13 th Annual Microbial Sciences Symposium

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1 13 th Annual Microbial Sciences Symposium April 16, 2016 Knafel Gymnasium Radcliffe Institute for Advanced Studies Harvard University Cambridge, MA Microbial Sciences Initiative at Harvard

2 Introduction Today s Symposium has been organized by the Microbial Sciences Initiative (MSI) at Harvard University. MSI is an interdisciplinary science program aimed at a comprehensive understanding of the richest biological reservoir of the planet, the microbial world. Microbes are ubiquitous and have an impact on every aspect of our existence. Yet, their intrinsic invisibility has meant that they have remained largely unknown, their effects and enormous potential often unrecognized. The recent realization of the vastness of microbial diversity and the genomics revolution have propelled the microbial sciences into an exciting new era of investigation. MSI is playing a key role in this emerging area by creating an organizational focal point for microbial studies with strong links to already existing science departments and schools at Harvard. MSI encourages broad interactions among microbial scientists across the Boston area and connects work on microbial sciences to ongoing work in related areas including molecular biology, medicine, biogeochemistry, evolutionary biology, and environmental engineering. Thus, MSI has built a community across the entire University including students, postdoctoral fellows, and faculty. MSI supports a variety of activities that foster interdisciplinary research, including colloquia, seminars, and weekly discussions of microbial science issues. Additionally, MSI runs several programs for students, such as a graduate consortium and, for undergraduates, a summer fellowship program and a secondary field. Further, the MSI has played a key role in the recruitment of several new faculty. It is our hope that this Symposium will, by presenting some of the breadth and depth of microbial sciences today, stimulate discussion among members of our scientific community that will help strengthen this integrative science initiative. We thank you for your attendance and welcome you to today s activities.

3 MSI PROGRAM Opening Remarks and Welcome 8:45 Session I 9:00-10:20 George Church Harvard Medical School, Dept. of Genetics Engineering eliminating endogenous and endemic Julie Huber Josephine Bay Paul Center for Comparative Molecular Biology & Evolution, Marine Biological Laboratory Microbes, fluids, and rocks: Subseafloor life Coffee Break 10:20-10:40 Session II 10:40-12:00 Emily Balskus Harvard Faculty of Arts and Sciences, Dept. of Chemistry and Chemical Biology Chemical discovery in the microbial world Jack Gilbert University of Chicago, Dept. of Surgery Applying ecology to human microbial exposure" Lunch 12:00-2:00

4 Session III 2:00-3:20 Sarah Fortune Harvard T.H. Chan School of Public Health, Dept. of Immunology and Infectious Diseases Meeting your match: Diversity in host and pathogen shapes infection outcome Michael Fischbach University of California at San Francisco, Dept. of Bioengineering and Therapeutic Sciences Small molecules from the human microbiota Coffee Break 3:20-3:40 Session IV 3:40-5:00 Eleftherios Mylonakis Alpert Medical School of Brown University, Depts. of Medicine, and Molecular Microbiology and Immunology Massachusetts General Hospital, Division of Infectious Diseases Antimicrobial drug discovery and repurposing using a whole animal C. elegans-based screen Lora Hooper University of Texas Southwestern Medical Center, Dept. of Immunology Bacteria-host interactions and the circadian clock Closing Remarks Reception

5 George Church Professor Department of Genetics Harvard Medical School B.A. Duke University Ph.D. Harvard University Member of the National Academy of Sciences Member of the National Academy of Engineering ASM Biotechnology Research Award World Economic Forum Technology Pioneer Award Howard Hughes Medical Institute Investigator Church is known for his professional contributions in the sequencing of genomes and interpreting such data, in synthetic biology and genome engineering, and in an emerging area of neuroscience that proposes to map brain activity and establish a "functional connectome." As a PhD student of Walter Gilbert, Church published the first methods for direct genome sequencing, molecular multiplexing, and barcoding. These strategies have contributed to most next-generation sequencing technologies, facilitating genome-scale sequencing and personal genomics. Later work as a principle investigator has focused on chip-dna-synthesis, gene editing, and stem cell engineering. Additionally, Church has helped pioneer new privacy, biosafety, environmental, and biosecurity policies.

