Jane M. Carlton,
Professor, Director, Center for Genomics and Systems Biology, New York University, USA
Dr. Jane Carlton is a Professor of Biology and Director of the Center for Genomics and Systems Biology at New York University. She received her PhD in Genetics at the University of Edinburgh, and has worked at several genomics institutions in the U.S. Her research involves comparative genomics of different species of malaria parasites, and the sexually transmitted protozoan, Trichomonas vaginalis. Professor Carlton’s ultimate goal is to cultivate and expand the science and use of genomics to improve global health.
“Mapping the Urban Microbiome of New York City’’
Microbes live in every part of the biosphere, and are crucial to ecosystems and to human life. However, the distribution of microbes and the drivers of microbial community assemblages are not well understood, especially in densely populated urban environments. We have used advances in environmental metagenomics to identify, characterize, and map the ‘urban microbiome’ of New York City (NYC), with a focus on protists. We have swabbed bicycle seats, ATM buttons, circulating paper currency, and analyzed samples of raw sewage collected from all 14 NYC waste-water treatment plants. Our current project analyzes samples from pets (cats and dogs) and pests (rats, cockroaches, and pigeons) in all five boroughs. These data are revealing intricate patterns and seasonal differences of the microbes in the city. For example, ATM keypads amalgamate microbial assemblages from different sources, including the human microbiome, eukaryotic food species, and potentially novel extremophilic taxa adapted to air or surfaces in the built environment. Microbes found on circulating paper currency have similar sources, and may also be recovered as viable organisms. DNA obtained from ATM keypads and paper bills thus provide a record of both human behavior, human health, and environmental sources of microbes.
Dr. Alexandra Graf is an Assistant Professor at FH Campus Wien where she heads the Bioinformatics Group. Dr. Graf studied Biology at the University of Vienna and obtained a Master’s in Human Ecology in Brussels before working in IT for 6 years. Combining her two fields of interest, she obtained her PhD in Bioinformatics at the University of Life Sciences and Natural Resources in Vienna. Her work focuses on the de-novo assembly and annotation of an industrial yeast genome, and on the development of a transcriptomics analysis platform for strain improvement. Dr. Graf’s interest are the de-novo assembly and annotation of microorganism genomes, transcriptomics, and analysis of gene regulation. Convinced of the benefits of communicating science to the general public, she regularly engages in citizen science projects.
“The Dark Matter in Urban Metagenomes’’
A large proportion of the reads from urban metagenome datasets cannot be assigned to known species. Therefore, all methods that depend on database searches can only successfully assign a small subset of reads. For some urban metagenome samples, the proportion of unclassified reads can reach up to over 90%. The use of assembly-based methods has the potential to include and characterize hitherto unknown species. Assembly tools are known to perform differently, depending on certain sample/data features, such as population diversity, sequencing quality, sequencing depth or input material. High community diversity, especially the presence of closely related microbial strains, can decrease assembly performance dramatically and is one of the main challenges in metagenomics analysis. Unfortunately, urban metagenome samples pose a challenge in that respect due to their limited sequencing depth, low input material and often high population diversity.
With the use of mock communities based on the properties and known taxonomic content of urban metagenome samples, it is possible to investigate the effect of technical and biological variance and bias in the datasets. Using the lessons learned from such mock communities we set out to investigate the dark matter in the dataset from an initial metro sampling study in Vienna.
Professor of Personalized Genomics, Fudan University, China
Leming Shi is a Professor at the School of Pharmacy and the School of Life Sciences of Fudan University in Shanghai, where he established the Center for Pharmacogenomics. Dr. Shi’s research focuses on pharmacogenomics, bioinformatics, and cheminformatics, aiming to realize their potentials in personalized medicine. As a Principal Investigator at the US Food and Drug Administration (FDA) from 2003 to 2012, Dr. Shi conceived and led the MicroArray and Sequencing Quality Control (MAQC/SEQC) project. Dr. Shi is a co-inventor on nine issued patents about novel therapeutic molecules and has published over 170 peer-reviewed papers (nine of them appeared in Nature Biotechnology). Dr. Shi received his Ph.D. in computational chemistry from the Chinese Academy of Sciences in Beijing.
