The Microbiome Immunity Project is a research collaboration between Dr. Ramnik Xavier of the Broad Institute of MIT and Harvard and the Massachusetts General Hospital, Dr. Rob Knight at the University of California San Diego (UC San Diego) and Dr. Rich Bonneau at the Simons Foundation’s Flatiron Institute.

Research Team

UC San Diego

Center for Microbiome Innovation

La Jolla, California, USA

The Center for Microbiome Innovation at UC San Diego is a concerted research and education effort that leverages the university’s strengths in science, medicine, engineering, and the humanities to produce a detailed understanding of microbiomes — distinct constellations of bacteria, viruses and other microorganisms that live within and around us — and methods for manipulating them for the benefit of human health and the environment.

Rob Knight, PhD

Professor, Departments of Pediatrics and Computer Science & Engineering
Director, Center for Microbiome Innovation
Co-Principal Investigator, Microbiome Immunity Project

Rob Knight is the founding Director of the Center for Microbiome Innovation, an Agile Center in the Jacobs School of Engineering with the School of Medicine and the Division of Biological Sciences as founding partners, and is Professor in UC San Diego’s Departments of Pediatrics and Computer Science & Engineering. Previously, he was Professor of Chemistry & Biochemistry and Computer Science in the BioFrontiers Institute of the University of Colorado at Boulder, and a Howard Hughes Medical Institute Early Career Scientist.

He is a Fellow of the American Association for the Advancement of Science and of the American Academy of Microbiology. In 2015, he received the Vilcek Prize in Creative Promise for the Life Sciences.

He is the author of “Follow Your Gut: The Enormous Impact of Tiny Microbes” (Simon & Schuster, 2015), and spoke at TED in 2014.

His lab has produced many of the software tools and laboratory techniques that enable high-throughput microbiome science, including the QIIME pipeline (cited over 5,000 times as of this writing) and UniFrac (cited over 3,000 times including its web interface). He is co-founder of the Earth Microbiome Project, the American Gut Project, and the company Biota, Inc., which uses DNA from microbes in the subsurface to guide oilfield decisions.

His work has linked microbes to a range of health conditions including obesity and inflammatory bowel disease, has enhanced our understanding of microbes in environments ranging from the oceans to the tundra, and made high-throughput sequencing techniques accessible to thousands of researchers around the world.

Tomasz Kosciolek, PhD

Assistant Professor, Małopolska Centre of Biotechnology, Jagiellonian University in Kraków, Poland
Research Associate, Knight Lab, University of California San Diego, USA

Tomasz Kosciolek is an Assistant Professor and a group leader of the Structural and Functional Genomics Group at Małopolska Centre of Biotechnology, Jagiellonian University, in Kraków, Poland; and a research associate at the Knight Lab, Department of Pediatrics, University of California San Diego, USA.

He holds an MSc in chemistry (2010) from the Jagiellonian University in Kraków, Poland; and a PhD in biological sciences (2015) from University College London, United Kingdom. His doctoral work was focused on the application of sequence covariation methods for protein structure prediction and computational predictions of dynamic properties in intrinsically disordered proteins. His postdoctoral work at the Knight Lab focused on studies of microbial proteins, method development for microbiome analyses, and studying the role of the microbiome in health and disease, especially in the context of the gut-brain axis – the impact of the gut microbiota on mental health.

The focus of his research group now is to integrate his prior expertise in structural biology and microbiome studies to build a comprehensive multi-scale understanding of the microbiome, from genes, through structures, to functions and therapies.

Broad Institute of MIT and Harvard

Cambridge, Massachusetts, USA

The Broad Institute of MIT and Harvard was launched in 2004 to empower this generation of creative scientists to transform medicine. The Broad Institute seeks to describe all the molecular components of life and their connections; discover the molecular basis of major human diseases; develop effective new approaches to diagnostics and therapeutics; and disseminate discoveries, tools, methods, and data openly to the entire scientific community.

Founded by MIT, Harvard, Harvard-affiliated hospitals, and the visionary Los Angeles philanthropists Eli and Edythe L. Broad, the Broad Institute includes faculty, professional staff, and students from throughout the MIT and Harvard biomedical research communities and beyond, with collaborations spanning over a hundred private and public institutions in more than 40 countries worldwide. For further information about the Broad Institute, go to

Massachusetts General Hospital

Boston, Massachusetts, USA

Massachusetts General Hospital is the original and largest teaching hospital of Harvard Medical School. Mass General conducts the largest hospital-based research program in the United States, is the top recipient of research funding from the National Institutes of Health, and has long been a leader in successfully bridging innovative science with state-of-the-art clinical medicine. With an annual research budget of more than $800 million, their research program spans more than 20 clinical departments and centers across the hospital. This research drives discoveries and breakthroughs in basic and clinical research, which translate into new and better treatments.

