Researchers


Ashfaqul Alam, Ph.D.

Assistant Professor, Pathology & Laboratory Medicine

My research programs focus on (1) the metagenomic study of the gut microbiome in health and diseases including colitis, obesity, and neurodegenerative diseases, and (2) the meta’omics analysis to elucidate the functions of microbial metabolites and small molecules during intestinal regeneration.



Jinbing Bai, PhD, MSN, RN

Assistant Professor, Nell Hodgson Woodruff School of Nursing, Emory University

My research focuses on the microbiome-gut-brain axis, cancer treatment-related outcomes, symptoms and toxicities. Using pipelines built by my team to analyze the gut microbiome, I study the impact of the gut microbiome on short-term and long-term side effects in children with cancer. I am currently holding a 5-year NIH K99/R00 award to understand the role of the gut microbiome on psychoneurological symptoms in chemotherapy. I also have experiences in studying the vaginal and gut microbiome in adult cancers.



Steven Bosinger, PhD

Assistant Professor, Dept. of Pathology and Laboratory Medicine
Director, Yerkes NHP Genomics Core, Div. Microbiology & Immunology

Our group is interested in understanding the relationship of intestinal and vaginal microflora and its relationship to HIV infection.  These studies fall into several categories: HIV transmission – in which we study the microflora in vulnerable humans populations in the US and Africa in the intestinal and vaginal tract and its association with susceptibility to HIV acquisition, and its interfence with prophylactic strategies. Vaccine responses: by comparing vaccine responses of adult macaques compared to those in infant receiving vaccines very early in life, before the diet-driven microbiome has been established, we are testing the ability of the microbiome to impact the breadth and immune dominance of the B cell repertoire. HIV pathogenesis: We recently discovered that sooty mangabeys, African green monkeys, and other non-human primate species that do not develop AIDS harbour a conserved mutation in TLR4 that dampen inflammatory reactions to bacteria. We are comparing the intestinal microbiota in natural host species to rhesus macaques (which develop AIDS) in diet-controlled conditions to determine if this mutation confers selection for divergent bacteria in natural hosts that help to maintain low levels of inflammation in the gut. Lastly, we are studying differences in the intestinal microbiome between captive and indigenous African primates.



Berry Brosi, PhD

Winship Distinguished AssociateProfessor,Department of Environmental Sciences, RSPH

Dr. Brosi is a biologist focused on the quantitative ecology of multi-species interactions in diverse biological communities. Much of his group’s work focuses on the functional consequences of diversity in biological systems, as well as the functional consequences of different network structures. While our work has not involved microbial systems to date, many of the questions and quantitative methods involved in our work are well suited to microbiome-related topics. We are also actively involved in using amplicon-basedmethods, analogous to 16S approaches in microbiology, to identify and quantify mixed-species pollen loads



Dr. Deborah Watkins Bruner, RN, PhD, FAAN

Senior Vice President for Research, Emory University
Robert W. Woodruff Professor of Nursing, Professor of Radiation Oncology.

Dr. Bruner’s latest work in the microbiome began as a natural extension of her research in symptoms and toxicities after cancer therapies for gynecologic malignancies. She works with a multidisciplinary team including Dr. Kostas Konstantinidis, Carlton S. Wilder Associate Professor, Georgia Institute of Technology, and expert in microbial genomic analysis and bioinformatics, as well as experts in gynecologic oncology and radiation therapy. Her team is also assessing associations among the gut and skin microbiome and cancer related outcomes.



Craig Coopersmith, MD, FACS, FCCM

Interim Director, Emory Critical Care Center and Professor of Surgery

The Coopersmith lab studies the role of the microbiome in sepsis. There is a rapid profound decrease in gut microbial diversity in sepsis, and this is associated with worsened outcomes in the disease. The laboratory is examining how the microbiome mechanistically alters the immune system and the gut epithelium in sepsis, and how these changes impact host survival. The ultimate goal of the research is to develop tools to alter the microbiome in patients in a disease which is the third most common cause of death in the United States.