“Precision Medicine and Standardization in Genomics and Bioinformatics’’
Precision medicine aims to deliver the right medicine to the right patient at the right dose at the right time, thus minimizing adverse drug reactions and maximizing drug efficacy. Realization of precision medicine depends on reliable and reproducible tools of genomics and bioinformatics for accurately characterizing patients at the genome scale. The MicroArray and Sequencing Quality Control (MAQC/SEQC) project is a community-wide effort to address concerns about the reliability of microarrays and next-generation sequencing. The first three phases of the MAQC/SEQC project focused on quality control and standardization on the generation and analysis of microarray and RNA-seq data, leading to the publication of three special issues by Nature Publishing Group (www.nature.com/nbt/focus/maqc/, www.nature.com/focus/maqc2/, and www.nature.com/nbt/collections/seqc/). The ongoing MAQC-IV (SEQC2) project is developing standard operating procedures for DNA-seq, aiming to improve the reliability of sequence variant calls and to increase the predictive power of genomics-based models using large cohorts of cancer patients. The MAQC/SEQC project is expected to build the foundation for the development of new diagnostic techniques and methods and foster close collaboration among international communities of precision medicine.
Distinguished University Professor, University of Maryland Institute for Advanced Computer Studies, USA
Rita Colwell is a distinguished University Professor at both the University of Maryland at College Park and at Johns Hopkins University Bloomberg School of Public Health, senior advisor and chairman emeritus at Canon US Life Sciences, Inc., and president and CEO of CosmosID, Inc. Her research interests are focused on global infectious diseases, water, and health. Colwell is currently developing an international network to address emerging infectious diseases and water issues, including safe drinking water for both the developed and developing world.
“Application of Next Generation Sequencing and Bioinformatics for Rapid and Accurate Pathogen Detection and Characterization of the Microbiome’’
Next generation sequencing (NGS) combined with high-resolution bioinformatics, offers a powerful method for detection, identification, and characterization of pathogenic microorganisms (bacteria, viruses, fungi, and parasites). This approach to diagnosis of infectious disease agents and infectious diseases offers accuracy, speed, and actionable information, the sequencing within one or two days and the bioinformatics analysis within minutes. We have applied this method in clinical studies, including retrospective case control studies comprising samples of known and unknown etiology, as well as samples from healthy individuals. The results are exciting and demonstrate detection and identification of pathogens can be accomplished well within the time frame of a single day or so. Furthermore, microbiome analysis can be used to differentiate healthy, diseased, and asymptomatic carriers, including individuals in early stages of infection and disease. Results of studies accomplished to date show that the disease state of patients reveals multiple pathogens, the microbial communities of healthy humans of diverse geographic locations tolerate different levels of pathogenic microorganisms and antibiotic resistance in their microbiomes. Different rates of antibiotic resistance were detected in geographically diverse populations. Analysis of the human microbiome and the microbial ecology of aquatic reservoirs and wastewater reuse treatment plants has provided insight into the complex interactions of the microbial populations of these ecosystems. Precision offered by next generation sequencing coupled with powerful bioinformatics makes possible a much more complete understanding of the microbiology of human populations and their environment.
Professor/ Senior Physician, Karolinska Institute, Sweden
Professor Lars Engstrand at the Karolinska Institutet, Stockholm has more than 25 years experience as a clinical microbiologist. His research interest includes the pathophysiology, diagnosis and treatment of gastrointestinal infections, and studies on cellular interactions and pathogenesis, particularly in the context of Helicobacter pylori infections. In a number of studies, population-based epidemiology has been combined with clinical and basic microbiological science, including molecular biology and genetics. Similar approaches have been applied on studies of the human microbiota in health and disease. Professor Engstrand has contributed to the Helicobacter field for 25 years and has published 140 scientific papers and book chapters on various aspects of this infection (out of 200). He has initiated the use of new diagnostic tools in clinical microbiology such as the next generation sequencing technology i.e. 454 pyrosequencing. Cross-departmental collaborations have been developed with a number research centers in Europe and USA. Prof. Engstrand currently holds faculty positions at the Department of Medicine, Baylor College of Medicine, Houston, TX and at Washington University, School of Medicine. St. Louis. Since 2012 he has been the Director of clinical omics at Science for Life Laboratory in Stockholm.
