Peter Belenky Ph.D. ( Founder ) 

Brown University

We are interested in how the microbiome changes its functional profile in response to the host environment. We are working with murine, human, and marine microbiomes. A particular focus of our work is on how antibiotics impact the metabolic function of the microbiome and how the metabolic environment within the host impacts the toxicity of antibiotics. Our hope is that by understanding the links between host metabolism, microbial metabolism, and antibiotic efficacy we can identify therapeutic methodologies to protect the microbiome from antibiotic-induced disruption. To profile microbiome function during antibiotic therapy, we utilize a multi-omic approach that includes shotgun metagenomics and metatranscriptomics as well as metabolomics.  Other interests in the lab include IBD, fungal infections, cross-domain interactions, HGT of antibiotic resistance, and the gut-brain axis. 

In our work, we utilize 16S rRNA amplicon sequencing, shotgun metagenomics, shotgun metatranscriptomics, anaerobic culture, and genome assembly.

Belenky Lab

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Pathobiology Graduate Program


Roxanne Beinart Ph.D.   

University of Rhode Island

Marine microbes critically influence global primary productivity, biogeochemical cycling, and oceanic food webs. We also recognize that the majority of eukaryotes are associated with microbes. The Beinart lab unites these two important ideas with the question: what are the roles of symbiotic microbes in marine ecosystems? Our research describes the mechanistic links among symbiont physiology, ecological processes, and biogeochemical cycles in order to advance knowledge of the function of microbes in marine ecosystems.

Beinart Lab



Richard Bennett Ph.D.   

Brown University

Our lab investigates the biology of commensal fungal species including Candida albicans and Candida tropicalis. We look to investigate how these species are able to adapt to their environment in the gastrointestinal tract, as well as how they can disseminate and cause opportunistic infections in the bloodstream. We are particularly interested in both the genetic and epigenetic mechanisms used by Candida species to generate phenotypic diversity, including their sexual cycles, and how these mechanisms can impact interactions with other commensal microbial species.

In our work, we utilize genome sequencing, RNA-seq, genetics and cell biology.



Alexandra Deaconescu Ph.D. 

Brown University

The overarching goal of research in the Deaconescu laboratory is to understand at a mechanistic and structural level the complexities of bacterial stress responses.  The cornerstone of our methodological approach is X-ray crystallography, but high-resolution crystallographic studies are synergistically combined with studies using small angle X-ray scattering, electron cryo-microscopy, biochemistry and other biophysical macromolecular characterization techniques. Currently, our work focuses on two distinct projects: (1) mechanisms of transcription-coupled DNA repair, and (2) transcriptional reprogramming induced by stress (including oxidative stress and DNA damage).
In the first case (transcription-coupled DNA repair) we are particularly interested in how ATP-dependent transcription-repair coupling factors are regulated by binding partners, how they may globally alter the distribution of elongating RNA polymerases found on the chromosome, and critically, on the structural characterization of their mechanochemical cycle.

In the second case, we are focusing on the master regulator of the bacterial stress response, RpoS, which globally redirects the transcription machinery to a subset of promoters to ensure survival under stress. Uniquely among stress-induced proteins, this master regulator is able to mount a response, which is global and so profound that it is effective in even protecting from stress signals not yet encountered. We aim to develop an atomic-resolution understanding of RpoS regulation, with direct implications for virulence and biofilm formation.

In our work, some of the tools that we use include X-ray crystallography, cryo-EM and other biophysical techniques

Deaconescu Lab



Marta Gomez-Chiarri Ph.D.

University of Rhode Island

Infectious diseases have a serious impact on shellfish and finfish, constraining the expansion of aquaculture and endangering wild fisheries. Our research interests include the use of multidisciplinary approaches to the prevention and management of infectious diseases in cultured and wild shellfish and finfish. These approaches include studying the patterns of disease prevalence and distribution using traditional and molecular diagnostic tools, investi-

gating host-microbial interactions, mechanisms of pathogenesis and disease resistance, and using all this information to develop novel strategies to prevent diseases in aquatic organisms. Examples of ongoing and past research projects in the laboratory include (1) the elucidation of the molecular immune responses of the Eastern oyster Crassostrea virginica to various pathogenic challenges, (2) development and testing of probiotics for commercial aquaculture, and (3) determination of the oyster microbiome and its response to disease, environment conditions, or pathogenic challenge.

