Appendix E

Speaker Biographies

Jill Banfield, Ph.D., is a professor in the Departments of Earth and Planetary Science and Environmental Science, Policy, and Management at the University of California, Berkeley. She studies natural microbial communities and their impact on biogeochemical processes. In part of her collaborative work, she is studying early colonization of the gut of premature human infants. The approaches used include community metagenomic (emphasizing reconstruction of near-complete genomes) and proteomic analyses (to emphasize activity, in situ).

Sam Brown, Ph.D., is a reader in evolutionary medicine at the University of Edinburgh (UK). His central research challenge is to understand the social lives of bacteria, and in particular how bacterial social strategies shape virulence and also present new opportunities for control. To pursue this multifaceted challenge, Dr. Brown’s lab takes an interdisciplinary approach, integrating molecular and biomedical microbiology with theoretical ecology and evolution. Having trained with theoretical epidemiologists and experimental microbiologists, and collaborated with veterinary and medical schools, Dr. Brown has developed the strong conviction that by closing the gap between molecular genetics, evolutionary ecology, and epidemiology, real progress in the management of infectious diseases can be made, while casting light on and expanding fundamental questions in ecology and evolution. Dr. Brown has a Ph.D. from Cambridge and has held fellowship positions in Montpellier, Austin, Texas, and Oxford.

Colleen Cavanaugh, Ph.D., is the Edward C. Jeffrey Professor of Biology in the Department of Organismic and Evolutionary Biology and co-director of the Microbial Sciences Initiative at Harvard University. Her research interests



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Appendix E Speaker Biographies Jill Banfield, Ph.D., is a professor in the Departments of Earth and Planetary Science and Environmental Science, Policy, and Management at the University of California, Berkeley. She studies natural microbial communities and their impact on biogeochemical processes. In part of her collaborative work, she is studying early colonization of the gut of premature human infants. The approaches used include community metagenomic (emphasizing reconstruction of near-complete genomes) and proteomic analyses (to emphasize activity, in situ). Sam Brown, Ph.D., is a reader in evolutionary medicine at the University of Edinburgh (UK). His central research challenge is to understand the social lives of bacteria, and in particular how bacterial social strategies shape virulence and also present new opportunities for control. To pursue this multifaceted challenge, Dr. Brown's lab takes an interdisciplinary approach, integrating molecular and biomedical microbiology with theoretical ecology and evolution. Having trained with theoretical epidemiologists and experimental microbiologists, and collabo- rated with veterinary and medical schools, Dr. Brown has developed the strong conviction that by closing the gap between molecular genetics, evolutionary ecology, and epidemiology, real progress in the management of infectious dis- eases can be made, while casting light on and expanding fundamental questions in ecology and evolution. Dr. Brown has a Ph.D. from Cambridge and has held fellowship positions in Montpellier, Austin, Texas, and Oxford. Colleen Cavanaugh, Ph.D., is the Edward C. Jeffrey Professor of Biology in the Department of Organismic and Evolutionary Biology and co-director of the Microbial Sciences Initiative at Harvard University. Her research interests 595

