Eric Alm Co-Director

Alm Eric Alm is an associate professor of bioengineering at MIT and an associate member of the Broad Institute. His research uses complementary computational and experimental methods to engineer the human microbiome, including data science, quantitative analysis, and novel molecular techniques. More broadly, the Alm lab emphasizes a systems-level approach to answering questions and solving problems in microbial ecology that have the potential to improve human health, develop sound bioremediation strategies, and uncover the global history of microbes. Dr. Alm also serves on the Board of Directors for the non-profit stool bank, OpenBiome.


Ramnik Xavier
Co-Director

XavierRamnik Ramnik Xavier, M.D, is Chief of the Division of Gastroenterology at Massachusetts General Hospital; Kurt Isselbacher Professor of Medicine, Harvard Medical School; and Senior Associate Member of the Broad Institute. In addition to his duties as a clinical gastroenterologist, he teaches medical students, residents in medicine, and gastroenterology fellows rotating through the Crohn’s Colitis Center at MGH. Dr. Xavier’s research combines basic science with translational approaches to study Crohn’s disease and ulcerative colitis. He directs the Center for the Study of Inflammatory Bowel Disease, a NIH-funded multidisciplinary program established to identify fundamental mechanisms underlying Crohn’s disease and ulcerative colitis, and co-leads an investigation to identify connections between the microbiome and inflammatory bowel disease, a project that is part of the second phase of the Human Microbiome Project (HMP), an NIH initiative first launched in 2008.


Vicki Mountain Assistant Director

vicki Vicki Mountain is the Assistant Director of the Center for Microbiome Informatics and Therapeutics. She works closely with the Directors to develop the greater scientific vision for the Center, while supporting current clinical and research collaborations, building a microbiome-focused research community, and overseeing Center communications. Dr. Mountain has an extensive background in scientific editing and project management having worked for Cell Press, and EBSCO Health, and independently consulted for Reflexion Pharmaceuticals, American Chemical Society, and the Max-Planck Institute for Colloids and Interfaces. She has a BSc from the University of Glasgow, and a PhD in Biochemistry from Dartmouth Medical School.


Emily Balskus, Harvard University

Dr. Balskus is the Morris Kahn Associate Professor of Chemistry and Chemical Biology. She is also an Associate Member of the Broad Institute of MIT and Harvard, a Faculty Associate of the Microbial Sciences Initiative at Harvard, and a member of the Harvard Digestive Diseases Center. She is the recipient of multiple awards, including the 2011 Smith Family Award for Excellence in Biomedical Research, the 2012 NIH Director’s New Innovator Award, and the 2013 Packard Fellowship for Science and Engineering. She is also a 2012 Searle Scholar, and was named one of MIT Technology Review’s 35 Innovators Under 35 in 2014.

Dr. Balskus’ goal is to transform our understanding of microbes and microbial communities, by dissecting microbial metabolism at the molecular level. Through integration of methods in chemistry and microbiology, the Balskus group is developing new and broadly useful approaches for studying the diverse chemical functions of microbes and microbial communities. Research is focused on 3 core areas of investigation: understanding the chemistry of the human microbiota, discovering novel enzymatic reactivity associated with unusual molecular architecture, and manipulating biological function with biocompatible chemistry. Ultimately, Balskus’ group would like to reveal how microbes contribute to human biology, and improving our ability to use and control their remarkable chemical capabilities.


