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 extensive collaboration.

To be added to this page, please contact andrew.goodman@yale.edu


Jason M. Crawford, PhD

Department of Chemistry

Department of Microbial Pathogenesis

Chemical Biology Institute

The Crawford group decodes orphan bacterial biosynthetic gene clusters in bacteria-insect and bacteria-human associations


Erol Fikrig, MD

Department of Infectious Diseases

Department of Microbial Pathogenesis

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


Richard A. Flavell, PhD, FRS

Department of Immunobiology

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.


Jorge Galán, PhD, DVM

Department of Microbial Pathogenesis

Mechanisms of enteric pathogen restriction by the gut microbiota.


Guadalupe Garcia-Tsao, MD

Department of 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.


Andrew Goodman, PhD

Department of Microbial Pathogenesis

Microbial Sciences Institute

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


Eduardo Groisman, PhD

Department of Microbial Pathogenesis

Microbial Sciences Institute

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


David Hafler, MD

Department of Neurology

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


Stavroula Hatzios, PhD

Department of Molecular, Cellular, and Developmental Biology

Microbial Sciences Institute

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


Kevan Herold, MD

Department of Immunobiology

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.


Farren Isaacs, PhD

Department of Molecular, Cellular, and Developmental Biology

Systems Biology Institute

Applying synthetic biology technologies to engineer clinical and ecological microbiomes.


Akiko Iwasaki, PhD

Department of Immunobiology

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


Caroline Johnson PhD

Department of Environmental Health

Understanding the role of microbial metabolites in human disease.


Barbara Kazmierczak, PhD, MD

Department of Microbial Pathogenesis, Department of Infectious Diseases

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


Martin Kriegel, MD, PhD

Department of Immunobiology

The Kriegel lab uses disease models, gnotobiotics and human gut, skin, and oral microbiomes to study host-microbiota interactions in immune-mediated diseases.


Andrew D. Miranker, PhD

Department of Molecular Biophysics and Biochemistry

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


Noah W. Palm, PhD

Department of Immunobiology

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


Melinda M. Pettigrew, PhD

Department of Epidemiology

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.


Jeffrey Powell, PhD

Department of Ecology and Evolutionary Biology

Our lab studies the microbial ecology of mosquito oviposition.


Alvaro Sanchez, PhD

Department of Ecology and Evolutionary Biology

Microbial Sciences Institute

Our lab studies the evolution of public goods based microbial communities, using a combination of mathematical modeling and experiments in vitro.


Paul Turner, PhD

Department 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


Li Wen, MD, PhD

Department of Endocrinology

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.


Hongyu Zhao, PhD

Department of Molecular, Cellular, and Developmental Biology

Laboratory of Epidemiology and Public Health

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