In our work, some of the tools that we use include genome sequencing and assembly, comparative genomics, 16S amplicon sequencing, shotgun (meta)genomicsshotgun (meta)transcriptomics, histology, disease challenges.



Amanda M. Jamieson Ph.D.  

Brown University

The main focus of our laboratory is on understanding host resilience mechanisms to infectious and non-infectious diseases of the lung and skin. Most research focuses on curing diseases by ridding hosts of a particular environmental insult, injury, cancerous cell, or clearing a pathogen. Another way to survive an infection is to tolerate the alterations to homeostasis that occur during a disease state; a process called host resilience or tolerance. We are focused on what mechanisms (including the microbiome, immune response, metabolism, etc.) are necessary to increase tolerance, and hence survival, to lung and skin diseases.

Jamieson Lab




Colleen R. Kelly M.D. 

Associate Professor of Medicine;

Lifespan Physician Group Gastroenterology Practice

The focus of my research and clinical practice is C. difficile infection (CDI) and fecal microbiota transplantation (FMT).  I was the principal investigator for a first placebo-controlled trial of FMT for treatment of recurrent CDI and one of the first investigators to sponsor of an investigational new drug (IND) application with the FDA. I have since served on several working groups focusing on regulatory issues related to FMT.  I am currently site PI for an industry-sponsored trial of an oral full spectrum microbiota for treatment of recurrent CDI and one of the PIs for an NIH-funded FMT National Registry which will answer important questions around the long-term safety of FMT.  FMT may prove beneficial for other diseases or conditions associated with dysbiosis and I am collaborating on several studies investigating the impact of FMT on patients with Inflammatory Bowel Disease, Nonalco-

holic Fatty Liver Disease and Alopecia Areata.  In addition to coauthoring current FMT guidelines I am serving as primary author for the forthcoming American College of Gastroenterology (ACG) 2019 C. difficile treatment guidelines.  I am a Fellow in the ACG and is a past member of the scientific advisory board for the American Gastroenterological Association Center for Gut Microbiome Research and Education.   




Richard T. Liu Ph.D. 

Bradley Hospital, and Brown University 

In our lab, we are interested in elucidating the potential role of the gut microbiome in the pathophysiology of depression and self-harm. In collaboration with Peter Belenky, Ph.D, I am currently conducting a study investigating whether gut dysbiosis prospectively predicts depressive symptoms over time in a sample of young adults, and whether pro-inflammatory cytokines may mediate this association.  




Eleftherios Mylonakis, M.D., Ph.D. 

Chief, Infectious Diseases Division, Alpert Medical School of Brown University and Rhode Island Hospital and The Miriam Hospital

We have an interdisciplinary and translational focus, and we use a variety of tools to answer complex scientific questions. This diverse approach includes areas such as molecular biology, immunology, biostatistics, decision-making analysis, risk assessment, outcomes research, and cost-effectiveness studies. Our host-pathogen and antimicrobial drug discovery studies utilize biostatistics, whole animal HTS, and screening by imaging, to identify lead compounds and study the fundamental molecular mechanisms that are employed pathogens against a widely divergent array of metazoan hosts.

In our work, some of the tools that we use include C. elegans bacterial colonization, HTS, and molecular biology.




Hollie Putnam, Ph.D.  

University of Rhode Island

Work in the lab is focused broadly on physiological ecology and epigenetic processes. We strive to understand how the immediate abiotic environment and biotic interactions drive organism phenotype, ecological patterning, and evolutionary processes through the interaction of symbiosis, genetics, and epigenetics. We study scleractinian, or reef-building corals, and other calcifying marine invertebrates. These organisms provide the foundation of ecosystems and fisheries and are ideal study systems to focus on biological response within the context of local environmental stress and a changing climate.