6 Julie Huber Associate Scientist & Associate Director Josephine Bay Paul Center for Comparative Molecular Biology & Evolution Marine Biological Laboratory B.S. Eckerd College Ph.D. University of Washington Neal Cornell Career Development Award L Oréal USA Fellowship for Women in Science NSF RIDGE 2000 Distinguished Lecturer National Research Council Research Associateship Award Huber is an oceanographer by training and is broadly interested in how basic earth processes- rocks forming, fluids moving, sediments accumulating- interact to create and maintain life in the oceans. Her research addresses some of the most central questions about the nature and extent of life on Earth in one of its least explored corners, the subseafloor habitat beneath the ocean floor. Her focus is on microorganisms, who for more than three billion years have served as engines of Earth s biosphere, driving essential biogeochemical cycles that shape planetary habitability. Huber investigates subseafloor microbial communities to resolve the extent, function, evolutionary dynamics, and biogeochemical implications of this relatively unexplored ecosystem. The questions her work addresses are universal for understanding the impact of microbial life on both human and planetary health and the selective forces that continue to allow life to establish, thrive, and diversify on Earth.

7 Emily Balskus Associate Professor Department of Chemistry and Chemical Biology Harvard Faculty of Arts and Sciences B.A. Williams College M. Phil. University of Cambridge Ph.D. Harvard University Packard Fellowship for Science and Engineering Damon Runyon-Rachleff Innovation Award Searle Scholar Award MIT Technology Review Innovator Under 35 The vast majority of life is microbial, and the metabolic functions of these organisms shape the environment, influence human health, and provide us with medicinally and industrially important molecules. However, the vast majority of microbial chemistry remains uncharacterized at a genetic and molecular level. Research in the Balskus lab explores the chemical diversity of microorganisms, with a particular focus on the human microbiota. Combining an understanding of enzyme mechanism with bioinformatics, the group identifies new metabolic pathways encoded in microbial genomes and metagenomes, revealing enzymes of both biological and chemical significance. Lab members also elucidate the roles these activities play in host microbes and microbial communities. Finally, the group develops new approaches for manipulating metabolic processes in individual microorganisms and the complex communities they inhabit. Ultimately, this research will not only improve our fundamental understanding of microbial metabolic capabilities, but may also reveal novel solutions to problems in chemistry, biology, and medicine.

8 Jack Gilbert Professor Department of Surgery University of Chicago B.S. University of London Ph.D. Nottingham University Genomic Standards Consortium Advisory Board Member Crain s Business Chicago s 40 Under 40 List Business Insider s 50 Most Influential Scientists List Popular Scientist s Brilliant Ten List Gilbert is a microbial ecologist who is interested primarily in how bacteria interact with each other and with their environment in myriad ecosystems. The group s current research portfolio uses the universality of bacteria to explore their interactions in humans, marine and fresh water, soils, plants and animals; but they also focus on anthropogenic environments such as homes and hospitals. Gilbert is profoundly interested in how communities assemble, and what keeps them stable in the face of complex external selection pressures.

Sarah Fortune Professor Department of Immunology and Infectious Diseases Harvard T.H. Chan School of Public Health B.S. Yale University M.D. Columbia University Alice B.

9 Sarah Fortune Professor Department of Immunology and Infectious Diseases Harvard T.H. Chan School of Public Health B.S. Yale University M.D. Columbia University Alice B. Hamilton Award Burroughs Welcome Foundation Investigator Award Doris Duke Foundation Clinical Scientist Developmental Award NIH New Innovator Award Fortune s work has focused on the overarching hypothesis that Mycobacterium tuberculosis (Mtb) infection is difficult to eliminate, either by antibiotics or immunity, in part because of the tenacity of a few cells that avoid clearance and fully regenerate disease. Mtb is likely to utilize a range of mechanisms to generate cells that differ functionally from one another. By integrating bacterial genetics, genomics, and single cell approaches, her lab has defined a number of mechanisms of bacterial diversification, ranging from genetic to epigenetic to mechanisms of high frequency phenotypic diversification through asymmetric growth and division. They have gone on to test the importance of bacterial diversity in allowing Mtb to escape selective pressures, including drug treatment and features of the host environment like hypoxic stress. The group s data suggests that different mechanisms of diversification are likely to be advantageous to the bacterial population depending on the force and stability of the selective pressures that the organism faces.

Michael Fischbach Associate Professor Department of Bioengineering and Therapeutic Sciences University of California at San Francisco A.B. Harvard University Ph.D. Harvard University NIH New Innovator Award David and Lucille Packard Foundation Fellowship W.

