Microbiome research in the Microbiology Graduate Program

The microbiota (the collection of bacteria, archaea, eukaryotes, and viruses that live in or on a host organism) impacts many aspects of human health. Microbiology Graduate Program faculty 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 extensive collaboration.

Faculty Affiliated with the Microbiology Graduate Program

Ronald Breaker, PhD, BS
Sterling Professor of Molecular, Cellular, and Developmental Biology and Professor of Molecular Biophysics and Biochemistry; Investigator, Howard Hughes Medical Institute, Molecular, Cellular and Developmental Biology
Dr. Breaker is a Sterling Professor of the Department of Molecular, Cellular and Developmental Biology at Yale University, is jointly appointed as a professor in the Department of Molecular Biophysics and Biochemistry, and is an Investigator with the Howard Hughes Medical Institute. His graduate studies with Dr. Peter Gilham at Purdue University focused on the synthesis of RNA and the catalytic properties of nucleic acids. As a postdoctoral researcher with Dr. Gerald Joyce at The Scripps Research Institute, Dr. Breaker pioneered a variety of in vitro evolution strategies to isolate novel RNA enzymes and was the first to discover catalytic DNAs or “deoxyribozymes” using this technology. Since establishing his laboratory at Yale in 1995, Dr. Breaker has continued to conduct research on the advanced functions of nucleic acids, including ribozyme reaction mechanisms, molecular switch technology, next-generation biosensors, and catalytic DNA engineering. In addition, his laboratory has established the first proofs that metabolites are directly bound by messenger RNA elements called riboswitches. Dr. Breaker’s research findings have been published in more than 220 scientific papers, book chapters, and patent applications, and his research has been funded by grants from the NIH, NSF, DARPA, the Hereditary Disease Foundation, and from several biotechnology and pharmaceutical companies. He is the recipient of fellowships from the Arnold and Mabel Beckman Foundation, the David and Lucile Packard Foundation, and the Hellman Family Trust. In recognition of his research accomplishments at Yale, Dr. Breaker received the Arthur Greer Memorial Prize (1997), the Eli Lilly Award in Microbiology (2005), the Molecular Biology Award from the U.S. National Academy of Sciences (2006), and the Merck Award from the American Society for Biochemistry and Molecular Biology (2016). Dr. Breaker was inducted into the U.S. National Academy of Sciences in 2014. He has cofounded two biotechnology companies and is a scientific advisor for industry and for various government agencies. He serves on the editorial board for the scientific journals RNA Biology, RNA, and Cell Chemical Biology.
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Jason Crawford, PhD
Associate Professor of Chemistry and Associate Professor 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?
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Erol Fikrig, MD
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.
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Richard Flavell, PhD, FRS
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.
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Jorge Galán, PhD, DVM
Lucille P. Markey Professor of Microbial Pathogenesis and Professor of Cell Biology
My laboratory studies the molecular mechanisms of host/pathogen interactions with special focus on the enteric pathogens Salmonella and Campylobacter jejun i. We use multidisciplinary approaches to define bacterial and host molecules involved in the pathogenic mechanisms and host defense. Of particular interest are the study of bacterial protein secretion machines, bacterial effector and toxin molecules, and their role in modulating host cellular functions, inflammation, and the host immune responses. I have been involved in training and teaching for my entire career and I have mentored 15 Graduate Students and more than 70 postdoctoral fellows.
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Andrew Goodman, PhD
C.N.H. Long Professor of Microbial Pathogenesis and Director of Microbial Sciences Institute; Interim Chair, Microbial Pathogenesis
Cooperation and competition in the human gut microbiome; role of the gut microbiota in drug metabolism and function.
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Eduardo Groisman, PhD
Waldemar Von Zedtwitz Professor of Microbial Pathogenesis
Our laboratory investigates gene control in Bacteroides thetaiotaomicron, a dominant member of the mammalian gut microbiota.
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Stavroula Hatzios, PhD
Assistant 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.
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Farren Isaacs, PhD
Professor of Molecular, Cellular and Developmental Biology
Applying synthetic biology technologies to engineer clinical and ecological microbiomes.
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Caroline Johnson, PhD
Associate Professor of Epidemiology (Environmental Health Sciences)
Understanding the role of microbial metabolites in human disease.
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Barbara Kazmierczak, MD, PhD
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.
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Liza Konnikova, MD/PhD
Assistant Professor
The Konnikova lab is interested in how the microbiome and the associated metabolome regulate immune development and homeostasis at barrier sites.
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Jun Liu, PhD
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.
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Ruslan Medzhitov, PhD
Sterling Professor of Immunobiology; Investigator, Howard Hughes Medical Institute
Medzhitov laboratory studies biology of inflammation, mechanisms of homoeostasis, allergic immunity and mechanisms of diseases.
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Michael O'Donnell
Assistant Professor in Molecular, Cellular and Developmental Biology
Wu Tsai InstituteOur 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.
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Noah Palm, PhD
Associate Professor of Immunobiology
The Palm lab is focused on illuminating the fundamental principles that govern immune-microbiota interactions in human health and disease.
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Melinda Pettigrew, PhD
Interim Dean of Yale School of Public Health and Anna M.R. Lauder Professor of Epidemiology (Microbial Diseases); Affiliated Faculty, Yale Institute for Global Health; 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.
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Paul Turner, PhD
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.
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Craig B. Wilen, MD, PhD
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
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Jing Yan, PhD
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.
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Additional microbiome research at Yale

