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
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Assistant Professor
I am a microbial community ecologist and my main interest is understanding how the environment shapes the structure of microbial communities. During my PhD at the University of Pisa, I worked under the supervision of Lisandro Benedetti-Cecchi, investigating the impacts of pulse perturbations and the occurrence of regime shifts in microbial biofilms and algal forests of intertidal habitats. After working in the field with natural communities, I decided to learn to perform experiments in the lab and I joined Jeff Gore’s group at MIT as a postdoc. My postdoctoral research focused on dissecting the effects of temperature and nutrient availability on the diversity and structure of microbial communities. I am fascinated by the possibility of harnessing metabolic principles and structures to understand how bacterial communities assemble and function in diverse environmental conditions.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, the USA National Academy of Medicine, and the USA Academy of Arts and Sciences. 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 both cause disease and further human health. I received an M.S. in Biochemistry from the University of Buenos Aires and a Ph.D. 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.Associate Professor of Molecular, Cellular and Developmental Biology and of Chemistry
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, (HHMI)
Akiko Iwasaki, Ph.D. is a Sterling Professor of Immunobiology at the Yale University School of Medicine. Her research focuses on the mechanisms of immune defense against viruses at mucosal surfaces, which are a major site of entry for infectious agents. Professor Iwasaki received her Ph.D. in Immunology from the University of Toronto and completed her postdoctoral training with the National Institutes of Health before joining Yale’s faculty in 2000. She has been a Howard Hughes Medical Institute Investigator since 2014. Professor Iwasaki has received many awards and honors including the Keio Medical Science Prize in 2025, Forbes 50 over 50 Innovation 2024, TIME 100 Most Influential People 2024, TIME 100 HEALTH Most Influential People Affecting Global Health 2024, and the Else Kröner Fresenius Prize for Medical Research 2023. She was elected to the National Academy of Sciences in 2018, to the National Academy of Medicine in 2019, to the American Academy of Arts and Sciences in 2021 and was appointed President of American Associations of Immunologists (AAI) in 2023. Professor Iwasaki has been a leading scientific voice during the COVID-19 pandemic and is also well known for her Twitter advocacy on women and underrepresented minorities in the science and medicine fields. She was named to the 2023 STATUS list of the ultimate list of leaders in life sciences. Professor Iwasaki is the director of the Center for Infection and Immunity and is at the forefront of several long COVID investigations including the Mount-Sinai Yale Long COVID study, Yale LISTEN study, and Yale Paxlovid trial.Associate Professor of Epidemiology (Environmental Health Sciences)
Caroline H. Johnson, PhD, is a Tenured Associate Professor of Epidemiology 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 colorectal cancer, with a focus on sex-specific differences.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.John F. Enders Professor of Microbial Pathogenesis; Enders Professor , Microbial Pathogenesis; Investigator, Howard Hughes Medical Institute
Joseph Mougous is an HHMI Investigator, the Enders Professor of Microbial Pathogensis and a member of the Microbial Sciences Institute. Dr. Mougous received his Bachelor’s degree in Biochemistry from Western Washington University and his PhD in Molecular and Cell Biology from the University of California-Berkeley. After completing postdoctoral studies in Microbiology at Harvard University, he was appointed an Assistant Professor of Microbiology at the University of Washington. He received tenure in 2013 and was promoted to Professor in 2018. Dr. Mougous joined the faculty at Yale in 2025. Dr. Mougous’s work on the molecular mechanisms underlying interbacterial interactions has been recognized by numerous honors, including the National Academy of Sciences Award in Molecular Biology, recognitions as a Blavatnik National Award Finalist for Young Scientists, election to the National Academy of Sciences and selection as a Howard Hughes Medical Institute Investigator.Professor
Noah W. Palm is a 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.Assistant Professor
Hualiang Pi, PhD, is an Assistant Professor in the Department of Microbial Pathogenesis and a member of the Microbial Sciences Institute. She received her doctoral training in Microbiology at Cornell University and completed her postdoctoral fellowship at Vanderbilit University Medical Center. Dr. Pi's research focuses on elucidating microbial stress defense mechanisms important for bacterial infection. Her work has been recognized through multiple competitive awards, including the NIH Pathway to Independence Award (K99/R00), the NIH Director’s New Innovator Award (DP2), and selection as a 2025 Searle Scholar.Associate Professor of Laboratory Medicine and of Immunobiology; 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 and his postdoctoral studies were conducted at Washington University School of Medicine. 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 mechanisms of viral entry, immunity, and pathogenesis for noroviruses, coronaviruses, and pre-emergent viruses with pandemic potential. The goals of this work are to enable improved risk stratification and to develop improved therapeutics and vaccines to reduce the disease burden from viruses. https://wilenlab.com