Faculty

Center Faculty

DMC faculty have primary appointments in a range of Schools and Institutes across Duke University, including the Duke School of Medicine, the Duke Center for Genomic and Computational Biology, the Nicholas School for the Environment, the Pratt School of Engineering, the Duke Marine Laboratories, Duke Departments of Biology and Evolutionary Anthropology, and the School of Arts and Sciences. Duke faculty members interested in affiliating with the Duke Microbiome Center please contact Pat Massard.

esb-headshotCindy Amundsen, MD
Roy T Parker Professor
Department of Obstetrics and Gynecology

My group studies the urinary microbiota and the differences between healthy populations and those with urologic diseases. We are particularly interested in lower urinary tract disorders of bladder pain, infection, and urgency incontinence which may have heterogeneous populations but with symptoms that often overlap. This results in failure of multiple treatments to ameliorate symptoms, high utilization of financial and personnel resources, delays adequate patient treatment, and provides no insight into improving treatment paradigms. Our current research is in recurrent urinary tract infections in post-menopausal women and considering the possible influences of the microbiome. New insights might provide an opportunity to predict risk of developing certain urologic diseases and innovative therapeutic strategies.
Emily Bernhardt, PhD
Professor
Department of Biology

Research in the Bernhardt lab focuses on the movement of elements and energy within and through Earth's ecosystems. Many of the biogeochemical processes that we study are driven by microbes (the microbial machines that drive Earth's global element cycles). We use a wide variety of tools to figure out what microbes are doing (enzyme analyses, process rate measurements, functional gene analyses, bioassays) and increasingly are using genomics approaches to figure out whether microbial identity and community composition can help us better understand how environmental change constrains and shapes the capacity of microbes to perform ecosystem processes.
esb-headshotStaci Bilbo, PhD
Haley Family Professor
Department of Psychology & Neuroscience and Neurobiology

We seek to understand the impact of environmental factors early in life on health and disease risk throughout the lifespan, with a particular emphasis on neuroimmune interactions with host physiology, including the critical role of the gut and its ecosystem.

Diego BohorquezDiego Bohorquez, PhD
Assistant Professor
Department of Medicine and Neurobiology

The Bohórquez Laboratory is dedicated to uncover neuronal mechanisms that could serve to treat the brain from the gut. The laboratory is recognized for its discovery of gut-brain neural circuits that transduce luminal stimuli to modulate appetitive behaviors. These circuits also serve to sense and transduce stimuli from bacteria and bacterial ligands in the gastrointestinal lumen.
Adela CardonesAdela Rambi Guanco Cardones, MD
Associate Professor of Dermatology
Lawrence David, PhD
Assistant Professor
Department of Molecular Genetics and Microbiology
Duke Center for Genomic and Computational Biology

Human epithelial surfaces are colonized by trillions of commensal microbes representing thousands of unique bacterial species, commonly refered to as the human microbiota. The David Lab seeks to understand, predict, and manipulate how human microbiota behave over time. We are particularly interested in how the dynamics of these human-associated microbial communities are shaped by human nutrition. Our research also includes developing tools and methods to pursue this interest.
Fred Dietrich, PhD
Associate Professor
Department of Molecular Genetics and Microbiology
Duke Center for Genomic and Computational Biology

In our laboratory, we are interested in using genomic technology to address what is the set of genes found in the fungi and how much genetic variation is there within a fungal pathogen species. Our main interest is in the human fungal pathogen Cryptococcus neoformans, where we want to investigate the diversity in clinical and environmental population and how regions of the genome or individual genes have diverged between isolates.
Christine Drea, PhD
Earl D. McLean Professor
Department of Evolutionary Anthropology