“Development of the resistome in a brand new hospital using a pipeline for large-scale microbiome mapping.’’
The recently established Center for Translational Microbiome Research at the Karolinska Institute/Science for Life Laboratory has established a broad technical, biological, clinical and epidemiological platform for studying complex microbiological communities in well-defined human materials http://ki.se/en/research/centre-for-translational-microbiome-research-ctmr A slightly modified collection, sample processing and bioinformatics analyses pipeline is also used for environmental samples obtained from different sources.New Karolinska Solna (NKS) is the project name for the state-of-the-art hospital currently under construction next to Karolinska Institutet in Stockholm. The new university hospital opened its doors to the first patients in November 2016. It will be fully operational in 2018. We identified a unique opportunity to study the development of the resistome in a brand new hospital by sampling sewage water from a defined central place in the hospitals sewage system before and after patients moved in. Culture is performed for identification of resistant bacterial strains of importance in clinical settings and hospital outbreaks. We perform taxa classification combined with functional and strain-level analyses including screening for antibiotic resistance markers; i.e. a longitudinal metagenomic profiling of the resistome. Increase knowledge about how the resistome is established in a new hospital may help to create a “smart hospital” in the future; i.e., a hospital that uses such information to improve planning, management, and promote human health by protecting against spread of resistance.
Professor, Georgia Tech and Emory University
Principal Investigator, FlyHealthy™
Howie Weiss is a Professor of Mathematics at Georgia Tech. He is also an Adjunct Professor of Biology and Global Health at Emory University. His current research projects include studying the bacterial genetics and phamacodynamics of antibiotics for bacteria growing in physically structured habitats, and studying the transmission of infectious diseases during air travel. Previously, Weiss made many significant contributions to the mathematical theory of dynamical systems. His most recent honors include being selected as a Georgia Power Professor of Excellence and a Fellow of the AAAS (American Association of Arts and Sciences).
‘‘Overview of the FlyHealthy Research Study’’
With over three billion airline passengers annually, the inflight transmission of infectious diseases is an important global health concern. Over a dozen cases of inflight transmission of serious disease have been documented, but, despite the sensational media stories and anecdotes, the true risks of transmission are largely unknown. Studies of Severe Acute Respiratory Syndrome (SARS) and pandemic influenza (H1N1p) transmission on airplanes indicate that air travel can serve as a conduit for the rapid spread of newly emerging infections and pandemics. It is believed that the movements of passengers and crew facilitate disease transmission.
In the FlyHealthy research study, we attempt to quantify the rates and routes of transmission of infectious diseases during air travel. Goals include characterizing the microbial communities in the cabin (in particular those in the air and on common touch surfaces), quantifying transmission opportunities, and constructing a data-driven, dynamic network transmission model of droplet mediated respiratory diseases. On ten transcontinental flights in the US, our team collected extensive movement and behavioral data of all individuals in the economy cabin, and also collected 229 environmental samples. We performed 16S rRNA sequencing on each sample, as well as a panel of PCR assays for common respiratory viruses.
