Microbiology Virtual Week 2022

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. Benbow joined the faculty of at Michigan State University in 2014 with a joint appointment in the Department of Department of Entomology and Department Osteopathic Medical Specialties. From 2008 - 2013 he was an assistant professor at the University of Dayton. His research ... program has developed around basic and applied insect and microbial ecology, with a history of studying disease in West Africa and more recent activities in building partnerships for food security in Malawi. He is the author or coauthor of over 140 peer-reviewed journal articles, 29 book chapters, three edited books and has received funding through NIH, NSF, NIJ, USDA, USGS, and USFS. Dr. Benbow has also served on three National Academy of Science, Engineering and Medicine appointed committees and is a regularly invited speaker to many international venues as a result of interactions with national and international scientists. He is a Fellow of the American Academy of Forensic Sciences and former president of the North American Forensic Entomology Association. Dr. Benbow is a community and disease ecologist, studying how complex communities (e.g., aquatic or carrion insects or microbes) contribute to ecological systems and can understanding these communities can be used in various applications in medicine, disease and forensics. One of the largest community ecology studies related to human health has been the Human Microbiome Project that showed much of the human body is composed of a wide diversity of prokaryotic cells and that these communities have significant importance to human health. Using the technological advances that came with the Human Microbiome Project, Dr. Benbow and colleagues have partnered with a medical examiner office to survey the postmortem microbiomes during routine autopsies and death investigations. The goal of this collaborative work is to determine how postmortem microbiomes can be used to make estimates of the postmortem interval and manner/cause of death. In addition to this work, Dr. Benbow's lab also does basic forensic research on how aquatic microbiomes can be used to estimate postmortem submersion intervals; consults for death investigations; and studies how insects and microbial communities interact in ways that could affect evidence during investigations. In addition to forensic research, Dr. Benbow's lab asks three general questions: 1) Is insect fitness influenced by the community of microbes living in or on them? 2) What are the ecological interactions of insects with the microbial communities associated with their habitat or food resources? and, 3) How can this information be used to inform resources management, human health and forensics? With a joint appointment in the College of Osteopathic Medicine, his lab seeks to answer these insect-microbe questions for translation into human health applications. Given the rich history of research in insect-microbe interactions that has focused on vectoring pathogens and co-evolved symbionts, coupled with the advanced ability to identify culturable and non-culturable bacteria using high throughput sequencing, a new generation of inquiry into the importance of the insect microbiome and their interactions in nature has tremendous potential for insect science. It is within this realm of inquiry where his students test explicit hypotheses at the individual, population and community levels to better understand the importance of insect-microbe interactions to the ecology and evolution of carrion, aquatic biology, forensics and disease systems. The research centers on the applied ecology of insect-microbial interactions within three systems: carrion decomposition (and forensics), aquatic ecological networks and disease systems.

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.

Dr. Fernandez-Sesma is currently a professor with tenure in the department of Microbiology at Icahn School of Medicine at Mount Sinai (ISMMS) in New York, NY, USA. She is interested on the modulation of innate immunity by viruses of human health interests, such as dengue (DENV) ... influenza (IAV), human immunodeficiency virus (HIV) and Zika (ZIKV) and in the past year also SARS-CoV-2. Her group uses mainly primary human systems, such as dendritic cells (DCs) and macrophages as well as primary lung epithelial cells and human tonsils for these studies combining molecular and immunological techniques. Their main goal is to understand the mechanisms of immune evasion used by these viruses to establish infection in humans. She currently participates in several multi-investigator projects on DENV and IAV that use OMICS technologies to study immune responses to infection. She also participated in several study sections for the National Institutes of Health (NIH/NIAD) and is currently a member of the Scientific Council of the Division of Microbiology and Infectious Diseases (DMID) at NIH/NIAID. Dr. Fernandez-Sesma is also the Chair of the NIAID Human Immunology Project Consortium (HIPC) Steering Committee. Dr. Fernandez-Sesma is also very dedicated to graduate education and mentoring. She co-directed the Microbiology Main Training Area of the Graduate School of Biomedical Sciences at ISMMS from 2010 to 2020. She has co-authored numerous publications in Virology and Immunology journals and is on the editorial board of Journal of Virology, mSphere and PLoS Pathogens.In 2021 she was Elected Fellow of the American Academy of Microbiology (AAM) and was also awarded the Jacobi Medallion from ISMMS.