Our interests in the mechanisms of mammalian social behavior have recently expanded to incorporate the study of symbiotic microbes that inhabit animal bodies and influence their host. To better understand the role of microbes in mediating host social interaction and health, one set of projects is focused on the bacterial assemblages in the scent glands of meerkats and lemurs and on (1) their developmental patterns in relation to host variables (e.g. age, sex, social status, group membership), (2) their role in modulating host volatile chemical signals (and hence olfactory communication), (3) their mode of acquisition (i.e. ‘inheritance’ vs. socioecological transfer), and (4) the broad consequences of their loss owing to antibiotic treatment. Another set of projects is focused on the gut microbiota of several lemur species in relation to host (5) phylogenetic relatedness and geographic sympatry or allopatry, (6) diet, habitat quality (at an active mine site in Madagascar), and health, and (7) age, antibiotic exposure, and antibiotic resistance across a habitat gradient from pristine to anthropogenically disturbed. The experimental investigation of animal-bacterial interactions is fundamentally changing our understanding of behavioral ecology, with relevance to wildlife management and conservation.
Holly DressmanHolly K. Dressman, PhD
Research Professor, Department of Molecular Genetics and Microbiology
Director, Duke Microbiome Shared Resource
Center for Genomic and Computational Biology

As Director of the Duke Microbiome Shared resource, our lab aims to provide investigators a variety of technologies and services that will enable them to study microbial communities, immune oncology, cancer research, infectious disease, and environmental health. My research area of interest has been intertwined with providing shared resources to investigators utilizing genomic and transcriptomic profiling as part of their research as well as being engaged as an investigator on several cancer, cardiovascular, radiation, and microbial studies.
Josh GranekJoshua Granek, PhD
Assistant Professor in Biostatistics and Bioinformatics

Dr. Granek interests are centered in interactions between organisms at the cellular and molecular scale, with a research focus on microbial communities and pathogens. Throughout his career, he has used a combination of experimental and computational approaches to address biological questions ranging from the structure, organization, and evolution of transcription regulatory sequences, through the development of GOMER, a software package for modeling transcriptional regulation on a genomic scale, to wet-lab experiments that analyzed the regulation of ploidy specific genes in the yeast Saccharomyces cerevisiae. He also developed S. cerevisiae colony biofilms as a model for understanding how microbes interact to generate multicellular behavior using a combination of genome-scale techniques, including next-generation DNA sequencing, high-throughput phenotyping, and computation. Dr. Granek’s current efforts are focused on supporting various microbial labs with the analysis of high-throughput genomic DNA and RNA sequencing data in both bacterial and fungal systems.
Claudia Gunsch, PhD
Associate Professor
Department of Civil and Environmental Engineering

Our research bridges environmental engineering and molecular biotechnology. We utilize a variety of genomic based methods to explore microbial interactions in natural and engineered settings with the goal of identifying the contributing factors which lead to bacteria acquiring negative (i.e., antibiotic resistance) and/or beneficial (i.e., ability to degrade a pollutant) genetic trait. Current research projects focus on investigating the impacts of emerging contaminants on biological treatment processes, developing genetic bioaugmentation technologies for improving the bioremediation efficacy of recalcitrant contaminants, studying microbial evolution following exposure to anthropogenic contaminants and developing innovative water treatment technologies for industrial and developing world applications.
Gianna Hammer, PhD
Assistant Professor
Department of Immunology

Although billions of microbes live inside the gut we know very little about what types of signals gut microbes deliver to the body, and how our body responds to them. To answer these questions our lab studies a special immune cell, called the dendritic cell. Dendritic cells can be considered the “head coach” of the immune system – their job is to study gut microbes, design a defensive play, and train other immune cells to execute these plays. Since dendritic cells have direct control over how other immune cells respond, we aim to identify the receptors and signals activated when dendritic cells detect gut microbes, the functions that gut microbes alter in dendritic cells, and determine how these control the immune response to gut microbes. While these dynamics normally maintain a healthy gut, we also seek to understand how, and which, gut microbes can drive disease. To study this we use mice whose dendritic cells’ responses to gut microbes are dramatically amplified. This amplification induces gut inflammation and we are now studying which specific dendritic cells, and microbes, drive this inflammatory disease. In addition to gut inflammation, we are also studying how dynamics between dendritic cells and microbes impact colon cancer and liver disease.
Joseph Heitman, MD, PhD
James B. Duke Professor
Department of Molecular Genetics and Microbiology

