Microbiology Major at the University of Michigan.  He teaches a series courses in microbial pathogenesis, host immunity & allergic disease, and microbial genomics to students ranging from sophomores to graduate students. He has written a book for a general audience, entitled "The Probiotics Revolution", as well as participated in television, radio, magazine and newspaper interviews on the topic.  In recognition of his efforts in both research and education, Dr. Huffnagle was awarded a Faculty Recognition Award from the President's and Provost's Offices at the University of Michigan in 2010.  His research career was initially dedicated to understanding the mechanisms underlying how the immune system eliminates microbes from the lungs and other mucosal sites. His laboratory then adopted new technologies and computational approaches to study the interactions of the microbiome in the lungs and gut with the immune system during health and disease, including respiratory diseases and food allergies.

Research Interests

Dr. Huffnagle's research interests fall into three areas: (1) the microbiome & respiratory diseases, (2) the mucosal immunobiology and microbiology of food allergies, and (3) the microbiology, immunology and microbial ecology of the yeast Candida albicans. 

  1. With over 200 species, Pseudomonas is one of the largest, most genetically diverse and ecologically adaptable of all Gram-negative genera. Despite this diversity, the only Pseudomonas species recognized as a common colonizer of humans is the opportunistic pathogen Pseudomonas aeruginosa. However, non-aeruginosa Pseudomonas species (NAPS) can often be detected in clinical specimens, but they have been assumed to be clinically insignificant. We have ongoing studies in humans and mice that pulmonary inflammation results in a bloom of two NAPS in the lungs that have the potential to act as co-factors in chronic inflammation and disease, as demonstrated by in vitroin vivo and in silico analyses.
  2. Our laboratory is interested in the role of the microbiota in shaping mucosal immunity and protection from food allergies. Epidemiologic and clinical data support the hypothesis that perturbations in the microbiota due to differences in "westernized" countries have disrupted the normal microbiota-mediated mechanisms of immunological tolerance in the mucosa, leading to an increase in the incidence of allergic diseases and other inflammatory conditions. Our laboratory demonstrated that mice can develop allergic responses to allergens if their endogenous microbiota is altered at the time of first allergen exposure. These experimental and clinical observations are consistent with other studies demonstrating that the endogenous microbiota plays a significant role in shaping the development of the immune system.
  3. In conjunction with our mucosal immunity interest, our laboratory also studies the microbial ecology of mucosal surfaces and how colonization by Candida albicans and other yeast can modify the resistance and resilience of the bacterial community structure in the gastrointestinal tract in response to ecologic stress or perturbation, as well as downstream effects on immune system regulation.

Research Opportunities for Rotating Students

In vivo and in vitro studies underlying mechanisms associated with food allergies