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. Svetlana Y. Folimonova received her PhD in Microbiology from Moscow State University, Moscow, Russia. She held a postdoctoral position at the S. R. Noble Foundation, Ardmore, Oklahoma and a postdoctoral position at the University of Florida, Citrus Research and Education ... Center, Lake Alfred, Florida. Dr. Folimonova was appointed Assistant Professor of Plant Pathology at the University of Florida, Gainesville, Florida, in 2012. In 2016, she was promoted to Associate Professor. Dr. Folimonova's research program focuses on viral and bacterial pathogens of citrus, with the main emphasis on Citrus tristeza virus (CTV) and Candidatus Liberibacter asiaticus, a causal agent of citrus greening [Huanglongbing (HLB)]. Her primary research effort is concentrated on understanding the mechanisms of the infection process, host responses to the pathogens, improving methods of detection, and developing management strategies for these diseases. In 2020, Dr. Folimonova received a prestigious Syngenta Crop Protection Award from the American Phytopathological Society for her outstanding contributions to research on CTV and, specifically, for the elucidation of the mechanism of the CTV superinfection exclusion and for the research accomplishments on the development of the CTV-based vectors for expression of antimicrobial proteins for management of citrus greening. Dr. Folimonova also serves as Councilor for Plant Virology at the American Society for Virology.

Dr. K. Leigh Greathouse is an Assistant Professor at Baylor University with appointments in Biology and Nutrition. Her background spands the fields of cancer biology, epidemiology, and nutrition. She recived her Ph.D. from the University of Texas and M.D. Anderson Cancer Center ... and her M.P.H. from Johns Hopkins Bloomberg School of Public Health. She completed her postdoctoral training at the National Cancer Institute in the laboratory of Curtis Harris, where she discovered a novel microbiome-gene interaction in lung cancer. The focus of her laboratory at Baylor is on elucidating the relationship between diet and the microbiome and its impact on cancer etiology and treatment. The goals of the Greathouse lab are focused on 1) delineating the dietary factors that modify the microbiome and its function, 2) developing microbial multi-omic classifiers that improve stratification of patients for cancer treatment, and 3) identify key functional pathways and mechanisms of microbiota-host communication. Dr. Greathouse has received multiple awards for her work, including a Merit Award from the National Insitutes of Health, Excellence in Research Leadership, and Rising Star at Baylor Univeristy. Most recenlty, she was awarded a career development award from Department of Defense to study the relationsihp between diet and the microbiome in colon cancer treatment response and toxicity. Ultimately, the goal of her lab is to discover dietary factors and microbial targets for the development of clinical tools to prevent cancer development, and reduce morbidity and mortality from colon cancer.

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.

Dorottya earned her MD and PhD in clinical medicine from Semmelweis University of Medicine in Hungary. Holding postdoctoral fellowships at Baylor College of Medicine/Texas Children's Hospital and Columbia University, she has 10+ years of experience in translational medicine ... pediatrics, gastroenterology, microbiology, and clinical metagenomics. She led cutting-edge clinical trials on fecal microbiome transplantation and developed a multicenter research program to understand the role of the gut-brain axis in the integrative neuroscience field. Currently, Dorottya is the Chief Medical Officer at Biotia, a NYC-based startup focusing on rapid infectious disease diagnostics, surveillance, and prevention of hospital-acquired infections powered by artificial intelligence.

Priscilla earned her PhD in Bio-organic Chemistry at the University of California, Berkeley. Following postdoctoral training in viral immunology at Scripps Research, she established her own research group combining chemical and pharmacological approaches to address fundamental ... and translational problems in virology. Her research interests and goals are centered on discovery and validation of new antiviral targets, identifying alternatives to combination therapy for avoiding antiviral resistance, and investigating the function of lipid membranes in RNA virus replication. She likes running and hiking, and when having kids meant finding a hobby she could do while watching the kids, she learned how to knit from her first graduate student. She is a strong advocate for diversity, equity, and inclusion in science. After many years at Harvard Medical School, she recently moved with her research group, husband, and three children back to the West Coast where she is Professor in the Department of Microbiology and Immunology at Stanford University School of Medicine.