Our studies focus on the defining the genomic diversity of various human fungal pathogens such as Cryptococcus and Candida species. This work has extended to an analysis of new hybrid fungal lineages that emerge in nature from sexual recombination and their implication to clinical settings. Parallel studies have focused on the structure, function, and evolution of the fungal mating type locus, which has implications for the origins of sex determination and the evolution of sex chromosomes.
Brenna Hughes, MD
Associate Professor
Obstetrics and Gynecology

Our team is a clinical research unit with the goal of preventing and treating infectious diseases in pregnancy for both mother and fetus. A major focus for our team is clinical trials for the prevention of congenital cytomegalovirus. We are also studying the vaginal microbiome and its impact on risk of HIV acquisition. Other areas of interest include chorioamnionitis and cesarean site infection and the impact of the microbiome of these conditions on disease in the mother and the fetus.
Dana Hunt, PhD
Associate Professor of Microbial Ecology
Nicholas School of the Environment

Our research focus is on understanding the ecology of microbes through examination of their genes and lifestyles and the role they play in cycling nutrients and energy. We are specifically studying bacterial interactions with the environment and the effect of temperature changes on bacterial population dynamics. Another area of active research is the response and adaptation of bacteria to emerging environmental pollutants such as antibiotics and nanomaterials.
Ru-Rong Ji, PhD
Director of Sensory Plasticity and Pain Research Laboratory
Co-Director of Center for Translational Pain Medicine
Professor of Anesthesiology, Cell Biology, and Neurobiology

Ji lab studies molecular and cellular mechanisms of chronic pain using mouse models, electrophysiology, and cell biology assays. We are interested in neuro-immune interactions in the context of inflammation and pain. We investigate how sensory neurons including nociceptor neurons interact with immune cells, cancer cells, and bacteria. We are also interested in studying microbiota dysregulation in chronic pain.
Zackary Johnson, PhD
Assistant Professor
Nicholas School of the Environment

The Johnson Lab broadly studies the abundance, diversity and activity of marine microbes. We are biological oceanographers, marine molecular ecologists, marine microbiologists, biogeochemists and aquaculturists. Our research, which is at the intersection of marine ecology and biogeochemistry, focuses on the marine cyanobacteria Prochlorococcus, the most abundant phytoplankton in the open oceans and an excellent model marine microbe. We also have a strong portfolio in developing the biotechnological applications of marine microalgae for the sustainable production of feed, food and fuel.
Matthew Kelly, MD, MPH
Assistant Professor
Department of Pediatrics
Duke Global Health Institute

Our research is broadly focused on elucidating the complex interactions that exist between the host microbiota and exogenous pathogens that cause infections in children. We have several ongoing projects and analyses: 1) evaluating the impact of the upper respiratory microbiota on the risk of colonization by bacterial respiratory pathogens among infants in Botswana; 2) identifying associations between the gut microbiota of pediatric stem cell transplant recipients and the risk of infections after transplant (bloodstream infection, C. difficile infection). Ultimately, we aim to develop strategies that use targeted modification of the microbiota for the prevention of infections in children.
Francois Lutzoni, PhD
Professor
Department of Biology

Research interests in the Lutzoni lab are centered on symbiotic systems involving fungi and photoautotrophic organisms. Lichens, including their microbiomes, have been our principal focus, but since 2005 our research program has expanded to include endophytic fungi found in all lineages of land plants, as well as symbiotic interactions between chytrids and algae. We have been studying these symbioses primarily from a macroevolutionary perspective, but since 2003 we have adopted an interdisciplinary approach bridging evolutionary biology, ecology, and genomics. Research in the Lutzoni lab spans the full spectrum of activities, from intensive fieldwork-based surveys, to experimental laboratory and computational work, across broad spatio-temporal scales.
Michael D. Lynch, PhD
Assistant Professor
Department of Biomedical Engineering