Bonnie Berger, Massachusetts Institute of Technology

Bonnie Berger is the Simons Professor of Mathematics at MIT, holds a joint appointment in Electrical Engineering and Computer Science, and serves as head of the Computation and Biology group at MIT’s Computer Science and AI Lab. After beginning her career working in algorithms at MIT, she was one of the pioneer researchers in the area of computational molecular biology and, together with the many students she has mentored, has been instrumental in defining the field. She continues to lead efforts to design algorithms to gain biological insights from recent advances in automated data collection and the subsequent large data sets drawn from them. Professor Berger has won numerous awards including a National Science Foundation Career Award and the Biophysical Society’s Dayhoff Award for research. In 1999 Professor Berger was named one of Technology Review Magazine’s inaugural TR100 as a top young innovator of the twenty-first century, in 2004, was elected as a Fellow of the Association for Computing Machinery, and in 2010, received the RECOMB Test of Time Award. She was recently elected to the American Academy of Arts and Sciences, received the Margaret Pittman Director’s Award at the NIH, was elected as Fellow of both the International Society for Computational Biology (ISCB) and American Institute of Medical and Biological Engineering (AIMBE), and received an Honorary Doctorate from EPFL. She currently serves as Vice President of the ISCB and Head of the steering committee for RECOMB. In addition, Professor Berger is an Associate Member of the Broad Institute, Faculty member of Harvard/MIT Health Science & Technology, and Affiliated Faculty of Harvard Medical School.


James J. Collins, Massachusetts Institute of Technology

James J. Collins is the Termeer Professor of Bioengineering in the Department of Biological Engineering, and Institute for Medical Engineering & Science at MIT. He is also affiliated with the Broad Institute of MIT and Harvard and the Wyss Institute for Biologically Inspired Engineering at Harvard.

His research program harnesses synthetic and systems biology, in combination with network biology approaches, to investigate antibiotic action, bacterial defense mechanisms, and the emergence of resistance. The Collins group focuses on enhancing our existing antibiotic arsenal and developing more effective means to treat resistant bacterial infections.

Professor Collins’ patented technologies have been licensed by over 25 biotechnology, pharmaceutical, and medical device companies, and he has helped to launched a number of other companies, including Sample6 Technologies, Synlogic, and EnBiotix.  He has received numerous awards and honors, including a Rhodes Scholarship, a MacArthur “Genius” Award, an NIH Director’s Pioneer Award, a Sanofi-Institut Pasteur Award, as well as several teaching awards. Professor Collins is an elected member of the National Academy of Sciences, the National Academy of Engineering, the Institute of Medicine, and the American Academy of Arts & Sciences, and is a charter fellow of the National Academy of Inventors.


Andrew Goodman, Yale University Medical School

Dr. Andrew Goodman is an Assistant Professor of Microbial Pathogenesis and a member of the Microbial Diversity Institute at Yale University’s West Campus. He was named a Burroughs Wellcome Fund Investigator in 2015, and received the Presidential Early Career Award for Scientists and Engineers in 2013, a Pew Scholar award in Biomedical Research in 2013, and a NIH Directors New Innovator Award in 2012.

Dr. Goodman studies the enormous community of microbes resident in and on the human body (the microbiome), that are known to play critical roles in our response to nutrients, toxins, and pathogens. In the gut, these microbes form a metabolic organ, and variation in the composition of this “organ” has important consequences for health.

The Goodman Group uses genomics and biochemistry to study the process of selection and competition that shapes these microbial communities. For many microbial communities, the great majority of organisms is unknown, or has not been well characterized. To characterize microbes for which the genome sequence is unavailable, the Goodman lab has have developed a generally applicable, new experimental approach (insertion sequencing, or INSeq) for functional genome-wide analysis of organisms. Furthermore, because many of these organisms have not yet been cultured in the laboratory, the group is developing high-throughput approaches to assemble large human gut culture collections from single healthy or diseased individuals, with the goal of re-uniting discrete components of these communities in germfree mice. These personalized culture collections will provide a new platform for studying resource sharing and competition in the gut.


Elizabeth Kujawinski, Woods Hole Oceanographic Institution

Dr. Kujawinski is an Associate Scientist with Tenure in the Department of Marine Chemistry and Geochemistry at Wood Hole Oceanographic Institution, where she also leads the Molecular Environmental Science Laboratory, and is Director of the Fourier Transform Mass Spectrometry Facility.