Vanessa Ezenwa
Professor
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Guadalupe Garcia-Tsao, MD, FRCP
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.
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David A. Hafler, MD, FANA
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.
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Kevan Herold, MD
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.
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Seth Herzon, PhD
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.
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Mark Hochstrasser, PhD
Eugene Higgins Professor of Molecular Biophysics and Biochemistry and Professor of Molecular, Cellular, and Developmental Biology
Part of the Yale faculty since 2000, Prof. Mark Hochstrasser is the Eugene Higgins Professor of Molecular Biophysics and Biochemistry and also holds appointments in the Department of Molecular, Cellular and Developmental Biology, the Yale Cancer Center, and the School of Medicine’s Biological and Biomedical Sciences Program. He earned his B.A. at Rutgers University and his Ph.D. at the University of California, San Francisco, and conducted postdoctoral research at the Massachusetts Institute of Technology.He has earned numerous honors for his scientific contributions, including a Young Investigator Award from the Cancer Research Foundation and designation as a Searle Scholar and a Fletcher Scholar. He is an elected Fellow of the American Academy of Arts and Sciences, the American Association for the Advancement of Science, and the Connecticut Academy of Science and Engineering.Prof. Hochstrasser holds several patents related to his work, which has been published in various scientific and medical journals, including Nature, the Journal of Cell Biology, Cell, the Proceedings of the National Academy of Sciences, Genetics and Nature Cell Biology.He has been a member of the editorial board of various journals, including Cell, EMBO Journal, Genes & Development, and Molecular Biology of the Cell and has served on several National Institutes of Health study sections. Prof. Hochstrasser has also helped organize numerous international and national scientific conferences and served as an ad hoc reviewer of various research and graduate programs around the country.
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Caroline Johnson, PhD
Associate Professor of Epidemiology (Environmental Health Sciences)
Caroline H. Johnson, PhD, is Assistant 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 colon cancer. She is also examining exposures during pregnancy.
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Liza Konnikova, MD/PhD
Assistant Professor
Dr. Konnikova's team focuses on the development of immunity at barrier sites such as the GI tract and the maternal-fetal interface and its role in the 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.
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Andrew Miranker, PhD
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.
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Michael O'Donnell
Assistant Professor in Molecular, Cellular and Developmental Biology
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Jeffrey Powell
Research Professor and Professor Emeritus of Ecology and Evolutionary Biology
Our lab studies the microbial ecology of mosquito oviposition.
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Aaron Ring, MD, PhD
Associate Professor of Immunobiology
Aaron Ring received his undergraduate training at Yale University and entered the Stanford Medical Scientist Training Program for his MD and PhD degrees. At Stanford, he worked in the laboratories of K. Christopher Garcia and Irving Weissman to use structure-based protein engineering to develop new cytokine and immune checkpoint therapies for cancer. Aaron joined the faculty of the Yale Department of Immunobiology in 2016 as the Robert T. McCluskey Yale Scholar. The focus of his research is to understand and manipulate the activity of immune receptors using precision immunopharmacology and systems immunology.
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Li Wen, MD, PhD
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.
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Hongyu Zhao, PhD
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.
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