Our work focuses on the design and optimization of synthetic biochemical and regulatory pathways to produce i) useful enzymes, ii) useful microbes and microbe communities and iii) useful molecules via fermentation. We are broadly interested in metabolic and biochemical engineering efforts using synthetic biology. Some application areas of interest include bioactive natural products, microbial biofilms, specialty and commodity chemicals and even biofuels. We are also interested in energetics of biological transformations including those of one carbon feedstocks including carbon dioxide, methane, and methanol.
Li Ma, PhD
Associate Professor
Department of Statistical Science

My group's research focuses developing statistical and computational tools for analyzing complex data sets. A particular area of research interest is developing methodology for effectively analyzing microbiome data sets to address several common and important inference objectives---including case-control comparison, adjustment for confounding, and the incorporation of time and covariate effects. A central statistical objective is to design data analytic tools that can effectively overcome the sparsity and high-dimensionality of microbiome data and produce both valid and powerful analysis.
Nancie MacIver, MD, PhD
Associate Professor
Department of Pediatrics

The MacIver Lab is broadly interested in how large changes in nutritional status (either undernutrition or overnutrition/obesity) alter T cell metabolism, differentiation, and function in the context of health and disease. We have several ongoing projects: (1) We have identified obesity-associated changes in T cell metabolism and T cell subsets. These changes are associated with impaired protective immunity, which we study in the context of influenza in collaboration with the Beck lab at UNC-Chapel Hill. Interestingly, weight loss does not reverse either obesity-associated T cell inflammation in adipose tissue or altered T cell metabolism, and weight loss does not restore protection against influenza. We are currently testing if targeting T cell metabolism can rescue T cell dysfunction in obesity. (2) We are identifying molecular mechanisms by which nutritionally regulated hormones and cytokines (insulin, insulin-like growth factor-1, leptin, and IL-6) communicate nutritional status to T cells and thereby influence T cell differentiation in under- and over-nutrition and in inflammatory disease. (3) We are studying the role of mitochondrial sirtuins in regulating persistent defects in T cell metabolism and function in the context of undernutrition, and we have identified mitochondrial sirtuins (especially sirtuin 3 and sirtuin 4) as critical regulators of T cell metabolism and cytokine response.
Amanda MacLeod, MD
Associate Professor of Dermatology

Our research studies focus on defining immune circuits in the skin barrier. Current projects investigate antimicrobial peptides and proteins in the skin, which comprise an ancient and conserved mechanism of innate host defense. This work has extended to identification and characterization of antiviral proteins, their transcriptional regulation and functional roles under homeostatic conditions and during skin injury. Additional studies are aimed at host-microbiome interactions and identifying the human cutaneous virome as well as emerging pathogens of the skin. Our long-term goal is to gain a better understanding of how skin innate and adaptive immune cells regulate microbes and associated diseases.
Paul Magwene, PhD
Associate Professor
Department of Biology
Center for Systems Biology

Genomic research in our lab is focused on characterizing genetic variation within and between species and exploring the consequences of that variation in terms of genetic networks and cellular phenotypes. We are interested in how eukaryotic microbes integrate signals from their external environment with information about their own internal state in order to make cellular decisions. We are using both experimental and mathematical approaches to tackle these problems.
Julia Messina, MD
Assisant Professor of Medicine


I am a Transplant Infectious Diseases physician scientist specializing in the care of immunocompromised patients with translational research interest in the impact of microbiome on clinical outcomes. My current research focuses on role that the bacteria Enterococcus plays within the gut microbiome of patients with hematologic malignancies in the propagation of bloodstream infections and graft-versus-host disease.
Charles Nunn, PhD
Professor
Evolutionary Anthropology