Elizabeth J. Corwin, MD

Nell Hodgson Woodruff School of Nursing

We investigate the association of the maternal vaginal, oral, and gut microbiome with symptom development and adverse outcomes in pregnant and postpartum women including preterm birth and postpartum depression, and with infant and toddler neurodevelopmental and physical outcomes including autism spectrum disorder and obesity. I am especially interested in the contribution of chronic stress exposure including racial discrimination, on the microbiome, and I focus my research on those most at risk for both chronic stress exposure and adverse health outcomes; African American women and their families.I am also interested in the contribution of the gut microbiome to the symptoms of fatigue, depression and anxiety and their associated metabolic pathways, experienced by African American adults suffering from multiple chronic health conditions.



Nicole Marie Gerardo, MD

Department of Biology

The Gerado lab studies the ecology and evolution of both beneficial and harmful host-microbe interactions, focusing on insect-associated systems that provide an opportunity to experimentally manipulate host and microbe pairings. Her research group has characterized how microbial associations of a number on insects, including aphids, squash bug, butterflies and beetles, shape host functioning, including protection from disease. Beyond fundamental research, she is currently working with Chris Beck (Emory) and Larry Blumer (Morehouse) to develop course-based undergraduate research experience for students to study the gut microbiome of bean beetles



Joanna B. Goldberg, Ph.D.

Professor, Department of Pediatrics
Division of Pulmonary, Allergy &Immunology, Cystic Fibrosis, and Sleep

I have worked in the field of the bacterial infections in cystic fibrosis (CF) for over 30 years.I am Director of Microbiologyat EmoryCF Biospecimen Registry, which includes bacterial isolates from people withCF,as well as sputum sampleswith available associated clinical data. I aminterested in the interactions of CF lung microbes and have investigated how the presence ofPseudomonasaeruginosaandStaphylococcus aureusimpact clinicaloutcome. More recentlymy laboratory started microbiome studies on sputumsamples from people withCF and are investigating theeffects ofpolymicrobial infections in these individuals.



Lisa Haddad, MD MS MPH

Assoc. Professor, Department of Gynecology and Obstetrics,Division of Family Planning,Emory University School of Medicine

Our research is evaluating the impact of the vaginal microbiome on HIV and STI risk. Further, we are evaluating the interaction of the microbiome on contraception associated changes in immunity in the lower genital tract. Additionally, we are interested in evaluating the impact of STI treatment on the vaginal microbiome and preterm delivery. These areas of inquiry have the potential for large public health impact.



Yijuan Hu, PhD

Associate Professor,Department of Biostatistics and Bioinformatics, RSPH

My research has been focused on developing statistical methods and tools for analyzing microbiome data, mainly 16S data for now.Working with Glen Satten at Centers for Disease Control and Prevention, we have developed methods for testing the overall association between microbiome and a (clinical, environmental) trait of interest and also detecting individual OTUs or taxa (species, genera, etc.) that are associated. We are working on methods that can analyze matched-pair, matched-set, and longitudinal data of the microbiome. I am also interested in meta-analysis of microbiome data from multiple studies that have similar traits of interest.



Rheinallt M. Jones PhD

Assistant Professor, Department of Pediatrics & Director Gnotobiotic Animal Core

My research interests include discovering the molecular mechanisms whereby beneficial bacteria known as ‘probiotics’ elicit their positive influences on health and disease. Specifically, we seek to discover the products released by beneficial bacteria, the host cell receptors that sense the products, and the downstream signaling events that are activated within host immune or epithelial cells. I am also the Director of the Emory Gnotobiotic Animal Core where we generate germ-free and gnotobiotic mice for the Emory research community.



Daniel Kalman, Ph.D.

Dept. of Pathology and Laboratory Medicine Emory University

My labuses the nematodeC. elegansas a biosensor to identify factors secreted by commensal bacteria (microbiota) that influence innate immunity, andhealth span.Importantly these molecules also influence innate immunity and immune tolerance in mammals, which we demonstrate using models of bacterial infection, environmental stress, and allogeneic bone marrow andT cell transplant. We haveshown that factors used byC. elegansare conserved across phyla, including in mammals.Wehave identified bacterial factors that influence mammalian immunity and can serve as the basis for therapeutics for auto-or allo-immune disorders or other diseases that result from dysbiosis. Our most recent work has shown that indoles augmenthealthspan and make older animals resemble younger ones, and that these same indoles can cure graft vs. host disease (Sonowal et al.,Indoles from commensal bacteria extend health span.2017 PNAS114(36):E7506-E7515.Swimm, A. et al.,Indoles Derived from Intestinal Microbiota Act via Type I Interferon Signaling to Limit Graft-versus-Host-DiseaseBlood2018in press)