10 Michael Fischbach Associate Professor Department of Bioengineering and Therapeutic Sciences University of California at San Francisco A.B. Harvard University Ph.D. Harvard University NIH New Innovator Award David and Lucille Packard Foundation Fellowship W.M. Keck Foundation Research Award Burroughs Wellcome Fund Investigators Award The Fischbach laboratory uses a combination of genomics and chemistry to identify and characterize small molecules from microbes, with an emphasis on the human microbiome. Small molecules from microbes are used widely in the clinic as antibiotics, anticancer agents, immunosuppressants, and cholesterol-lowering drugs. The group focuses on three emerging principles that are changing the understanding of which microbes make natural products, what roles they play in the biology of their producers, and how best to discover them: 1) small molecules from the underexplored niche of the human microbiota, 2) computational tools for small molecule discovery, such as an algorithm that identifies small-molecule-producing genes in bacterial genomes, and 3) using synthetic ecology to control microbiome metabolism.

Eleftherios Mylonakis Professor Departments of Medicine, and Molecular Microbiology and Immunology, Division of Infectious Diseases Alpert Medical School of Brown University, Massachusetts General

11 Eleftherios Mylonakis Professor Departments of Medicine, and Molecular Microbiology and Immunology, Division of Infectious Diseases Alpert Medical School of Brown University, Massachusetts General Hospital M.D. National University of Athens Ph.D. National University of Athens IDSA Oswald Avery Award Maxwell Finland Award for Excellence in Infectious Disease Research ICAAC Young Investigator Award American Society for Clinical Investigation representative for Brown and Lifespan Dr. Mylonakis is a physician-scientist that uses a variety of tools, such as molecular biology, immunology, biostatistics, decision-making analysis, risk assessment, outcomes research and cost effectiveness studies, in order to answer complex scientific questions. His studies have included clinical and laboratory studies and the use of mammalian and invertebrate model hosts. These surrogate hosts fill an important niche in pathogenesis research and provide us with a unique opportunity to identify novel antimicrobial compounds and study basic, evolutionarily conserved aspects of microbial virulence and host response. His investigations have identified novel virulence factors, cross kingdom pathogen-pathogen interactions, novel agents and evolutionarily conserved traits that are involved in host virulence and immune responses during infection. These studies have resulted in whole animal C. elegans-based high throughput assays for the identification and characterization of antimicrobial compounds. Taken in their totality, these results indicate that a common, fundamental set of molecular mechanisms is employed by pathogens against a widely divergent array of metazoan hosts.

12 Lora Hooper Professor Department of Immunology University of Texas Southwestern Medical Center B.S. Rhodes College Ph.D. Washington University Howard Hughes Medical Institute Investigator Member of the National Academy of Sciences Edith and Peter O'Donnell Award Burroughs Wellcome Fund Career Award The human intestine is inhabited by nearly 100 trillion intestinal bacteria that are essential for health. Millions of years of coevolution have molded this human-microbe interaction into a symbiotic relationship in which gut bacteria make essential contributions to human nutrient metabolism and in return occupy a nutrient-rich environment. The goal of the Hooper lab is to understand the mechanisms that regulate host-microbial interactions at the epithelial surfaces of the intestine and how these mechanisms promote symbiotic relationships with resident intestinal bacteria. A major focus is on secreted epithelial cell derived antimicrobial proteins, which directly lyse bacteria and promote host-microbial relationships by restricting bacterial interactions with host tissues. The lab s approach is multidisciplinary, ranging from the creation of new animal models with altered epithelial innate immune function to detailed biochemical and structural analyses of epithelial antibacterial proteins. The lab is continuing to explore the molecular consequences of bacterial-host interactions in the intestine through biochemistry, structural biology, and mouse genetics.

9 th Annual. Microbial Sciences. Symposium. April 14, 2012 Radcliffe Gym Radcliffe Institute for Advanced Studies Harvard University Cambridge, MA

9 th Annual. Microbial Sciences. Symposium. April 14, 2012 Radcliffe Gym Radcliffe Institute for Advanced Studies Harvard University Cambridge, MA 9 th Annual Microbial Sciences Symposium Microbial Sciences Initiative at Harvard April 14, 2012 Radcliffe Gym Radcliffe Institute for Advanced Studies Harvard University Cambridge, MA Introduction Today