Research in the Nunn lab investigates "why we get sick" from both evolutionary and ecological perspectives. We study infectious diseases in humans and our closest living relatives, the ecology of the skin microbiome in non-Western populations, and how evolution makes humans susceptible to infectious and non-infectious diseases. We investigate these topics using phylogenetic methods, mathematical modeling, and through fieldwork in Madagascar, Kenya and other locations.
William Parker, PhD
Associate Professor
Department of Surgery

In our laboratory, we examine the role of the gut “biome” in a variety of inflammatory conditions, including cardiovascular disease and neuropsychiatric disorders (i.e. major depressive disorder and anxiety disorders). We are interested in the entire gut biome, which entails all life associated with the gut’s ecosystem, both microscopic and otherwise. Our lab continues exploration of the relationship between bacteria and the immune system, a long term interest of ours. However, much of our recent work has focused on intestinal worms, which, based on available data, have a greater therapeutic potential than do bacteria. At the present time, we have projects aimed at making "therapeutic helminths" available to everyone, and, using laboratory rodent models, we are looking at the intersection between the microbiota, immune function, colonization with complex eukaryotic symbionts (helminths), and diet.
Sallie Permar, MD, PhD
Professor
Pediatrics, Immunology, Molecular Genetics and Microbiology, Pathology

Our laboratory group focuses on prevention of perinatal infections such as HIV and cytomegalovirus, which can result in lifelong debilitating diseases,. We are investigating systemic and mucosal immune landscapes of infants and pregnant women and how these can be harnessed to develop maternal and pediatric vaccine strategies to eliminate perinatal viral pathogen transmission. Additionally, we also focus on the role of the early life commensal microbiologic signatures towards the development of protective immune responses and viral acquisition. We utilize both human cohorts and nonhuman primate models of mother-to-child infections to define protective immune responses and vaccine approaches that can prevent vertical transmission of important perinatal pathogens.
John Rawls, PhD
Associate Professor
Department of Molecular Genetics and Microbiology

We seek to understand how the intestinal microbiome contributes to vertebrate physiology and disease. To that end, we leverage complementary zebrafish and mouse models to study the integrative physiology of host-microbiome interactions. This work has identified novel and conserved mechanisms by which intestinal bacteria regulate dietary fat metabolism and systemic innate immunity. We also apply genomic approaches in these animal models to understand the transcriptional regulatory pathways utilized by the intestinal epithelium to mediate host responses to the microbiome. These studies have identified mechanisms of transcriptional and chromatin regulation that have been conserved during vertebrate evolution and also contribute to modern human diseases such as the inflammatory bowel diseases, obesity, and diabetes. We are also engaged in translational research in humans and animal models to define microbial and metabolic determinants of obesity and efficacy of weight loss intervention.
Daniel Rittschof, PhD
N.L. Christensen Distinguished Professor of the Enviroment

After just a few decades of research Professor Rittschof has seen the light. Microbes and especially products of microbial exoenzymes, predominantly serine proteases organize estuarine communities and habitat webs and inform floating oyster aquaculture with respect to biofouling, pathogens and parasites. Though the ultimate research targets are the microbiomes that organize large communities like oyster reefs, shorter term goals are smaller symbiotic communities like individual worm associated micro-reefs and generation of pheromones and cues from biological glues. In related work on the toxicology of plastics Rittschof is using microbiomes to inform the nature of proprietary toxic additives used in every day plastics and polymer coatings. This forensics approach complements modern analytical chemistry techniques and provides clues to additives in plastics and polymer coatings.
Jatin Roper, MD
Assistant Professor
Department of Medicine
Department of Pharmacology and Cancer Biology

