Skip to Main Content

Microbiome

The microbiota (the collection of bacteria, archaea, eukaryotes, and viruses that live in or on a host organism) impacts many aspects of human health. Track faculty explore these relationships using a wide range of systems and tools.

Microbiome

  • Waldemar Von Zedtwitz Professor of Medicine (Infectious Diseases) and Professor of Epidemiology (Microbial Diseases) and of Microbial Pathogenesis; Affiliated Faculty, Yale Institute for Global Health; Section Chief, Infectious Diseases, Internal Medicine

    My laboratory investigates vector-borne diseases. Studies are directed toward understanding Lyme disease, flaviviral infections including dengue and West Nile viruses, and malaria. Efforts on Lyme disease include exploring immunity to Borrelia burgdorferi, selective B. burgdorferi gene expression in vivo, and the immunobiology of Lyme arthritis. Flaviviruses and Plasmodium are used as models  to understand the molecular interactions between pathogens, their arthropod vectors and their mammalian hosts. Finally, we are developing new  approaches to prevent ticks and mosquitoes from feeding on a vertebrate host, thereby interfering with pathogen transmission.
  • Sterling Professor of Immunobiology; Investigator, Howard Hughes Medical Institute

    Dr. Flavell is Sterling Professor of Immunobiology at Yale University School of Medicine, and an Investigator of the Howard Hughes Medical Institute. He received his B.Sc. (Honors) in 1967 and Ph.D. in 1970 in biochemistry from the University of Hull, England, and performed postdoctoral work in Amsterdam (1970-72) with Piet Borst and in Zurich (1972-73) with Charles Weissmann. Before accepting his current position in 1988, Dr. Flavell was first Assistant Professor (equivalent) at the University of Amsterdam (1974-79); then Head of the Laboratory of Gene Structure and Expression at the National Institute for Medical Research, Mill Hill, London (1979-82); and subsequently President and Chief Scientific Officer of Biogen Research Corporation, Cambridge, Massachusetts (1982-88). Dr. Flavell is a fellow of the Royal Society, a member of the National Academy of Sciences as well as the National Academy of Medicine. Richard Flavell uses transgenic and gene-targeted mice to study Innate and Adaptive immunity, T cell tolerance and activation in immunity and autoimmunity,apoptosis, and regulation of T cell differentiation.
  • Associate Professor of Laboratory Medicine and Immunobiology

    Dr. Ellen Foxman, M.D., PhD. is an Associate Professor of Laboratory Medicine and Immunobiology at the Yale School of Medicine. Her laboratory studies antiviral defense in the human respiratory tract, focusing on innate immunity, an inborn system of protective mechanisms that guards against harmful viruses or bacteria, even when the body has never encountered the infection before. The overarching goal of this research is to improve the diagnosis, treatment, and prevention of illnesses caused by respiratory viruses. Background. Dr. Foxman trained in medicine and immunology at Stanford University. She became interested in respiratory viruses during her residency training in clinical pathology at Harvard's Brigham and Women's Hospital, due to the advances in testing that were beginning to reveal a previously unappreciated very high prevalence of these viruses. She later joined Dr. Akiko Iwasaki’s group at Yale as a postdoctoral associate, where she demonstrated suppression of innate immune responses in the airway epithelium by cool ambient temperature. In 2016, she established her independent research group at Yale. Contributions of the Foxman Lab include defining biomarkers to track innate immune responses in the human respiratory tract and uncovering evidence for viral interference, in which general antiviral defenses triggered by common cold viruses protect against unrelated viruses such as influenza and COVID-19.  Dr. Foxman’s recognitions include the 2018 Hartwell Foundation Individual Biomedical Research Award, the 2021 ASCI Young Physician-Scientist Award, and the 2021 Rita Allen Foundation Scholars Award.
  • Lucille P. Markey Professor of Microbial Pathogenesis and Professor of Cell Biology