Colleen F. Kelley MD, MPH

Associate Professor of Medicine, Division of Infectious Diseases, Department of Medicine

I have a multi-disciplinary background and experience in clinical HIV/STI medicine, HIV/STI epidemiology and clinical outcomes research, and laboratory-based research. The primary focus of my research is on mucosal HIV susceptibility in sexual and gender minority populations with a particular interest in biomedical prevention interventions. I am currently conducting several studies examining mucosal immunology and how real-life, human, sexual contexts can influence rectal mucosal susceptibility to HIV.  My translational immunology laboratory has specific expertise in flow cytometry and explant HIV challenge experiments with human mucosal tissues and the relationship of the microbiome to mucosal inflammation.



Colleen S. Kraft, MD, MSc

Associate Professor, Department of Pathology and Laboratory Medicine
Associate Professor, Division of Infectious Diseases,Emory University Hospital

Dr. Colleen Kraft is an infectious diseases physician and medical microbiologist and along with Dr. Tanvi Dhere started the Emory Fecal Transplant Program in 2012.This program has recreated itself as the Emory Microbiota Enrichment Program, and serves to bring in studies and funding to support microbiome therapeutics at Emory Hospital.Dr. Kraft has over 20 publications on fecal microbiota transplantation, and currently is the site PI on 4 industry trials to study various microbiome therapeutics forC. difficile.She is also the PI for investigator initiated research looking at descriptive microbiome studies in returning travelers and organ transplant recipients.She is also the PI for the PREMIX study (NCT02922816) which utilizes fecal enema to eliminate multi-drug resistant organism carriage in renal transplant recipients



Karen Levy

Associate Professor, Department of Environmental Health, Rollins School of Public Health

My  research program focuses on the ecology and epidemiology of enteric (food and waterborne) diseases.  Our group examines environmental determinants of the gut microbiome and how interactions between the gut microbiome and enteric pathogens shape acute and chronic child health outcomes. I currently co-direct two projects focused on the infant gut microbiome, enteric pathogens and child health outcomes, one in Ecuador and the other in Mozambique.  Both are funded by major grants from the National Institute for Allergy and Infectious Diseases.



Vincent Marconi, MD

Professor of Medicine and Global Health,Division of Infectious Disease,Emory University School of Medicine
Department of Global Health,Rollins School of Public Health
Emory Vaccine Center,Yerkes National Primate Research Center

Our research team is interested in identifying the drivers of viral persistence and chronic inflammation for individuals living with HIV. Alterations in the oral and gut microbiome can contribute to systemic inflammation and immune activation which can result in AIDS progression and serious non-AIDS diseases as well as persistence of the HIV viral reservoir.



Jan Mead, PhD

Professor, Department of Pediatrics

Cryptosporidiosis can be severe in immunocompromised patients and is the 2nd leading cause of diarrheal illness in children in developing countries.  Our laboratory is examining how changes in the microbiome affect susceptibility and Infection levels to the gut pathogen cryptosporidium.  In collaboration with our co-investigators (Dr. Rheinallt Jones, Dr. Colleen Kraft) we are developing a “Humanized” Microbiome Mouse Model using fecal transplants from individuals and engrafting them into germ-free mice.



Andrew S. Neish, MD

Professor of Pathology

Dr. Neish is interested in mechanistic study of the role of the microbiota in a spectrum of human diseases. He oversees projectsinvestigating inflammatory bowel disease and gut homeostasis, systemic metabolic and hepatic disorders, neuroinflammation, infectious disease,and reproductive biology. The laboratory utilizes human, murine and model systems including gnotobiotics, and employs a variety of analytic methods, including metagenomics, metatranscriptomics, and metabolomics.