Ramnik Xavier, MD

Chief, Gastrointestinal Unit, Massachusetts General Hospital (MGH)
Director, Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital
Kurt J. Isselbacher Professor of Medicine, Harvard Medical School
Institute Member and Co-Director of the Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard
Co-Director, Center for Microbiome Informatics and Therapeutics, MIT
Co-Principal Investigator, Microbiome Immunity Project

Ramnik Xavier is Chief of Gastroenterology at Massachusetts General Hospital, Kurt Isselbacher Professor of Medicine at Harvard Medical School, and an Institute Member at the Broad Institute of MIT and Harvard. In addition to his roles as Director of the Center for the Study of Inflammatory Bowel Disease at MGH, Co-Director of the Center for Microbiome Informatics and Therapeutics at MIT, and Co-Director of the Microbiome and Infectious Disease program at the Broad Institute, he is also a founding member of the Center for Computational and Integrative Biology at MGH.

As a clinical gastroenterologist and molecular biologist, he studies the specific molecular mechanisms involved in innate and adaptive immunity, as well as the genetic variants associated with Crohn’s disease and ulcerative colitis. The overall goal of his laboratory is to understand how the balance between microbes, immunity, and the human host contributes to disease. He directs a multidisciplinary research effort involving microbiome research, genome-wide association studies, mouse models, functional genomics, systems biology, basic immunology, and high-throughput screens.

Hera Vlamakis, PhD

Group Leader/Research Scientist, Broad Institute of MIT and Harvard

Hera Vlamakis is working with Dr. Ramnik Xavier at the Broad Institute, leading microbiome projects relevant to health and diseases such as Type 1 diabetes and inflammatory bowel disease. She received her PhD in 2004 in Molecular and Cell Biology at the University of California, Berkeley and performed her postdoctoral research at Harvard Medical School studying bacterial communities called biofilms. Her expertise is in bacterial signaling and communication and she is now focusing on understanding how bacteria interact with each other and with host cells in the human gut.

Tommi Vatanen, PhD

Research Associate, Broad Institute of MIT and Harvard

Tommi Vatanen is a postdoctoral research associate in Ramnik Xavier's laboratory at the Broad Institute of MIT and Harvard. He holds a PhD in computational biology from Aalto University, Finland. During his PhD, he studied the development of the infant gut microbiota and established a mechanistic connection between bacterial surface molecules, lipopolysaccharides, and type 1 diabetes. In his current role as a postdoctoral researcher, he is interested in microbial proteins and other bioactive molecules implicated in health and disease.

Simons Foundation's Flatiron Institute

New York, New York, USA

The mission of the Flatiron Institute is to advance scientific research through computational methods, including data analysis, modeling and simulation. The institute, an internal research division of the Simons Foundation, is a community of scientists who are working to use modern computational tools to advance our understanding of science, both through the analysis of large, rich datasets and through the simulations of physical process.

Rich Bonneau, PhD

Professor of Biology, Computer Science; Faculty Director of Bioinformatics, New York University (NYU)
Group Leader for Systems Biology, Center for Computational Biology, Simons Foundation's Flatiron Institute
Co-Principal Investigator, Microbiome Immunity Project

Dr. Bonneau completed his PhD working with David Baker, Professor of Biochemistry at the University of Washington, on protein structure prediction and was an initial author on the Rosetta structure prediction code (the core code used to predict protein structure in this project). Dr. Bonneau is a professor at NYU and a group leader in Systems Biology at the newly formed Center for Computational Biology at the Flatiron institute. His laboratory works on methods for predicting and using protein and bio-molecular structure and methods for predicting and modeling biological networks from genomics data. His body of scholarly work can be viewed here.

Douglas Renfrew, PhD

Research Scientist, Simons Foundation's Flatiron Institute
Visiting Scholar, Bonneau Lab, New York University

Dr. Doug Renfrew is a research scientist in the Center for Computational Biology at the Flatiron Institute and has almost 15 years of experience developing computational methods to predict, design, and analyze the complex 3-dimensional structure of proteins and other polymers. His primary research tool is the Rosetta Macromolecular Modeling Suite, a computer program developed by more than 50 different groups around the world to computationally model macromolecules and their interactions.