My laboratory is interested in studying how stem cells in the intestine are regulated by organismal diet, the immune system, and the gut microbiome. We seek to understand how stem cell behavior is linked to diseases such as inflammatory bowel disease and colorectal cancer. We are focused on the role of toll-like receptors in intestinal stem cell function. We predict that toll-like receptors respond to local bacterial and viral signals to regulate stem cell differentiation and oncogenic transformation.
Laurie Sanders Laurie H. Sanders, PhD
Assistant Professor
Department of Neurology, Divisions of Movement Disorders and Translational Brain Sciences
Center for Neurodegenerative Diseases & Neurotherapeutics

The Sanders Laboratory studies the underlying mechanisms of age-related neurodegenerative diseases, with a particular emphasis on Parkinson’s disease. We seek to understand gene-environment interactions, including gut microbiome alterations that contribute to the initiation, potentiation of pathology and progression of Parkinson’s disease.
Amy Schmid, PhD
Associate Professor
Department of Biology
Center for Genomics and Computational Biology
Duke Microbiome Center

We explore how sensory and regulatory mechanisms in microbes integrate environmental signals to adapt and survive in fluctuating environments. We use systems approaches in archaeal extremophiles to understand the regulation of cellular physiology at the limits of sustainable life. Ultimately, we aim to model transcriptional and posttranscriptional regulatory networks to quantitatively predict phenotypic changes in response to environmental perturbation.
Keri Seymour, DO
Assistant Professor of Surgery
Metabolic and Weight Loss

As a general and bariatric surgeon, my primary research interests include understanding obesity and surgery as a treatment for obesity-related diseases. Our group studies the metabolic effects of surgery on gastrointestinal physiology and obesity-related diseases including non-alcoholic fatty liver disease (NAFLD), type 2 diabetes mellitus, and gut microbiota dysbiosis. We are investigating the impact of surgery on modification of gastrointestinal hormones, liver disease, and alteration of the gut microbiome.
Xiling Shen, PhD
Associate Professor
Department of Biomedical Engineering

Our group studies the interaction between microbiota and disease in the gut. In particular, how colon cancer, inflammation, stem cells, and the enteric nervous system impact the microbiome and how the microbiome in turn affect disease progression. We also explore whether new technology like peripheral neuromodulation, metabolic reprogramming, in vivo imaging and synthetic biology can modulate microbiota-host interaction to improve therapy.
Nazema Siddiqui, MD
Associate Professor
Division of Urogynecology & Reconstructive Pelvic Surgery
Division of Reproductive Sciences
Department of Obstetrics & Gynecology

Our team studies associations between urinary microbiota and bladder conditions such as recurrent urinary tract infection (UTI) and overactive bladder (OAB). We also study how the urinary microbiome changes with aging and in the context of estrogen. We are using this information to design new strategies to mitigate urinary symptoms and maintain health in the aging bladder.
Anthony Sung, MD
Department of Medicine
Duke Cancer Institute

As a hematopoietic stem cell transplant (HCT) physician, my group is interested in the effect of the microbiota on HCT outcomes such as infections and graft-versus-host disease. On the clinical side, we study samples from patients undergoing HCT or enrolled in our cell therapy protocols; on the laboratory side, we study a murine model of HCT (C57BL/6 -> BALB/c). Primary research questions include how the environment affects the microbiota (e.g. co-housing and shared bedding; home vs. hospital-based HCT); how the microbiota affect HCT outcomes (e.g. disruptions in the microbiota lead to GVHD, intestinal dominance leads to translocation and bacteremia); and what microbial regulatory mechanisms mediate these changes (e.g. anti-microbial peptides).
Neil SuranaNeil Surana, MD, PhD
Assistant Professor
Departments of Pediatrics, Molecular Genetics & Microbiology, and Immunology