Roberto Pacifici, MD

Garland Herndon Professor of Medicine
Director of the Division of Endocrinology, Metabolism and Lipids, Emory SOM

Dr. Pacifici is one of the founders of the field of osteoimmunology and an expert on the mechanism of action of estrogen and PTH in bone. The overall goal of the lab is to determine the contribution of the gut microbiome to bone health and disease. The Pacifici’s lab focuses on the regulatory effects of the microbiome on immune cells, which are relevant to the regulation of bone turnover and the mechanism of action of probiotics in bone. Using germ-free mice, antibiotic treated mice and stool transfer techniques, we are investigating the mechanism by which estrogen deficiency alters gut permeability, immune cell activation in the gut, the trafficking of lymphocytes from the gut to the bone marrow, and the components of the gut microbiota that are relevant for bone loss.



Pretesh Patel, MD

Assistant Professor
Dept of Radiation Oncology, Winship Cancer Institute

We study the impact of radiotherapy on the human microbiome and its influence on the patient symptom experience.We specifically study microbiota of the skin, vagina, and gut in patients with breast cancer, GYN malignancies, and GI malignancies.



Glen A Satten PhD

Senior Statistician,Division of Reproductive Health,Centers for Disease Control and Prevention
Adjunct Professor, Emory University: Department of Biostatistics & Bioinformatics; Department of Environmental Health; Department of Human Genetics

I do research developing methods for analyzing data from microbiome studies, especially 16S studies.Working with Yijuan Hu in the Department of Biostatistics & Bioinformatics, we have developed an approach that unifies overall tests of microbiome effect withtests of the effects of individual OTUs or ASVs.We are interested methods to analyze complex epidemiologic studies such as matched/clustered/longitudinal microbiome data or studies with important confounders.I am also interested in questions about how to normalize or standardize 16S data using control samples.



Guido Silvestri, M.D.

SOM Pathology and Yerkes

Our laboratory studies HIV/AIDStransmission andpathogenesis using comparative pathogenic and non-pathogenic models of SIV infection in non-human primates. A number of studies have shown thatthose events are influenced by specific features of the microbiome in mucosal tissues such as the gastro-intestinal and genital tracts. In particular, the relationship between the microbiome and the HIV/SIV-associated chronic immune activation is the topic of intense studies.



Alicia K. Smith, Ph.D.

Associate Professor &Vice Chair for Research
Gynecology and Obstetrics, Emory University School of Medicine

My main area of microbiome work is optimization of experimental methods and bioinformatic approaches for human microbiome studies, particularly as it applies to the vaginal microbiome and women’s health.



Lynn Marie Trotti, MD, MSc

Associate Professor of Neurology, Emory Sleep Center

I am a sleep neurologist evaluating causes of and treatments for disorders of excessive daytime sleepiness, such as idiopathic hypersomnia and narcolepsy.  We have previously shown that the macrolide antibiotic, clarithromycin, reduces sleepiness in patients with these disorders, but the mechanism of action is currently unknown.  We are about to begin an NIH-funded mechanistic clinical trial of clarithromycin vs placebo to evaluate potential mediators of treatment benefit, including changes in the microbiome. 



Despina Tsementzi, PhD

Nell Hodgson Woodruff School of Nursing

My main research interest is the understanding of how microbes function and interact within microbial communities in natural and engineered ecosystems and which are the underlying ecological and evolutionary processes that shape natural microbial assemblages. I have been employing and advancing cutting edge “omic” techniques (metagenomics, meta-transcriptomics, single cell genomics, viromics) to study microbial communities within environmental, clinical, and engineered settings. My current work  focuses on the human microbiome and how it affects human health, disease and recovery from cancer therapies. Our most recent work aims to understand the dynamics and functional potential of the vaginal microbial communities in postmenopausal women that undergo radiation therapy for gynecological cancers, and the extent and mechanism by which the microbiome affects treatment outcomes and related symptoms.



Nic Vega, PhD

Assistant Professor, Biology Department

The Vega lab uses a combination of experiments and modeling to understandmicrobial ecology in the host environment. We are particularly interested in understanding the assembly and evolution of commensal and pathogenic microbial communities and in determining the factors that make host-associated communities resilient to stress, including antibiotic perturbation and invasion by pathogens. To this end, we use the nematode wormC. elegansas a tractable experimental system for microbial community assembly.