The Kujawinski research group applies cutting-edge mass spectrometry to better understand metabolic dynamics of individual marine microorganisms, and the role of chemical compounds in structuring microbial communities in disparate environments. Their goal is to detect and quantify those molecules that are central to microbial interactions.

Marine microbes interact with one another through the medium of dissolved organic matter, or the complex mixture of molecules dissolved in the surrounding seawater. Using ultrahigh resolution mass spectrometry, and statistical analyses Kujawinski’s group has identified novel molecules and compound classes that are important for microbial carbon cycling in the surface and in deep oceans, beneath the Greenland Ice Sheet, and in groundwater systems. With this approach they were first to identify polar dispersant components in the deep Gulf of Mexico during the Deepwater Horizon oil spill. By integrating molecule discovery and quantification with gene-based omics, the group has characterized biochemically and ecologically relevant compounds that had not been previously quantified in the ocean. These molecules have diverse roles in processes such as the degradation of oil in seawater, the physiological response of eukaryotic algae to phosphorus limitation, and the metabolic restructuring in heterotrophic bacteria associated with shifts in free-living vs. cooperative lifestyles.


Timothy Lu, Massachusetts Institute of Technology

Timothy Lu, M.D., Ph.D. leads the Synthetic Biology Group (SBG) in the Department of Electrical Engineering and Computer Science and the Department of Biological Engineering at MIT. He is a core member of the Synthetic Biology Center at MIT, an Associate Member of the Broad Institute of MIT and Harvard, and co-founder of Sample6 Technologies. He has received the Henry L. and Grace Doherty Professorship, NIH New Innovator Award, Lemelson-MIT Student Prize for Invention, Army Young Investigator Award, Ellison New Scholar in Aging Award, and Presidential Early Career Award for Scientists and Engineers (PECASE).

Dr. Lu’s Synthetic Biology Group is focused on advancing fundamental designs and applications for synthetic biology. Using principles inspired by electrical engineering and computer science, new techniques are being developed to construct, probe, modulate, and model engineered biological circuits. The Lu Group is focused on applying novel methods for biomedical applications and to tackle problems in infectious disease, amyloid-associated conditions, and nanotechnology.


Hidde Ploegh, The Whitehead Institute of Biomedical Research

Dr. Ploegh is a Member of The Whitehead Institute of Biomedical Research, and a Professor of Biology at MIT. A contributor to over 400 papers, he was elected Fellow of the American Academy of Arts and Sciences in 2000, and has received many awards including most recently, a NIH Director’s Pioneer award in 2012, and an AAI-Life Technologies Meritorious Career Award in 2011. In addition, he was nominated in 2009 to deliver a NIH Director’s Lecture and the Harvard University John Edsall Lecture.

The Ploegh Group studies the various tactics that viruses employ to evade our immune responses, and the ways in which our immune system–both innate and adaptive–distinguishes friend from foe. Their findings have illuminated not only host-pathogen interactions, but also aspects of protein quality control, an area to which the lab continues to apply chemistry-based strategies. Other technologies include new methods for protein labeling and for the production of mouse models by somatic cell nuclear transfer (“cloning”).

Ploegh’s research has uncovered new mechanisms by which dendritic cells sense the presence of antigens and instruct the immune response, using Class II MHC-eGFP knockin mice and live cell imaging.  In addition, Ploegh has helped elucidate how products of the major histocompatibility complex (MHC) are assembled and are delivered to the right destination to help an immune response kick in. Herpesviruses such as HCMV evade the immune system by selective destruction of Class I MHC products. A recent innovation is the generation of cloned mice with lymphocytes specific for pathogens such as Toxoplasma and herpesviruses, using the technique of somatic cell nuclear transfer.

Ploegh and his coworkers have emphasized the generation of the chemical tools with which to probe the ubiquitin-proteasome system. These tools include bacterially derived transacylases (sortases) as convenient tools for protein modification.