    Dr. Jorge E. Galán earned his DVM from the National University of La Plata (Argentina) and his Ph.D. in Microbiology from Cornell University. He completed postdoctoral studies at Washington University in St. Louis, and was in the Faculty at SUNY Stony Brook before coming to Yale in 1998. He is currently the Lucille B. Markey Professor of Microbiology and Professor of Cell Biology at the Yale University School of Medicine. Dr. Galán is the recipient of numerous honors and awards including the Pew Scholar in Biomedical Sciences, the Searle Scholar Award, the National Institutes of Health MERIT award in 2000 and 2015, the Hans Sigrist Prize, the Alexander M. Cruickshank Award, and the Robert Koch Prize.  He is a member of the American Academy of Microbiology, the German Academy of Sciences Leopoldina, a fellow of the American Association for the Advancement of Sciences, and a member of the USA National Academy of Science and the USA National Academy of Medicine.  He is a member of several Scientific Advisory Boards and has authored more than 200 publications in the field of bacterial pathogenesis and molecular biology.
  • C.N.H. Long Professor of Microbial Pathogenesis and Director of Microbial Sciences Institute; Chair, Microbial Pathogenesis

    Andrew L. Goodman, PhD, is the C. N. H. Long Professor and Chair of the Department of Microbial Pathogenesis and Director of the Yale Microbial Sciences Institute. Goodman received his undergraduate degree in Ecology and Evolutionary Biology from Princeton University, his PhD in Microbiology and Molecular Genetics from Harvard University, and completed postdoctoral training at Washington University. His lab uses microbial genetics, gnotobiotics, and mass spectrometry to understand how gut microbes interact with their host during health and disease. The lab is also interested in how the microbiome impacts the efficacy and toxicity of medical drugs. The lab’s contributions have been recognized by the NIH Director New Innovator Award, the Pew Foundation, the Dupont Young Professors Award, the Burroughs Wellcome Foundation, the Howard Hughes Medical Institute Faculty Scholars Program, the ASPET John J. Abel Award, and the Presidential Early Career Award in Science and Engineering.
  • Waldemar Von Zedtwitz Professor of Microbial Pathogenesis

    I am a geneticist who studies the mechanisms that enable bacteria to cause disease and to further human health.  I received a MS in Biochemistry from the University of Buenos Aires and a PhD from the University of Chicago.  After spending 20 years in the faculty of the Washington University School of Medicine, I joined the Yale School of Medicine in 2010.  For 19 years, I was a member of the Howard Hughes Medical Institute.
  • Sterling Professor of Immunobiology and Professor of Dermatology and of Molecular, Cellular, and Developmental Biology and of Epidemiology (Microbial Diseases); Investigator, Howard Hughes Medical Institute

    Akiko Iwasaki, Ph.D., is a Sterling Professor of Immunobiology and Molecular, Cellular, and Developmental Biology at Yale University, and an Investigator of the Howard Hughes Medical Institute. She received her Ph.D. from the University of Toronto in Canada and her postdoctoral training from the National Institutes of Health. Her research focuses on the mechanisms of immune defense against viruses at the mucosal surfaces, and the development of mucosal vaccine strategies. She is the co-Lead Investigator of the Yale COVID-19 Recovery Study, which aims to determine the changes in the immune response of people with long COVID after vaccination. Dr. Iwasaki also leads multiple other studies to interrogate the pathobiology of long COVID, both in patients, and through developing animal models of long COVID. Dr. Iwasaki was elected to the National Academy of Sciences in 2018, to the National Academy of Medicine in 2019, to the European Molecular Biology Organization in 2021, and to the American Academy of Arts and Sciences in 2021.
  • Associate Professor of Epidemiology (Environmental Health Sciences)