In our work, we utilize RNASeq, Methylome Sequencing, ITS2, 16S, and ecophysiology.




Matthew M. Ramsey Ph.D.  

University of Rhode Island

My laboratory is interested in polymicrobial interactions in the human oral microbiome. Many oral bacteria are dependent on these multispecies interactions for survival. Our work includes finding bacterial interactions of interest in both health and disease and identifying the mechanisms underlying these interactions so we can exploit them as future targets for anti- or probiotic therapy to either treat or prevent oral infections.

In our work, we utilize 16S sequencing, RNA-Seq, and  Microbiome data analysis.   

      Ramsey Lab



Jason M. Shapiro, M.D.   

Hasbro Children’s Hospital, Rhode Island Hospital, and Brown University 

Defining the significance of the human microbiome in health and disease is a rapidly evolving field. I have developed a specific interest in understanding how changes in the gut microbiome contribute to the immunopathogenesis of inflammatory bowel disease (IBD). As co-investigator of the multicenter Pediatric RISK stratification study, I was a co-author on one of the first papers to demonstrate specific microbial markers of disease outcomes in a prospective cohort of pediatric patients with Crohn’s disease. I am currently a principal investigator of a collaborative study aimed at defining the immunologic and clinical relevance of IgA-coated bacteria in IBD.

In our work, we focus on translational research, patient enrollment, sample collection, and interpreting microbial datasets in a clinical context.




Koty Sharp, Ph.D.   

Roger Williams University

Our research explores the microbial ecology and chemical ecology of marine invertebrate-bacterial symbioses, with a focus on the microbiome’s role in shaping the host animal’s response and resilience to change. We study symbiotic acquisition and transmission, patterns of microbial community diversity and dynamics, and the factors that regulate and organize microbial assemblages in and on benthic marine invertebrates, most notably, corals and coral reef organisms.

Some of the tools that we use include 16S amplicon sequencingfluorescence and confocal microscopy, aerobic culturing, molecular biology, and field experiments

Sharp Lab



Shipra Vaishnava Ph.D.  

Brown University 

Our lab focuses on the following areas of research to gain a better understanding of the complex and dynamic nature of host-microbe interaction at the intestinal mucosal surface:  1. Role of adaptive immunity in regulating host-microbe interaction. Intestinal microbiota provides a strong selective pressure for the host to evolve adaptive immunity.  We are interested in studying the role of adaptive immunity in regulating composition and geographical location of the intestinal bacteria. 2. Bacteria regulated vitamin A 

metabolism. Complex communities of bacteria inhabit the mammalian intestines that are continuously interacting with the host. Our goal is to define the molecular mechanism by which gut bacteria modulate vitamin A metabolism in the intestine and how this regulates RAR signaling dependent immune function in the mucosal tissues. 3. Stratification of bacterial communities within the intestinal mucus layer. Intestinal bacteria play a critical role in regulating the metabolic potential of the host and greatly influences host biochemistry and susceptibility to disease. Our goal is to determine how bacterial communities are stratified within the intestinal lumen in order to better understand how they might influence host physiology and susceptibility to disease.

In our work, we utilize animal models, gnotobiotic mice, 16S sequencing, and laser capture microscopy. 

Vaishnava Lab



Ying Zhang, Ph.D.   

University of Rhode Island

Metabolism is an important process that governs the homeostasis of individual cells, multicellular organisms, and complex multi-organismal interactions. In human, animals, insects, and marine invertebrates, metabolism of host-associated microbiomes is essential for mediating food digestion and is correlated with the health and disease of the host. In the marine environment, metabolism of microbial communities mediates diverse ecosystem function and is essential for the circulation of carbon nutrients and energy flow. The Zhang Laboratory works on the development of computational tools to study the metabolism and evolution of microbiomes. Applying our in-house open-source software, PSAMM, we aim to construction genome-to-ecosystem models for diverse microbiome communities.

Zhang Lab GitHub