Skip to Main Content


The scientific focus of the Department of Microbial Pathogenesis is to study microbial pathogens through multidisciplinary approaches. Understanding the mechanisms by which microbial pathogens cause disease requires understanding the pathogenic microorganisms themselves as well as the cellular and immune responses they stimulate in the host. We are researching these interactions for a wide variety of important viral, bacterial and parasitic pathogens.

Research Community

The Department of Microbial Pathogenesis is part of a larger community: Microbiology Track Faculty in the Yale Combined Program in the Biological and Biomedical Sciences (BBS) and Microbiome Research at Yale.

Microbiome Research at Yale

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

These groups belong to many departments and interact through research seminars, graduate student advising, and collaboration.

To be added to this page, please contact Andrew Goodman.

Faculty and Labs

  • Professor of Chemistry and of Microbial Pathogenesis

    The Crawford laboratory focuses on Metabolism at the Human-Microbe Interface. High-throughput genome sequencing of bacteria (and fungi) has revealed many highly unusual “orphan” biosynthetic gene clusters suspected of synthesizing novel, structurally diverse, and biologically active small molecules. These types of naturally produced molecules often regulate complex interactions with their animal hosts, hold a rich history of being utilized as human drugs, and serve as excellent molecular probes for identifying new drug targets for a wide variety of diseases. Additionally, there are still many novel metabolites of functional relevance in well-characterized animals, such as humans and mice. Using a blend of small molecule chemistry, protein biochemistry, cell biology, and microbiology, the lab exploits the natural interactions between bacteria and animals to discover new molecules with signaling, antimicrobial, immunomodulatory, and anticancer activities. The lab also connects these products to their underlying biosynthetic genes, characterizes the biosynthetic enzymes involved in their construction, and investigates their roles in biology and medicine.

    In this context, we address two major biological questions at the host-bacteria interface, one from the microbe perspective and one from the host perspective:

    How do bacterial human/mouse microbiome members regulate host responses, such as inflammation, signal transduction, and DNA damage, at the metabolic level?

    How do human and mouse immune cells, such as macrophages, rewire immunometabolism in response to microbial insults?

  • 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

    We study how the microbiota of ticks and mosquitoes influences the transmission of arthropod-borne diseases.

  • Sterling Professor of Immunobiology; Investigator, Howard Hughes Medical Institute

    The Flavell lab studies the relationship between the microbiota and the immune system, particularly in the context of human diseases such as IBD, metabolic syndrome and cancer and their mouse models.

  • Lucille P. Markey Professor of Microbial Pathogenesis and Professor of Cell Biology

    Mechanisms of enteric pathogen restriction by the gut microbiota.

  • Professor of Medicine (Digestive Diseases)

    Microbiome research in experimental cirrhosis to identify measures to decrease bacterial translocation, a mechanism that leads to systemic inflammation and decompensation in patients with cirrhosis.

  • C.N.H. Long Professor of Microbial Pathogenesis and Director of Microbial Sciences Institute; Chair, Microbial Pathogenesis

    Cooperation and competition in the human gut microbiome; role of the gut microbiota in drug metabolism and function.

  • Waldemar Von Zedtwitz Professor of Microbial Pathogenesis

    Our laboratory investigates gene control in Bacteroides thetaiotaomicron, a dominant member of the mammalian gut microbiota.

  • William S. and Lois Stiles Edgerly Professor of Neurology and Professor of Immunobiology; Chair, Neurology; Neurologist-in-Chief, Yale New Haven Hospital

    Our lab is investigating the interplay between human diet, microbiome, genetics, and immune reponses in inflammatory disease.

  • Associate Professor of Molecular, Cellular and Developmental Biology and of Chemistry

    My lab applies chemical biology to the discovery of enzymes and other proteins whose biochemical activity shapes host-microbe dynamics in the context of gastrointestinal infections and the gut microbiota.

  • C.N.H. Long Professor of Immunobiology and of Medicine (Endocrinology)

    My lab is interested in looking at the effect of the microbiome on responses to biologics and in understanding how the microbiome regulates immune tolerance.

  • Milton Harris ’29 Ph.D. Professor of Chemistry

    Our research focuses on the structure elucidation and mode of action of small molecules encoded in the human microbiome. We are particularly interested in secondary microbiota metabolites that have been implicated in human cancers.