My research innovatively integrates gnotobiotic murine models, immunology, microbiology, and characterization of the microbiota with the ultimate aim of identifying specific commensal bacteria with immunomodulatory potential and subsequent characterization of their biologic effects. We have recently developed an inventive approach for identifying with high specificity organisms within the microbiota that are causally related to the phenotype of interest. Using this approach of microbe–phenotype triangulation, we identified Clostridium immunis, a new bacterial species that protects against colitis in murine models, and two bacterial species that induce host expression of a critical antimicrobial peptide. We are now investigating the molecular mechanisms—from both the bacterial and host perspectives—that underlie these host–commensal relationships. Furthermore, we are extending our discovery platform to human samples and additional disease processes to identify more causal microbes.
David Tobin, PhD
Assistant Professor
Department of Molecular Genetics and Microbiology

Tuberculosis (TB) can have many different presentations in humans, ranging from active pulmonary disease to subclinical infections that can persist for decades. These widely different manifestations of TB depend on both host and bacterial genotypes. Our laboratory works to understand how bacterial genotype influences the course of infection. We are currently using whole genome sequencing to analyze circulating Mycobacterium tuberculosis strains (in collaboration with Drs. Jason Stout, Duke Infectious Diseases and Sunhee Lee, Duke Human Vaccine Institute). We aim to understand the evolution and transmission patterns of extant strains and to link genetic strain variation to specific clinical phenotypes.
We are using the zebrafish/M. marinum infection model to identify and understand both bacterial and host genetic determinants of disease severity and host susceptibility.
Jenny Tung, PhD
Assistant Professor
Department of Evolutionary Anthropology

Our research focuses on the relationship between social behaviors and social structure on one hand, and genetics and genomics on the other. Recently, we’ve become interested in how social relationships shape the structure of the gut microbiome, focusing on nonhuman primate populations that are models for human behavior, health, and disease. For example, in close collaboration with Beth Archie’s lab at the University of Notre Dame, we’ve found that baboons that groom more often share more similar gut microbiome composition. Socially mediated transmission may thus have an important role in shaping the microbiome, a relationship that also has ramifications for the evolution of social living.
Raphael Valdivia, PhD
Associate Professor
Department of Molecular Genetics and Microbiology

One of the focuses of my laboratory is to understand how individual microbial genes contribute to establishing pathogenic or mutualistic interactions between microbes and their vertebrate hosts. We are particularly interested in developing methods to study "non–model" microbes, such as obligate pathogens, emerging infectious agents and microbial species in the vertebrate gut microbiome. These organisms are of significant importance in clinical and environmental settings, yet very little is known about the function of their genes because these microbes are difficult to culture and genetically manipulate in the laboratory. We combine chemical mutagenesis and NextGen DNA sequencing technologies to perform genome-wide association studies and establish genotype-phenotype links in these "genetically-intractable" microbes. In this manner, we seek to identify microbial genes required for host colonization, metabolic adaptation, establishing mutualism, and how they ultimately impact human health.
Rytas Vilgalys, PhD
Professor, Biology

Our lab studies genetics and natural history of fungi using a variety of field-based and experimental approaches. Research areas include: 1) Fungal biodiversity, molecular systematics, and comparative genomics; 2) Molecular epidemiology and population genetics of fungal mating systems and life history including mushrooms and human pathogens; and 3) Metagenomic studies of plant-fungal symbiosis in forest ecosystems and responses of fungal communities to environmental change.

Jennifer Wernegreen, PhD
Associate Professor
Nicholas School of the Environment

Our work focuses on bacterial genome evolution, particularly in the context of symbiotic associations with animal hosts. Many of our current projects center on bacterial partners of ants and other insects, including diverse gut microbiota as well as long-term nutritional mutualists that have lived exclusively within insect cells for millions of years. Using comparative genomics, population genetics, and experimental approaches, we are examining fundamental evolutionary and ecological processes that shape these host-microbe associations, their functional significance in variable natural environments, and long-term consequences on rates and patterns of genome change.
Paul Wischmeyer, MD, EDIC
Professor of Anesthesiology and Surgery