    Caroline H. Johnson, PhD, is an Associate Professor of Epidemiology (on term) in the Department of Environmental Health Sciences at Yale School of Public Health. She graduated from Imperial College London in 2009 with a PhD in Analytical Chemistry. Since then she has held postdoctoral and staff appointments at the National Cancer Institute and The Scripps Research Institute. Dr. Johnson's research uses mass spectrometry-based metabolomics to understand the role of metabolites in human health. Her primary research interest is to investigate the relationship between genetic and environmental influences (diet, hormones and microbiome) in colon cancer. She is also examining exposures during pregnancy.
  • Gustavus and Louise Pfeiffer Research Foundation M.D.-Ph.D. Program Director and Professor of Medicine (Infectious Diseases) and of Microbial Pathogenesis; Professor, Microbial Pathogenesis; Director, MD-PhD Program, Yale University

    Dr. Kazmierczak received her PhD from Rockefeller University (1993) and her MD from Cornell University Medical College (1994), both in New York City. She completed an Internal Medicine residency and Infectious Diseases fellowship training at the University of California, San Francisco, and joined the Yale faculty in 2001. She is currently a Professor of Medicine and Microbial Pathogenesis, and Director of the MD-PhD program at Yale. Dr. Kazmierczak's research program is broadly focused on bacterial and host factors that allow opportunistic infections to occur. Using Pseudomonas aeruginosa as a clinically relevant model, her lab addresses fundamental questions of how cell-envelope spanning bacterial machines - the Type 3 secretion system, Type 4 pili and polar flagellum - are assembled, regulated, and used during infection. She has also identified host responses directed at components of these virulence associated structures, in particular those mediated by the NLRC4 inflammasome. Inflammatory responses to bacteria are also a focus of her work on microbiome-host interactions in infants with Cystic Fibrosis, where her lab has used longitudinal data acquired over five years from cohorts of patients and controls to understand gut microbiome composition and the inflammatory and metabolic responses at this site. Dr. Kazmierczak has been recognized as a Burroughs-Wellcome Fund Investigator in the Pathogenesis of Infectious Diseases (2007), a Donaghue Investigator (2002), and a Hellman Family Fellow (2002). She is a Fellow of the Infectious Diseases Society of America and an elected member of the American Society for Clinical Investigation and the American Academy for Microbiology.
  • Associate Professor; CyTOF Core Director, Medicine

    Dr. Konnikova's team focuses on the development of early life immunity particularly at barrier sites such as the GI tract and the maternal-fetal interface with a particular focus on T cell biology. Using multi-omic approaches, the group investigates how mucosal homeostasis is developed and what contributes to pathogenesis of diverse diseases such as sepsis, preterm labor, necrotizing enterocolitis (NEC), very early onset (VEO) and pediatric IBD. The Konnikova lab is further interested in how the microbiome and the associated metabolome regulate immune development and homeostasis at barrier sites. Her group is also interested in how early life events alter circulating immune cells. To this end, in collaboration with the NOuRISH team they are enrolling infants in a longitudinal study of peripheral blood development.
  • Sterling Professor of Immunobiology; Investigator, Howard Hughes Medical Institute

    Medzhitov laboratory studies biology of inflammation, mechanisms of homoeostasis, allergic immunity and mechanisms of diseases.
  • Associate Professor of Immunobiology

    Noah W. Palm is an Assistant Professor of Immunobiology at the Yale University School of Medicine. His laboratory focuses on illuminating the myriad interactions between the immune system and the gut microbiota in health and disease. Dr. Palm performed his doctoral work with Ruslan Medzhitov and his postdoctoral work with Richard Flavell, both at Yale University.
  • Professor Adjunct; Affiliated Faculty, Yale Institute for Global Health