Martin Polz,Massachusetts Institute of Technology

Dr. Polz is Professor in the Department of Civil and Environmental Engineering, and is affiliated with the Woods Hole Center for Oceans and Human Health, and the Earth Systems Initiative and Microbial Systems Group at MIT. He is the recipient of numerous awards including the Eli Lilly and Company Elanco Research Award in 2013, the Frank E. Perkins Award for Excellence in Graduate Advising in 2013, and was elected a Fellow of the American Academy for Microbiology in 2012.

Dr. Polz studies environmental microbiology, primarily looking at three areas: the dynamics that govern microbes’ interactions and evolution to learn the role of individual populations within the community, the range of genomic similarity that defines a functional unit, and what mechanisms govern diversification of microbial populations in the environment. The Polz group addresses these questions using a combination of quantitative molecular approaches, genomics, physiological techniques and mathematical modeling. Research focuses primarily on bacteria of the genus Vibrio since these are a longstanding model of heterotrophic bacteria in the Ocean and contain many pathogenic variants. In this context, they are interested in understanding the mechanisms of evolutionary emergence and persistence of pathogens among otherwise harmless environmental bacteria. The Polz group is also developing population genetic models for human pathogens in the context of complex microbiomes.


Aviv Regev, The Broad Institute of MIT and Harvard

Aviv Regev is a Core Member of the Broad Institute, Professor of Biology at MIT, and a Howard Hughes Medical Institute Investigator.

Dr. Regev studies biological circuits, gene regulation, and evolution using a combination of experimental and computational methods. This combinatorial approach allows her researchers to systematically decode the mechanisms and principles that underlie the rewiring of regulatory networks controlling gene transcription, and answer questions about how transcriptional networks are rewired at different timescales. In addition, it allows them to learn how gene regulation changes when cells adapt to changing growth conditions, when cells differentiate, and when species evolve. In this way, Regev’s group has helped make sense of the complex regulatory pathways and networks in yeast cells, dendritic cells (the watchdogs of the immune system), and immune cells called T helper 17 (Th17) cells, which are implicated in autoimmune disorders, such as multiple sclerosis (MS) and rheumatoid arthritis.

The Regev group now is developing microfluidics, or lab-on-a-chip, techniques to chart gene expression in hundreds—and eventually many thousands—of single cells every day. Dr. Regev also directs a new project called the Cell Observatory at the Broad Institute to identify and map all the circuits in human cells and ultimately hopes this work will open the door to new treatments for disease.


Alex Shalek, Massachusetts Institute of Technology

Dr. Shalek is a Core Member of the Institute of Medical Engineering and Science (IMES), an Instructor in Health Sciences and Technology (HST), and an Assistant Professor of Chemistry at MIT. He is also affiliated with The Broad Institute of MIT and Harvard, the Ragon Institute, and Massachusetts General Hospital. He is a Hermann L.F. Von Helmholtz Career Development Professor, and the recipient of numerous awards including the NIH Director’s New Innovator Award, the Beckman Young Investigator Award, and the Searle Scholar Award.

Dr. Shalek’s interdisciplinary research focuses on understanding how cells collectively perform systems-level functions in healthy and diseased states. To this end, Dr. Shalek and his group is developing and utilizing nanoscale manipulation and measurement technologies to understand how small components (molecules, cells) drive systems of vast complexity (cellular responses, population behaviors). With respect to technology development, the group is leveraging recent advances in nanotechnology and chemical biology to establish a host of core, cross-disciplinary platforms that will collectively enable them to extensively profile and precisely control cells and their interactions within the context of complex systems. With respect to biological applications, the group is focusing on how cellular heterogeneity and cell-to-cell communication drive ensemble-level decision-making in the immune system, with an emphasis on “two-body” interactions (e.g., host cell-virus interactions, innate immune control of adaptive immunity, tumor infiltration by immune cells). The goal is to not only provide broadly applicable experimental tools but also help transform the way in which we think about single cells, cell-cell interactions, diseased cellular states and therapeutics so as to create a new paradigm for understanding and designing systems-level cellular behaviors in multicellular organisms.

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