  • Professor of Molecular, Cellular and Developmental Biology

    Applying synthetic biology technologies to engineer clinical and ecological microbiomes.

  • 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

    The Iwasaki laboratory studies the role of microbiome and virome on immunity and inflammatory diseases. Our research showed that signals from the microbiome help optimize the immune response in the respiratory tract against influenza virus infection.

  • 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

    Acquisition and maturation of the gut and airway microbiomes in infants with Cystic Fibrosis.

  • Associate Professor; CyTOF Core Director, Medicine

    The Konnikova lab is interested in how the microbiome and the associated metabolome regulate immune development and homeostasis at barrier sites.

  • Professor of Microbial Pathogenesis

    We are developing a high-throughput cryo-electron tomography (cryo-ET) pipeline for high-resolution structure determination of molecular machines in cells, in order to gain molecular insights into fundamental biochemical processes.

  • Professor of Molecular Biophysics and Biochemistry and of Chemical and Environmental Engineering

    Provenance and authentication of works of art and other forms of cultural heritage.

  • Associate Professor of Genetics and of Internal Medicine (Medical Oncology).; Member, Yale Cancer Biology Institute; Scientific Director, Center for Gastrointestinal Cancers at Smilow Cancer Hospital and Yale Cancer Center; Co-Director of Pancreas Program, Center for Gastrointestinal Cancers at Smilow Cancer Hospital and Yale Cancer Center; Associate Professor of Internal Medicine, Medical Oncology

    The Muzumdar Lab is an inclusive team that seeks to understand how genetic alterations cooperate with environmental and host factors to drive the progression of the most recalcitrant cancers in hopes of devising novel strategies for cancer prevention, interception, and therapy. We strive to train the next generation of cancer research scientists in a diverse work environment that fosters belonging and growth. Using sophisticated genetically engineered and dietary models, we are exploring how obesity shapes the intestinal microbiome to drive the development of pancreatic cancer and other obesity-associated cancers.

  • Assistant Professor in Molecular, Cellular and Developmental Biology

    Wu Tsai Institute

    Our lab studies how gut microbes affect sensory behaviors, such as smell and taste. We primarily use the nematode C. elegans to identify microbial metabolites that alter nervous system function.

  • Professor

    The Palm lab is focused on illuminating the fundamental principles that govern immune-microbiota interactions in human health and disease.

  • Professor Adjunct; Affiliated Faculty, Yale Institute for Global Health

    The Pettigrew research lab conducts clinical epidemiologic studies of the respiratory and gastrointestinal microbiota in order to facilitate progress towards the goal of manipulating the microbiota for control of antibiotic resistance and transmission of multi-drug resistant organisms.

  • Research Professor and Professor Emeritus of Ecology and Evolutionary Biology

    Our lab studies the microbial ecology of mosquito oviposition.

  • Rachel Carson Professor of Ecology and Evolutionary Biology

    The Turner Lab is interested in the role of bacteriophages in the ecology and evolution of microbiomes, especially phage therapy approaches to targeting bacterial pathogens in/on the human body and whether such treatment affects community composition of resident phages and non-target bacteria inhabiting the microbiome.

  • Professor of Medicine (Endocrinology); Director of Core Laboratory of Yale Center for Clinical Investigation (YCCI)

    We study the role of the microbiome in the pathogenesis of type 1 diabetes and obesity, focusing on their interaction with immune cells in mouse models and humans.

  • Assistant Professor, Molecular, Cellular and Developmental Biology

    Our lab is interested in how commensal bacteria determine the outcome of infections by gut pathogens such as Vibrio cholerae, and what the role bacterial biofilm plays in the interaction between the pathogen and the resident bacteria.

  • Ira V. Hiscock Professor of Biostatistics, Professor of Genetics and Professor of Statistics and Data Science; Affiliated Faculty, Yale Institute for Global Health

    Development and application of statistical methods for the analysis of microbiome data.

Advanced Training

The impact of viruses such as AIDS and SARS-CoV-2 cannot be overstated; emerging microbial pathogens and the spread of antibiotic resistance are clear indications that infectious diseases remain a significant health problem. In the United States, infectious diseases are the third leading cause of death, and the situation is even more serious worldwide. A concerted effort is needed to deal with the growing threat of infectious diseases, and a central component of this effort is the training of scientists in the fields of microbiology and microbial pathogenesis.