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596 THE SOCIAL BIOLOGY OF MICROBIAL COMMUNITIES focus on microbial diversity and bacteria-animal symbioses, including trans- mission strategy and host-symbiont coevolution, and the origin and evolution of autotrophy. With emphasis on "chemosynthetic symbioses" between marine invertebrates and chemoautotrophic bacteria, she has participated in research cruises worldwide with deep-sea dives on the submersible Alvin. With expertise in the study of "unculturable" bacteria, her research has recently expanded to the characterization of the microbiome of humans and human model animals and their role in health and disease. She received her bachelor's degree from the University of Michigan and her M.A. and Ph.D. from Harvard. She was a junior fellow at Harvard and currently is a fellow of the American Association for the Advancement of Science (AAAS) and the American Academy of Microbiology, and a member of the Cambridge Scientific Society. Dr. Cavanaugh is a visit- ing investigator at the Woods Hole Oceanographic Institution, a member of the Marine Biological Laboratory Corporation, Committee on Courses, and Science Council, and an associate member of the Broad Institute. Cameron Currie, Ph.D., is an associate professor in the Department of Bacte- riology at the University of WisconsinMadison. He received his bachelor's and master's degrees from the University of Alberta, and his Ph.D. from the Univer- sity of Toronto. Dr. Currie spent 3 years as a faculty member in the Department of Ecology and Evolutionary Biology at the University of Kansas before moving his group to Wisconsin. His training and research is highly interdisciplinary, spanning the fields of microbiology, genomics, ecology, and evolutionary biology. His lab studies the ecological and evolutionary dynamics of symbiotic associa- tions, with a particular focus on the interactions that occur between insects and microbes. His research, including extensive work with the charismatic leaf-cutter ants, has potential applications in fields as diverse as bioenergy development and drug discovery. He has received several significant awards, including a Presiden- tial Early Career Award for Scientists and Engineers and a Government of Canada National Sciences and Engineering Research Council Doctoral Dissertation Prize. In 11 years as a faculty member, Dr. Currie has published more than 80 papers and been awarded more than $6 million in extramural funds, including a 2010 NIH RC4 American Recovery and Reinvestment Act (ARRA) award. Jonathan Eisen, Ph.D., is a professor at the Genome Center at the University of California (UC), Davis, and holds appointments in the Department of Evolution and Ecology in the College of Biological Sciences and Medical Microbiology and Immunology in the School of Medicine. His research focuses on the mechanisms underlying the origin of novelty (how new processes and functions originate). Most of his work involves the use of high-throughput DNA sequencing methods to characterize microbes and then the use and development of computational methods to analyze this type of data. In particular, his computational work has focused on integrating evolutionary

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APPENDIX E 597 analysis with genome analysis--so-called phylogenomics. Previously, he applied this phylogenomic approach to cultured organisms, such as those from extreme environments and those with key properties as they relate to evolution or global climate cycles. Currently he is using sequencing and phylogenomic methods to study microbes directly in their natural habitats (i.e., without culturing). In par- ticular, he focuses on how communities of microbes interact with each other or with plant and animal hosts to create new functions. Dr. Eisen is also coordinating one of the largest microbial genome sequencing projects to date--the "Genomic Encyclopedia of Bacteria and Archaea" being done at the Department of Energy (DOE) Joint Genome Institute, where he holds an adjunct appointment. In addition to his research, Dr. Eisen is also a vocal advocate for "open access" to scientific publications and is the academic editor-in-chief of PLoS Biology. He is also an active and award-winning blogger/microblogger (e.g., http://phylogenomics.blogspot.com, http://twitter.com/phylogenomics). Prior to moving to UC Davis he was on the faculty of The Institute for Genomic Research (TIGR) in Rockville, Maryland. He earned his Ph.D. in biological sciences from Stanford University, where he worked on the evolution of DNA repair processes in the lab of Philip C. Hanawalt and his undergraduate degree in biology from Harvard College. E. Peter Greenberg, Ph.D., received his bachelor's degree from Western Washington University, his master's from the University of Iowa, and his Ph.D. from the University of Massachusetts. After a postdoctorate at Harvard, he joined the faculty at Cornell University, eventually moved back to the University of Iowa, and finally returned to the Pacific Northwest as a member of the University of Washington Medicine Microbiology faculty. He is an elected fellow of the National Academy of Sciences, the American Academy of Arts and Sciences, the American Association for the Advancement of Science, and the American Academy of Microbiology. Dr. Greenberg has spent his scientific career uncov- ering the world of microbial social behavior. Due in part to his efforts we now understand that bacteria possess a chemical language for communication and we understand mechanisms of bacterial communication. Bacterial communication controls virulence in a variety of pathogenic bacteria and has thus become a target for development of new therapeutic strategies. Bacteria have also become models for studies of selection for and evolution of cooperative behavior. Jo Handelsman, Ph.D., is Howard Hughes Medical Institute Professor in the De- partment of Molecular, Cellular and Developmental Biology at Yale University. She received her Ph.D. in molecular biology from the University of Wisconsin (UW)Madison in 1984 and served on the UW faculty from 1985 until moving to Yale in 2010. Her research focuses on the genetic and functional diversity of microorganisms in soil and insect gut communities. She is one of the pioneers of functional metagenomics, an approach to accessing the genetic potential of

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598 THE SOCIAL BIOLOGY OF MICROBIAL COMMUNITIES unculturable bacteria in environmental samples for discovery of novel antibiotics and other microbial products. In addition to her research program, Dr. Handelsman is nationally known for her efforts to improve science education and increase the participation of women and minorities in science at the university level. She co-founded the Women in Science and Engineering Leadership Institute at UWMadison, which has designed and evaluated interventions intended to enhance the participation of women in science. Her leadership in women in science led to her appointment as the first President of the Rosalind Franklin Society and her service on the National Academies' panel that wrote the 2006 report Beyond Bias and Barriers: Fulfilling the Potential of Women in Academic Science and Engineering . Dr. Handelsman is co-author of three books about teaching: Entering Men- toring, Scientific Teaching, and Biology Brought to Life. She co-edits the series Controversies in Science and Technology. She is a fellow in the American Acad- emy of Microbiology, Wisconsin Academy of Arts and Sciences, and the AAAS; member of the Connecticut Academy of Science and Engineering; director of the Center for Scientific Teaching at Yale; and co-director of the National Academies Summer Institute on Undergraduate Education in Biology. She was elected to serve as president of the American Society for Microbiology (ASM) 2013-2014; has received numerous awards in recognition of her mentoring, teaching, and research contributions; and in 2009, Seed magazine named her "A Revolution- ary Mind" in recognition of her unorthodox ideas. In 2011, she was one of 11 individuals selected by President Barack Obama to receive the Presidential Award for Excellence in Science, Mathematics, and Engineering Mentoring and recently co-chaired a working group that produced the report to the President, Engage to Excel: Producing One Million Additional College Graduates with Degrees in Science, Technology, Engineering, and Mathematics, about improving STEM education in postsecondary education. Susan Holmes, Ph.D., is professor in statistics at Stanford University and is a specialist in nonparametric complex multivariate data analyses. She has special- ized in combining spatiotemporal multivariate information with abundance and clinical data. In particular, she has studied the genetic network perturbation prob- lem, providing the open-source software GXNA for finding a small subnetwork that is the most perturbed between two conditions. This has led to important ap- plications in cancer biology. She has also designed methods that extend ordinary correlation analyses to multitable approaches using relevant weighting schemes and the multitable RV coefficient. This enables the user to do a "PCA" of PCAs and thus integrate many different tables, seeing what they have in common and what differentiates them. This is particularly useful for combing metagenomic, phylogenetic, and metabolic data in the microbiome context. Her group has de- veloped a Bioconductor tool, Phyloseq, specifically for combining phylogenetic tree, abundance, and clinical data into a unique structure. This package enables

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APPENDIX E 599 the user to provide useful interpretations of data structure and decomposition of the variability into patient/clinical/time-series components. Her other area of expertise, nonstandard applications of the bootstrap to trees, networks, and com- plex combinatorial structures, provides confirmatory validation of the exploratory findings using computer-intensive methods in a nonparametric setting. Colin Ingham, Ph.D., gained Ph.D. at University College London (1988) on chemotaxis in photosynthetic bacteria. His postdoctoral work was on E. coli chemotaxis, Streptomyces bacteriophage genetics, and transcription termination in Gram-positive bacteria, both within the United Kingdom and as a Damon Runyon Fellow at Madison, Wisconsin. He was senior scientist at PamGene BV until 2003 and in 2008 won the Zilveren Zandloper prize for innovation from the Dutch Biotechnology society (NBV). He is currently chief security officer and founder of the Dutch biotechnology start up Microdish BV, a position held since 2007. In addition, he pursues a longstanding fascination with collective bacterial motility--particularly swarming in the utterly beautiful pattern-forming bacte- rium Paenibacillus vortex. Jared Leadbetter, Ph.D.'s research program at the California Institute of Tech- nology focuses on interspecies microbial interactions and has had two distinct thrusts. One is the mutualistic symbiosis formed between termites and their diverse gut microbiota. The other is the biodegradation of an important class of bacterial signaling molecules, acyl-homoserine lactones. He has published in Nature, Science, Nature Biotechnology, the Journal of Bacteriology, Applied and Environmental Microbiology, and Molecular Microbiology, among others. Dr. Leadbetter graduated with a B.A. with honors in the biological sciences from Goucher College (Towson, Maryland) and with a Ph.D. in microbiology from Michigan State University (East Lansing, Michigan), where he was a participant in the National Science Foundation (NSF) Science and Technology Center for Microbial Ecology under the tutelage of John Breznak. He joined the Caltech faculty in the year 2000 after spending 2 years at the University of Iowa (Iowa City) in the laboratory of National Academician E. Peter Greenberg (now at Uni- versity of Washington, Seattle), where he was an NSF postdoctoral fellow in the Biosciences Related to the Environment. Simon A. Levin, Ph.D., is the Moffett Professor of Biology at Princeton Uni- versity and the director of the Center for BioComplexity in the Princeton Envi- ronmental Institute. His principal research interests are in understanding how macroscopic patterns and processes are maintained at the level of ecosystems and the biosphere, in terms of ecological and evolutionary mechanisms that operate primarily at the level of organisms. Dr. Levin is a fellow of the American Academy of Arts and Sciences and the AAAS, a member of the National Academy of Sciences and the American

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600 THE SOCIAL BIOLOGY OF MICROBIAL COMMUNITIES Philosophical Society, and a foreign member of the Istituto Veneto. He is a University Fellow of Resources for the Future, a fellow of the Beijer Institute of Ecological Economics, and a fellow of the Society for Industrial and Applied Mathematics. He has nearly 500 publications and is the editor of the Encyclope- dia of Biodiversity and the Princeton Guide to Ecology. He serves on the Science Board of the Santa Fe Institute, which he co-chaired from 2007 to 2010. Dr. Levin's awards include the Heineken Prize for Environmental Sciences, the Kyoto Prize in Basic Sciences, the Margalef Prize for Ecology, and the Eco- logical Society of America's MacArthur and Eminent Ecologist Awards. David Low, Ph.D., received his bachelor of science in biology from University of California (UC), San Diego, his master of science in microbiology from San Diego State University, and his Ph.D. in cellular biochemistry from UC Irvine, and he did postdoctoral work at Stanford University in molecular microbiol- ogy. He was a professor for 13 years at the University of Utah Health Sciences Center before moving to UC Santa Barbara in 1998. He became co-founder of Remedyne in 2000 and was elected fellow of the AAAS in 2005. He spent his first 20 years as an independent scientist investigating the roles of DNA methylation in controlling bacterial gene expression. His current research interest concerns bacterial cellular communication. Specifically, his laboratory focuses on the biol- ogy and mechanisms involved in contact-dependent growth inhibition (CDI), a phenomenon in which one bacterial cell touches another, injecting a small peptide effector/toxin called the CdiA-CT. CdiA-CTs have diverse activities, primar- ily nucleases. CDI systems are expressed by many bacterial species including important pathogens and can play important roles in intraspecies competition. Recent data indicate that CDI systems play roles in the coordination of cellular activities such as biofilm formation. Their goal is to determine how these contact- dependent systems contribute to the lifestyles of different bacterial species and to determine their mechanisms of action. Paul Rainey, Ph.D., is professor of evolutionary genetics and James Cook Re- search Fellow at the New Zealand Institute for Advanced Study. He is also a member of the Max Planck Society and honorary director at the Max Planck Institute for Evolutionary Biology in Pln, co-director of the Hopkins Microbial Diversity Program at Stanford, Principle Investigator at the Allan Wilson Centre for Molecular Ecology & Evolution, and a Fellow of the Royal Society of New Zealand. He completed his Ph.D. at the University of Canterbury in 1989 and moved to Cambridge, where he worked as a postdoctoral fellow. In 1994 he received a BBSRC Advanced Research Fellowship, which he took to the Depart- ment of Plant Sciences at the University of Oxford. In 1996 he was appointed to a faculty position at Oxford and a fellowship at St. Cross College. With much dedication, he also ran his college's wine cellar. In 2003 he returned to New Zealand as Chair of Ecology and Evolution at the University of Auckland, but

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APPENDIX E 601 retained a fractional professorial position at Oxford until the end of 2005. In 2007 he moved his lab to Massey University's Albany campus. David A. Relman, M.D., is the Thomas C. and Joan M. Merigan Professor in the Departments of Medicine and Microbiology and Immunology at Stanford Univer- sity and chief of Infectious Diseases at the VA Palo Alto Health Care System in Palo Alto, California. He received an S.B. (biology) from MIT (1977) and M.D. (magna cum laude) from Harvard Medical School (1982), completed his clinical training in internal medicine and infectious diseases at Massachusetts General Hospital, served as a postdoctoral fellow in microbiology at Stanford University, and joined the faculty at Stanford in 1994. Dr. Relman's current research focus is the human indigenous microbiota (mi- crobiome), and in particular, the nature and mechanisms of variation in patterns of microbial diversity within the human body as a function of time (microbial succession), space (biogeography within the host landscape), and in response to perturbation, e.g., antibiotics (community robustness and resilience). One of the goals of this work is to define the role of the human microbiome in health and disease. This research integrates theory and methods from ecology, population bi- ology, environmental microbiology, genomics, and clinical medicine. During the past few decades, his research directions have also included pathogen discovery and the development of new strategies for identifying previously unrecognized microbial agents of disease. This work helped to spearhead the application of molecular methods to the diagnosis of infectious diseases in the 1990s. His re- search has emphasized the use of genomic approaches for exploring host-microbe relationships. Past scientific achievements include the description of a novel approach for identifying previously unknown pathogens, the identification of a number of new human microbial pathogens, including the agent of Whipple's disease, and some of the first broad, molecular analyses of the composition of the human indigenous microbiota. Dr. Relman advises the U.S. government, as well as nongovernmental orga- nizations, in matters pertaining to microbiology, emerging infectious diseases, and biosecurity. He currently serves as a member of the National Science Advi- sory Board for Biosecurity and as a member of the Defense Advanced Research Projects Agency Synthetic Biology Panel, and he advises several U.S. government departments and agencies on matters related to pathogen diversity, the future life sciences landscape, and the nature of present and future biological threats. He has served as chair of the Board of Scientific Counselors of the National Institute of Dental and Craniofacial Research (NIH) and is currently (2011-2012) president- elect of the Infectious Diseases Society of America (IDSA). Dr. Relman served as vice-chair of a National Academy of Sciences (NAS) study of the science underlying the FBI investigation of the 2001 anthrax mailings, and he co-chaired a 3-year NAS study that produced a widely cited report entitled Globalization, Biosecurity, and the Future of the Life Sciences (2006). He is a fellow of the

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602 THE SOCIAL BIOLOGY OF MICROBIAL COMMUNITIES American Academy of Microbiology, a fellow of the AAAS, and a member of the Association of American Physicians. Dr. Relman received the Squibb Award from the IDSA in 2001 and was the recipient of both the NIH Director's Pioneer Award and the Distinguished Clinical Scientist Award from the Doris Duke Chari- table Foundation, in 2006. He was elected a member of the Institute of Medicine (NAS) in 2011. Thomas M. Schmidt, Ph.D., is a professor of microbiology and molecular ge- netics at Michigan State University. His research focuses on the distribution of microbial populations in nature and the link between community structure and function. In particular, his research group is establishing links between the flux of greenhouse gases from soil and the composition of microbial communities that catalyze these ecosystem-level processes and is exploring the role of microbes in the human microbiome related to health and disease. A unifying theme of these studies is a postulated trade-off between metabolic power and efficiency that would dictate microbial fitness and the distribution of microbes in the environ- ment. Schmidt, a fellow of the American Academy of Microbiology, was honored with the 2010 ASM Graduate Microbiology Teaching Award in recognition of his dedication to students and for fostering an intellectually stimulating environment in his laboratory and the courses he has taught. Vanessa Sperandino, Ph.D., received her Ph.D. in 1995. She did her postdoc- toral training in the University of Maryland School of Medicine from 1997 to 2001, when she joined the faculty at the Microbiology Department at Univer- sity of Texas Southwestern Medical Center as an assistant professor. In 2007 Dr. Sperandino was promoted to associate professor with tenure. In September 2011 she was promoted to full professor. She was a Pew Fellow in biochemical sciences, an Ellison Foundation New Scholar Award in Global Infectious Dis- eases, a Burroughs Wellcome Fund Investigator in Pathogenesis of Infectious Diseases, and Kavli Frontiers of Science Fellow. Joan E. Strassmann, Ph.D., is professor of biology at Washington University in St. Louis. Until 2011, she was professor of ecology and evolutionary biology at Rice University. She studies the evolution of cooperation, how conflict is con- trolled in cooperative systems, and the evolution of altruism and organismality. With David C. Queller, she has investigated genetic relatedness and kin selec- tion in numerous species of social wasps and bees at field locations in Texas, Venezuela, Brazil, and Italy. They have applied theories of social evolution to Dictyostelium discoideum, a social amoeba previously studied from develop- mental and cell biology perspectives. They have identified many social genes, have elucidated processes of cooperation, and have shown that high relatedness is essential for maintaining altruism, using experimental evolution. A new direc- tion explores the discovery of a Dictyostelium--bacteria farming and protection

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APPENDIX E 603 symbiosis. Her work has resulted in more than 150 publications, including more than 15 papers in Science or Nature. Dr. Strassmann is also active in science edu- cation at several levels. She has held a Guggenheim Fellowship. She is a fellow of the American Academy of Arts and Sciences, the AAAS, and the Animal Behavior Society, of which she currently serves as president. Edith Widder, Ph.D., is a deep-sea explorer and MacArthur Fellow who com- bines expertise in oceanographic research and technological innovation with a commitment to reversing the worldwide trend of marine ecosystem degradation. A specialist in bioluminescence (the light chemically produced by many ocean organisms), she has been a leader in helping to design and invent new submersible instrumentation and equipment to enable unobtrusive deep-sea observations. She is the CEO, senior scientist, and co-founder of the Ocean Research & Conserva- tion Association, an organization dedicated to the study and protection of marine ecosystems and the species they sustain through development of innovative tech- nologies and science-based conservation action. Joao Xavier, Ph.D., graduated as a chemical engineer in 1998 (Technical Uni- versity of Lisbon) and, after that, moved into quantitative biology for his Ph.D. (New University of Lisbon). There he developed an interest in emergent proper- ties of microbial systems. For his thesis and subsequent postdoctoral work (Delft University of Technology), he developed a mathematical modeling framework for the behavior of bacterial biofilms, which he applied to problems in environ- mental biotechnology such as wastewater treatment. In July 2006 he decided to shift his research focus to more fundamental questions in evolutionary biology and joined Kevin Foster as a postdoc of the FAS Center for Systems Biology in Harvard University in order to study the evolution of cooperation in biofilms, again using complementary experimental and computational approaches. In late 2009, he joined the faculty at Memorial Sloan-Kettering Cancer Center, where he continues his work on bacterial interactions now applied to biomedical problems.

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