Professor at Department of Ecology and Genetics, Limnology, Uppsala University, Sweden
Stefan Bertilsson is a Professor of Biology at the Department of Ecology and Genetics and Director for the SciLifeLab Microbial Single Cell Genomics Facility hosted by Uppsala University. His fields of research include Aquatic Microbial Ecology, Biogeochemistry, Environmental Genomics, and single cell methodology. His ongoing research projects include microbial transformation and cycling of Carbon, Nitrogen, Mercury and associated elements in freshwaters, oceans, and the deep terrestrial biosphere. His research specifically focus on the role of microorganisms in nature and their ability foremost to transform and redistribute central elements (e.g. carbon, nitrogen, mercury). His research group relies on a combination of molecular (DNA and RNA-based) methods, isotope tracers, and analytical chemical tools to understand processes such as nitrogen fixation, autotrophic carbon fixation, mercury methylation (and demethylation), and degradation of biopolymers and organic pollutants.
“Understanding the interactive nature of aquatic microbial communities from genomic data”
In this talk I will provide a synthesis and overview of how we have used a combination of amplicon based biomarker assays, metagenomics, and single cell genomics to learn more about the dynamics and functioning of aquatic microbial communities. Using examples from ecological observatories in freshwater lakes, brackish systems, and deep aquifers, I will highlight the interactive nature of such microbiomes and discuss the role of metabolite exchange, auxotrophies and other interactions controlling the biogeography and functioning of the microorganisms that populate aquatic biomes.
Assistant Professor, University of Pittsburgh
Professor Bibby received his bachelor’s degree from Notre Dame in 2008. He is currently an assistant professor in the Department of Civil and Environmental Engineering at the Swanson School of Engineering at the University of Pittsburgh. Dr. Bibby’s research interests center around understanding the presence, ecology, and diversity of microorganisms, such as viruses and bacteria, in an environmental engineering context. Microorganisms are by far the most abundant and genetically diverse biological entities on our planet. They are at the core of many of society’s environmental challenges, including sustainable energy production, waste treatment, and environmentally transmitted disease. In Dr. Bibby’s lab, emerging molecular biology techniques such as proteomics, genomics, metagenomics, and transcriptomics are integrated with fundamental, quantitative environmental engineering practices to develop new insights and solutions to these problems.
“Lessons and Questions About the Microbiomes of Buildings’’
The relatively recent explosion of interest in the ‘microbiome’ coupled with the rapid expansion of DNA sequencing ability has revolutionized our ability and understanding of the microbiota that surround our daily lives. Humans in the developed world spend approximately 90% of their time indoors, suggesting the importance of understanding the exposure to microorganisms in the built environment. In this talk I will review recent lessons about factors that shape the microbiomes of buildings, including building operation and occupancy, and how microorganisms in buildings influence human health and well-being. In addition, I will highlight important remaining questions about the microbiomes of buildings based upon a recently published review (Ten questions concerning the microbiomes of buildings, Adams et al., 2016). Finally, I will close with some perspectives about the direction of the field.
Ellen Jorgensen, PhD
Co-founder and Director of Genspace, USA
Dr. Ellen Jorgensen is the co-founder and Executive Director of Genspace. Her efforts to develop Genspace into a haven for entrepreneurship, innovation, and citizen science have been chronicled by Nature Medicine, Science, Discover Magazine, BBC News, Dan Rather Reports, PBS News Hour, The Discovery Channel, and The New York Times. Dr. Jorgensen has a Ph.D. in Molecular Biology from New York University, spent many years in the biotechnology industry, and is currently adjunct faculty at New York Medical College, the School of Visual Arts, and a Visiting Professor at The Cooper Union. Her talk ‘What you Need to Know about CRISPR’ has reached over 1 million views on TED.com.
“Into the Gowanus Canal: A Community Lab Partnership with MetaSUB’’
Community labs are a relatively new phenomenon. They are independent organizations, mostly non-profits, that provide laboratory space to the general public at a greatly reduced price. They function as informal research collectives, with shared safety standards, equipment and supplies. Research projects are initiated by lab members, who may or may not be degree-holding scientists, and efforts are self-funded. Given the limited resources of these labs, many have chosen to collaborate with university research groups on projects requiring sophisticated equipment. When a member of the Genspace community lab in Brooklyn NY was curious about what lived in a local polluted canal, Genspace reached out to a MetaSUB partner for help. The mechanics of this partnership and other similar collaborations will be discussed.
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