Vladimir Gligorijevic, PhD

Research Scientist, Center for Computational Biology, Simons Foundation's Flatiron Institute

Vladimir Gligorijevic is a Research Scientist in Richard Bonneau’s lab in the Center for Computational Biology at the Flatiron Institute. Gligorijevic received his PhD in computer science from Imperial College London in 2017. During his PhD, he worked on developing novel machine learning methods for integration of large-scale, heterogeneous biological networks with applications in computational biology and medicine. His current research focuses on studying the structure and function of microbial proteins using geometric deep learning techniques.

Julia Koehler Leman, PhD

Research Scientist, Center for Computational Biology, Flatiron Institute, Simons Foundation
Visiting Scholar, Bonneau lab, New York University

Dr. Koehler Leman is a research scientist in the Center for Computational Biology at the Flatiron Institute. After she completed her Master’s degree in Physics in Germany she spent most of her career developing computational methods to help elucidate and model membrane protein structures. That ranged from sequence-based methods for secondary and transmembrane span prediction using machine learning techniques to structural tools for membrane protein modeling which are based on a framework she implemented in the Rosetta software suite. She also focuses on prediction of deleteriousness of genetic variations using sequence and structure-based features. She completed her PhD at Vanderbilt University and her postdoctoral training at Johns Hopkins University.

Daniel Berenberg

Research Analyst, Center for Computational Biology, Simons Foundation's Flatiron Institute

Daniel Berenberg is a research analyst in Richard Bonneau’s systems biology group. Prior to joining the lab, Daniel completed his BS in mathematics and Master’s in computer science at the University of Vermont where his research focused on network data mining through natural language inference and crowdsourcing. His current work explores aspects of protein structure and function prediction by integrating self- and semi-supervised deep learning methods.

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Rommie Amaro, PhD

Professor of Chemistry and Biochemistry, UC San Diego

Dr. Rommie Amaro started her independent research career in the Departments of Pharmaceutical Sciences, Computer Science, and Chemistry at the University of California, Irvine in 2009. In 2010 she was selected as an NIH New Innovator for her work developing cutting-edge computational methods to help discover new drugs. The following year, she received the Presidential Early Career Award for Scientists and Engineers. In 2012, Dr. Amaro opened her lab at UC San Diego in the Department of Chemistry and Biochemistry. Research in the Amaro lab is broadly concerned with the development and application of state-of-the-art computational methods to address outstanding questions in drug discovery and molecular-level biophysics. Her lab focuses mainly on targeting neglected diseases, Chlamydia, influenza, and cancer, and works closely with experimental collaborators to catalyze the discovery of new potential therapeutic agents. The Amaro lab is also keenly interested in developing new multiscale simulation methods and novel modeling paradigms that scale from the level of atoms to whole cells, and beyond.

Matthew Redinbo, PhD

Distinguished Professor, Chemistry, Biochemistry and Genomics, University of North Carolina at Chapel Hill

Professor Redinbo is a structural and chemical biologist focusing on the gut microbiota as a source of therapeutic drug targets. His previous crystallographic studies of human and microbial systems have morphed into probing the symbiotic relationship between the microbiota and the mammalian host. The lab now employs the full translational arc from small molecule inhibitor design to animal models of disease, and also includes human clinical and metagenomic studies.

Previous Research Team Members

Bryn C. Taylor

Graduate Student

Bryn Taylor is a biomedical sciences graduate student at UC San Diego, co-advised by Drs. Rob Knight and Rommie E. Amaro. She uses tools from the fields of computational chemistry and biophysics (protein folding, molecular dynamics, Markov state models, and more) to investigate microbial proteomes and elucidate the function of the microbiome.

Emily Koo

Graduate Student, Bonneau Lab, New York University

Emily Koo is a graduate student in Richard Bonneau's lab in the Department of Biology at New York University. Her research is focused on developing methods for protein function prediction and she is interested in incorporating structural features as a means to localize protein-level annotations to their functional regions.

Meet Barot

Associate Software Engineer, Center for Computational Biology, Simons Foundation's Flatiron Institute

Meet Barot received his bachelor's degree in Chemistry and Computer Science from New York University where he did research in DNA computation. His current work involves prediction of protein function using deep learning techniques.