    Melinda Pettigrew, PhD, is a Professor of Epidemiology. She completed a fellowship from the Hedwig van Ameringen Executive Leadership in Academic Medicine (ELAM) Program for Women and was a Public Voices Thought Leaders Fellow. Professor Pettigrew has an international reputation in the molecular epidemiology of infectious diseases. Professor Pettigrew's research focuses on pathobionts of the respiratory and gastrointestinal tracts (e.g., Haemophilus influenzae and Pseudomonas aeruginosa) and the growing public health threat of antibiotic resistance. Her current work utilizes a combined approach involving microbiology and infectious disease epidemiology to identify factors that influence whether pathobionts asymptomatically colonize or cause diseases such as pneumonia and exacerbations of chronic obstructive pulmonary disease (COPD). Additional projects focus on how disruptions of homeostasis in the respiratory and gastrointestinal microbiome influence colonization resistance, development of antibiotic resistance, and risk of both hospital and community acquired infections. Current projects utilize next-generation sequence technologies (e.g., whole-genome sequencing, 16S rRNA gene microbial profiling, and RNA-sequencing) to examine the complex relationships between the microbiota, antibiotic exposure, and risk of infections. She serves on the Steering and Executive Committees for the Antibiotic Resistance Leadership Group (ARLG). As the Associate Director of the Scientific Leadership Core, focusing on Diversity, Professor Pettigrew leads efforts implement and integrate principles of diversity, access, equity, and inclusion throughout the ARLG. Professor Pettigrew serves on the editorial board of mBio.
  • Assistant Professor

    Hualiang Pi, PhD, is an Assistant Professor in the Department of Microbial Pathogenesis and member of the Microbial Sciences Institute. Hualiang received her PhD in Microbiology from Cornell University and conducted her postdoctoral training at Vanderbilit University Medical Center. The Pi lab focuses on elucidating microbial stress defense mechanisms important for bacterial infection. She is also the recipient of an NIH Pathway to Independence Award (K99/R00).
  • Associate Professor Term; Medical Director, Immune Monitoring Core Facility

    Dr. Wilen is an Associate Professor in Laboratory Medicine and Immunobiology and is focused on the host-pathogen interactions of RNA viruses including coronavirus and norovirus. Dr. Wilen received his A.B in Biology and Economics at Washington University in St. Louis, his MD and PhD from the University of Pennsylvania. His residency training was in clinical pathology at Barnes-Jewish Hospital in St. Louis, MO. His postdoctoral studies were conducted in the laboratory of Herbert "Skip" Virgin at Washington University School of Medicine where he studied the pathogenesis of norovirus, the leading cause of acute gastroenteritis. Dr. Wilen discovered CD300lf as the first receptor for a norovirus and identified intestinal tuft cells as the physiologic target cell for mouse norovirus infection. Current work in the Wilen lab is focused on identifying novel therapeutic targets for SARS-CoV2 and elucidating mechanisms COVID-19 pathogenesis. The Wilen lab utilizes a diverse array of techniques to achieve these goals with SARS-CoV2 in the BSL3 including single-cell RNA sequencing, genome-wide CRISPR screening, organoid culture, and transgenic mouse models.https://wilenlab.com
  • Assistant Professor, Molecular, Cellular and Developmental Biology

    Jing Yan is currently an Assistant Professor of Molecular, Cellular and Developmental Biology and a member of the Quantitative Biology Institute (Qbio) at Yale. Originally from Shanghai, China, he obtained his B.S. degree from the College of Chemistry and Molecular Engineering at Peking University in China, with extensive undergraduate research experience in organic synthesis. In 2009, he switched to the field of soft matter physics and pursued Ph.D. degree in the Department of Materials Science and Engineering at the University of Illinois at Urbana-Champaign. In 2014, he stumbled into microbiology at Princeton as a joint postdoctoral researcher in the department of Molecular Biology and Mechanical and Aerospace Engineering. in 2019, he started his independent lab at Yale. His lab focuses on bacterial biofilms, surface-attached communities of bacteria surrounded by an extracellular matrix. His lab combines state-of-art imaging techniques, biochemical tools, genetics, mechanical measurements, and computer simulations to understand how bacteria build multicellular communities cell by cell, what unique materials they use to do so, and what characteristics emerge at the level of the collective. Ultimately, the lab aims to solve biofilm-related problems in medicine and in industry and to enhance the use of beneficial biofilms. Jing received the Career Award at the Scientific Interface from Burroughs Wellcome Fund (BWF) in 2016, NIH Director’s New Innovator Award in 2021, Sloan Research Fellowship in 2023, and Investigator in Pathogenicity from BWF in 2023.