3rd Annual Metagenomics and Metadesign of Subways and Urban Biomes (MetaSUB) Conference
18-19 July – Royal Academy of Engineering Sciences, Grev Turegatan 16, Stockholm (www.iva.se)
20 July – Stockholm University, Svante Arrhenius väg 20C, Stockholm (www.su.se)
Tuesday, July 18, 2017 – Royal Academy of Engineering Sciences
10:00-10:45 Arrival at the Royal Academy of Engineering Sciences & Registration & Coffee
10:45-12:55 Plenary Session (5 minutes for Q&A after each speaker)
Dr. Rita Colwell, Former Director of the U.S. National Science Foundation (NSF) (10:45 – 11:05)
Dr. Alexandra Graf, Assistant Professor, FH Campus Wien, Austria; PI for MetaSUB Vienna (11:05 – 11:35)
Dr. Ellen Jorgensen (Co-founder and Director of Genspace, USA, Bio-hacker lab) (11:35 – 11:55)
Dr. Lars Engstrand, Professor/Senior Physician, Karolinska Institute, Sweden (11:55 – 12:15)
Dr. Kyle Bibby, Assistant Professor, University of Pittsburgh (12:15 – 12:35)
Dr. Stefan Bertilsson, Professor of Ecology and Genetics, Uppsala University (12:35-12:55)
12:55-13:20 Networking Reception
13:20-13:40 Updates from The Second Annual Global City Sampling Day (GCSD 2017)
Sofia Ahsanuddin, Executive Director of MetaSUB International Consortium
13:40-14:00 Sponsored Talk by Promega
14:00-14:20 Sponsored Talk by Zymo Research
14:20-14:50 Coffee and Tea Break
14:50-16:00 Breakout Sessions
- Library Methods in Metagenomics
- Sampling methods for sampling air, subways, buses, sewage systems, beaches, and rivers
- Strategies of NGS Sequencing of unique sample types
- Novel approaches to library synthesis and sequencing
- Alternative sequencing approach methods-Epigenetics and the Virome
- Validation of Metagenomics and Sequencing Data
16:00-16:40 Reports from Breakout Groups
Moderated by Dr. Klas Udekwu and Sofia Ahsanuddin
16:40-17:10 Sponsored Talk by QIAGEN
Distinguished Conference Hosts; PIs for MetaSUB Stockholm and MetaSUB New York City
17:30 Depart for Dinner
18:30-22:00 Shrimp Cruise Dinner
Wednesday, July 19, 2017 – Royal Academy of Engineering Sciences
8:00-8:30 Precision Interplanetary Metagenomics; Dr. Christopher Mason
Associate Professor of Computational Biology at Weill Cornell Medicine; PI for MetaSUB New York City
8:30-9:00 Keynote Address by Dr. Jane Carlton
Professor, Director, Center for Genomics and Systems Biology, New York University, USA
9:00-10:00 Thematic Session I (panel discussion): Metagenomics and Health Surveillance
Dr. Gaston Gonnet, Professor of Computer Science at ETH Zurich and Institut Pasteur Montevideo, Montevideo, Uruguay
Dr. Lynn Schriml, Associate Professor of Epidemiology and Public Health at the Institute for Genome Sciences at University of Maryland School of Medicine, Baltimore, USA
Dr. Torsten Semmler, Assistant Professor at Robert Koch Institute, Berlin, