Microbiology Virtual Week 2020

Meredith Ashby is the Director of Market Strategy for Microbial Genomics, Cancer and Immunology at Pacific Biosciences. She completed her Ph.D. at Caltech mapping the gene regulatory networks that direct sea urchin development just as the sea urchin genome was being sequenced ... Inspired by the impact of genome sequencing on her research, she joined PacBio after a postdoc at UCSF. She has been with the company since 2009 and has worked in R&D on both sequencing optimization and bioinformatics application development. She is now focused on facilitating the use of PacBio long read sequencing to solve the unmet needs of scientists seeking to understand the incredibly diverse range of microbes that live in, on and around us and the systems we depend on.

Dr Ivan Brukner entered into genomic era back in 1989 (ex-Yugoslavia), trying to describe and solve repeating sequence "branching motif problem" in building whole genome sequence. Next 5-10 years, his research was targeting sequence-dependent DNA structural problems, where ... contradictory puzzle about origin of DNA curvature and bending (crystallographic versus soft biochemistry data) was resolved (Italy, Germany and Canada). In 2000-2007, focus was directed toward design of nucleic-acid-based "ideal" point of care diagnostic device. Robust, multiplex, hybridization-based diagnostic device (which operates at standard "room" temperatures - in spite of ~90% sequence cross-similarity) was constructed and functionally tested. The universal protocol for selection of "robust" hybridization probes was result of this adventure. After joining Jewish General Hospital in Montreal (~2009), his work was becoming more clinically applicable, focusing on high volume molecular assays with strong financial and/or diagnostic impact (MRSA, C.difficile, VRE). He realized the strong need for applicability of new molecular techniques in emergency, including NGS, and definition of technological bottlenecks is subject of his talk in this secession.

Dr. Ehrlich is Professor of Microbiology and Immunology, and Otolaryngology-Head and Neck Surgery at Drexel University College of Medicine (DUCoM) in Philadelphia, PA, USA. He also directs: the Center for Genomic Sciences (CGS); the Center for Advanced Microbial Processing ... (CAMP); and the Center for Surgical Infections and Biofilms within the Institute for Molecular Medicine and Infectious Disease at DUCoM. In addition, he directs the Core Genomics Facility for the Drexel University as a whole. CGS scientists utilize a broad array of comparative genomic techniques and bioinformatic tools, many developed in-house, to identify and characterize both virulence genes within pathogens, and susceptibility genes to pathogens within their hosts. Dr Ehrlich is also one of the founders of the field of Clinical Molecular Diagnostics (MDx), having been involved in the original application of PCR for the detection of human retroviruses in 19851. He founded the MDx Division at UPMC and used these experiences to author the first textbook/lab manual for infectious disease (ID) MDx2. Together with a team of like-minded pioneers he was one of the founders of the Association for Molecular Pathology and served as the first co-chair of the ID section. Dr Ehrlich counts among his major contributions to science the mapping and cloning of several major human disease genes3,4, and the re-writing of much of our understanding of chronic bacterial pathogenesis5,6. The latter began with his promulgation of the biofilm paradigm to explain many facets of chronic mucosal microbial infections7-9. Working with Chris Post, he started his explorations into chronic middle-ear disease in children in the early 90's which he has since repeatedly generalized such that it is now widely accepted that the vast majority of all chronic microbial infections are biofilm-associated10,11. He also advanced the Distributed Genome Hypothesis (DGH12,13) to explain the enormous clinical variability among strains of a bacterial species, which together with the biofilm paradigm form the bases for his rubric of Bacterial Plurality6. His work in human genetics combined with the laboratory resources necessary to test the DGH have resulted in his having played a role in the development of several waves of genomic technology over the last quarter century including microsatellite mapping, microarrays, and next-generation sequencing. More recently he has developed the concept of bacterial population-level virulence factors and has for the first time within the field of bacterial genomics used statistical genetics and machine learning algorithms approaches to identify unannotated distributed genes that are associated with virulence. These computational methodologies provides a non-biased, top-down approach to prioritize the annotation of hypothetical genes14. Coincident with the recent relocation of his research enterprise to DUCOM he founded CAMP which functions as a collaborative multi-discipline facility for exploitation of a suite of technological advances, many developed within the CGS, which permit the identification, cloning, heterologous expression, and biochemical verification of commercially important biosynthetic and biodegradative pathways from what he refers to as the "Genomic Dark Matter". This approach came out his successful collaborative studies with Dr. David Sherman at the University of Michigan wherein they used multiple omics technologies (and developed the term meta-omics) to isolate and characterize all of the genes for a novel biosynthetic pathway for an important anti-cancer drug from an unculturable endosymbiotic bacterium of a tunicate15. Over the past several years Dr Ehrlich has overseen the development of a novel ultra-high-fidelity microbiome assay that provides quantitative, species-specific analyses of microbial consortia using whole-gene 16S amplification and sequencing on the Pacific Biosciences third generation long-read sequencing platform16. When combined with a state-of-the art bioinformatics pipeline that takes advantage of novel pathway- algorithms and a custom database, developed in-house, this system provides unprecedented accuracy. In collaboration with Dr Curtis Harris at the NCI, Dr Ehrlich and his team applied this high-fidelity microbiome assay to identify bacterial species-specific changes to the lung microbiome associated with a specific TP-53 mutation - providing the first microbial biomarker for cancer17. Dr Ehrlich's lifelong interest in emergent MDx and "omic" technologies led to his recent appointment as Director of the Meta-Omics Core Facility at the Sidney Kimmel Cancer Center, a consortium NCI-designated Cancer Center involving Thomas Jefferson University and Drexel University. Dr Ehrlich's latest paradigm-changing hypothesis is that Alzheimer's disease results from a combination of chronic bacterial infections of the brain (primarily originating from the periodontium) and the brain's anti-microbial and inflammatory responses to these infections. Dr. Ehrlich was elected as fellow of the American Association for the Advancement of Science in 2014 and has won numerous awards for his research and teaching.

Jennifer M. Fettweis, Ph.D. is the founder and director of the Research Alliance for Microbiome Science (RAMS) Registry and assistant professor in the Departments of Microbiology and Immunology and Obstetrics and Gynecology at Virginia Commonwealth University. From 2009-2019, she ... served as the project director for two projects funded through the NIH's Human Microbiome Project: the Vaginal Human Microbiome Project (VaHMP) and the Multi-Omic Microbiome Study: Pregnancy Initiative (MOMS-PI). Dr. Fettweis was awarded a B.A. in Mathematics and Economics from the University of Virginia and a Ph.D. in Microbiology and Immunology from Virginia Commonwealth University. As an international leader in the microbiome science, Dr. Fettweis studies how the microbiome impacts risk for pregnancy complications with a focus on the microbiome's influence on health disparities. She also investigates how human health is influenced by the transmission of the microbiome from mother to child and across generations.

Matt entered the research field over 20 years ago as a lab animal technician at the TSI/Mason contract research facility. He has worked at both contract facilities such as TSI and OREAD Biosafety as well in industry at Pharmacia, Pfizer, and Sanofi-Aventis. During that period he ... has performed a variety of surgical procedures including device implantation, transplants, orthopedic defect, ocular and vascular implants, cardiac surgery, and brain and spinal procedures. His experience ranges from mice and rats to non-human primates and livestock. In addition, he holds four patents for novel surgical devices and implants and has been training technicians, scientists, veterinarians, and physicians in surgical techniques and procedures for over 15 years. Outside of the surgical realm, he has been a study director, sonographer, Safety Pharmacology scientist, and manager. Currently Matt supervises a team of technicians and surgeon-technicians at Genzyme who support the Boston hub and perform over 1250 surgical procedures a year. Matt was also on the board of directors for the Academy of Surgical Research for over ten years, serving as their program chair for three of them as well as educational chair for two. Currently he is the program chairman for the New England branch of AALAS.

Dr. García-Sastre is Professor in the Departments of Microbiology and Medicine and in the Tisch Cancer Center at Icahn School of Medicine Mount Sinai (ISMMS) in New York,. He is also Director of the Global Health and Emerging Pathogens Institute at ISMMS, and Principal ... Investigator for the Center for Research on Influenza Pathogenesis (CRIP), one of five NIAID Centers of Excellence for Influenza Research and Surveillance (CEIRS). For the past 30 years, his research interest has been focused on the molecular biology, virus-host interactions, innate immunity and pathogenesis of influenza viruses and several other RNA viruses, as well as on the development of new vaccines and antivirals. He has more than 500 peer-reviewed publications in these areas of research. He has been President of the International Society for Vaccines in 2014-2015. He is Editor for the scientific journals PLoS Pathogens, Journal of Virology and Virus Research. In 2017, he has been elected a fellow of the Royal Academy of Pharmacy in Spain. In 2019, he was recognized with a Honorary Doctor Degree from the University of Burgos, Spain. Also in 2019, he was elected a member of the National Academy of Sciences.

Dr. Emily Hollister is a microbial ecologist and serves as the Vice President for Information Technology & Analytics at Diversigen, Inc. Prior to joining Diversigen, Dr. Hollister served as an Assistant Professor in the Department of Pathology & Immunology at Baylor College of ... Medicine and as the Director of Microbial Ecology and Bioinformatics at the Texas Children's Microbiome Center at Texas Children's Hospital. Her microbiome experience ranges from soils and biofuel production systems to the human microbiome, built environment, and pre-clinical models of disease.

Jonas Korlach was appointed Chief Scientific Officer of Pacific Biosciences in July 2012. He was previously a Scientific Fellow, supporting commercial development of the PacBio RS II system and performing research aimed at developing new applications for SMRT technologies. He ... co-invented the SMRT technology with Stephen Turner, Ph.D., Pacific Biosciences Founder and Chief Technology Officer, when the two were graduate students at Cornell University. Dr. Korlach joined Pacific Biosciences as the company's eighth employee in 2004. Previously, he was a Postdoctoral Researcher at Cornell University. Dr. Korlach is the recipient of multiple grants, an inventor on 70 issued U.S. patents and 61 international patents, and an author of over 70 scientific studies on the principles and applications of SMRT technology, including publications in Nature, Science, and PNAS. In 2013, Dr. Korlach was honored by the Obama White House as an Immigrant Innovator "Champion of Change." He received both his Ph.D. and his M.S. degrees in Biochemistry, Molecular and Cell Biology from Cornell, and received M.S. and B.A. degrees in Biological Sciences from Humboldt University in Berlin, Germany.

Stephen S. Morse, Ph.D., is Professor of Epidemiology at the Columbia University Mailman School of Public Health, where he also serves as Director of the Infectious Disease Epidemiology certificate and as chair of the Columbia University Institutional Biosafety Committee (IBC) ... He was founding Director of the CDC-funded "Center for Public Health Preparedness" (2000-2005). Before coming to Columbia, Dr. Morse was Assistant Professor (virology) in The Rockefeller University (1985-1995), and Program Manager for Biodefense at DARPA (the Defense Advanced Research Projects Agency) from 1995 to 2000. He was appointed in 2014 to the U.S. government's National Science Advisory Board for Biosecurity (NSABB). His research interests focus on infectious disease surveillance, and the epidemiology and assessment of emerging infectious diseases, including influenza. He was Chair of the NIH "Conference on Emerging Viruses" (1989), for which he originated the concept of emerging viruses/infections, was founding chair of ProMED (the Program to Monitor Emerging Diseases, best known for originating outbreak reporting on the Internet in 1994); and served on the Institute of Medicine (now National Academy of Medicine) Committee on Emerging Microbial Threats to Health (1990-1992), and chaired its Virology Task Force. His book Emerging Viruses (Oxford University Press, 1993) was selected by American Scientist as one of "The Top 100 Science Books of the [20th] Century". He was a founding member of the National Academies' "Forum on Emerging Infections" (later renamed the "Forum on Microbial Threats"), a founding section editor of the CDC journal Emerging Infectious Diseases, former Editor-in-Chief of the Pasteur Institute's virology journal, and global co-Director of PREDICT (a USAID project to strengthen global capacity for surveillance and detection of new infectious disease threats) from 2009 to 2014. He is currently an Associate Editor of Disaster Medicine & Public Health Preparedness, and serves on the Editorial Board of several journals, including Health Security and Viral Immunology. He also serves on committees at the National Academies of Sciences and the World Health Organization (WHO), including the WHO Expert Group on Pandemic Influenza Preparedness Planning in the Eastern Mediterranean Region. He is a Fellow of the American Association for the Advancement of Science (AAAS), the American Academy of Microbiology, the American College of Epidemiology, the New York Academy of Medicine, the New York Academy of Sciences (and was Chair of its Microbiology Section), and other professional societies, and is a Life Member of the Council on Foreign Relations. He received his Ph.D. (in microbiology) from the University of Wisconsin-Madison.

Dr. Roossinck received a PhD in 1986 from the University of Colorado School of Medicine in Microbiology and Immunology, studying Hepatitis B virus, on an National Institutes of Health fellowship. Following a postdoctoral fellowship at Cornell University, where she began studying ... plant viruses, she moved to the Samuel Roberts Noble Foundation as a principal investigator, and focused her research on plant virus evolution and ecology. After the discovery of a novel plant-fungus-virus three-way mutualistic symbiosis that allows plants to grow in geothermal soils in Yellowstone National Park her interests expanded to include viruses of fungi. Currently she is a member of the Center for Infectious Disease Dynamics, and a Professor of Virus Ecology, in the Department of Plant Pathology and Environmental Microbiology at the Pennsylvania State University. She and her team have been studying virus ecology and experimental evolution for 25 years using plant and fungal viruses as models, and have published a number of seminal papers in this area. She is an expert in virus diversity and biodiversity, and has done extensive work on complex interactions between beneficial viruses and their hosts that are involved in adaptation of plants and fungi to extreme environments.

Professor Emeritus John G. Thomas, PhD, is recognized as an "International Educator and Global Microbiologist " (www.globalbugs.com) having lectured in more than 43 countries while a clinical microbiologist in pathology (Professor), dentistry (Clinical Professor) and ... Graduate School Education (Adjunct Professor) for 54 years , his translational research emphasizing biofilms and medical devices. He has focused upon micro 3-D- bio Printing of contour fitting gauzes using bio-plastics and unique Prebiotics with Therapeutic Bacteria (Beneficial Bacteria) for chronic wound intervention (SMarT Gauze); this integrates a common pathway, visualized through his 'Microbial Clock' and recently created Center of Hologenomic Clinical Studies (www.globalbugs.com/Hologenomic Center) which underscores a "Dual Citizenship" and co evolution of symbiotic microbes and human ecosystems. "MICROBES MATTER". His Probiotic Solutions integrates Computer Decision Support for Probiotic (Beneficial Bacteria) Guidelines combining AI, Artificial Intelligence and Precision Medicine, expanded recently to emphasize Aging, hypothesized now as a disease by the NIH. He has over 50 publications, multiple book chapters and significant grant support. His military obligation (1969-71)(wounds) and his sabbatical at Cardiff University, Wales, UK (2007)(oral health, biofilms) have remained a driving catalyst. He has been a member of the American Dental Association Scientific Advisory Committee for 8 years and American Society of Microbiology for 54 years. As Faculty at 3 national (Northeastern Ohio Universities College of Medicine, Rutgers University and West Virginia University) and 2 international Universities ( National University of Singapore and Cardiff University) during his career , he has received multiple Alumni and University awards for research and Student Mentoring ; retiring from West Virginia University in 2013 after 23 years as Professor Emeritus , he presently is expanding his research/teaching utilizing the advanced resources of the Allegheny Health Network (Center of Excellence in Biofilm Research) and Carnegie -Mellon University, Pittsburg, PA, and Mass. Gen. Hospital (Dept. of Anesthesia and Critical Care) with Harvard University, Boston, MA, all under the umbrella of his Global Microbiology Consulting. (GMC) (www.globalbugs.com). He was Acting Director of Microbiology, Laboratory Medicine, Allegheny General Hospital, Pittsburgh, PA, 2013-2016.