Our laboratory¹s interest is exploring the role of the microbiome and probiotic/bacterial based nterventions in perioperative care, critical care, and other illness states. We are excited to partner with groups looking for large scale single and multi-center clinical microbiome sample collection that can be paired with extensive clinical outcome data- including mortality and morbidity, nutritional variables, cognitive function, functional/physical status and other translational science endpoints. Our current collaborators include work carried out with the Rob Knight Lab and we hope to grow our work partnering with other fundamental microbiome labs. We hope our collaborative work will allow for microbiome signatures to be used as diagnostic markers and guides to therapeutic interventions in patients to repopulate the normal, "health-promoting" microbiome with probiotics therapies to improve patient outcomes. We also have a key interest in the role of probiotics and other nutrition interventions that effect dysbiosis to promote recovery from illness in both clinical trials and laboratory
models of illness/injury.
Anne Yoder, PhD
Braxton Craven Professor of Evolutionary Biology
University Program in Genetics and Genomics

The Yoder Lab has a long-standing interest in the evolution of the highly endemic biota of Madagascar. Ongoing projects are investigating the differential impacts of diet, ecology, and phylogenetic history on the gut microbiome of Madagascar's iconic lemurs. One finding of tremendous consequence has been the discovery that the majority of microbial lineages found within the lemuriform gut are unique to Madagascar, in keeping with the signal of long-term independent evolution among host organisms. Future projects will focus on understanding the role of the gut microbiome in driving and maintaining speciation among vertebrate lineages, providing insight into the ecological principles that govern microbial community assemblage, niche partitioning, maintenance, defense and recovery over the life of the vertebrate host.
Lingchong You, PhD
Associate Professor, Biomedical Engineering

A major focus of our work is on using engineered bacteria as models to address unresolved biological questions. We pioneered the use of cell-cell communication to regulate survival and killing of one or multiple populations. Using these engineered systems, we have examined the critical factors that underlie the stability and evolution of microbial populations in time and space. Analysis of these engineered systems has led to new insights into how bacteria cope with stress and mechanisms underlying self-organized pattern formation. These insights have laid the foundation for our ongoing research in investigating the collective antibiotic tolerance by bacterial pathogens, bacterial-mediated fabrication of patterned materials, and in engineering novel hybrid biological-biomaterial systems for sustained protein synthesis and delivery.
Noelle Younge, MD, MHS
Assistant Professor of Pediatrics, Neonatology

Our research interests focus on understanding the factors dictating microbiome assembly in infancy and the effects of host-microbiome interactions on infant health and development. We are studying the influence of the intestinal microbiota on metabolism and postnatal growth of extremely preterm infants, perinatal acquisition of microbiota from maternal and other environmental sources, and the effects of bioactive components of human milk on microbial succession and immune responses.


Nancy Zucker, PhD
Associate Professor
Child & Family Mental Health and Dev Neuro

Our laboratory is interested in how individuals learn to detect and decipher the signals from their bodies (e.g., of hunger, of emotional experience) and use these signals to guide their behavior. We study individuals for whom this learning somehow goes awry: individuals struggling with eating disorders (e.g. anorexia nervosa, ARFID, selective eating, pediatric binge eating), those with chronic medical conditions that may disrupt or complicate this learning (e.g. pediatric gastrointestinal disorders or pediatric cancer) or neurodevelopmental disorders such as autism. Using this information, we strive to develop interventions that manipulate afferent input from the viscera (particularly the gut), help individuals to decipher and utilize afferent input from the viscera, or some combination of these factors. For instance, our group is currently conducting interventions that help young children with abdominal pain learn to decipher visceral signals (rather than be afraid of their bodies); using probiotics as a treatment for anxiety in anxious 9-13 year olds with abdominal pain, and are using exercise as a form of biofeedback to improve body image in anorexia nervosa.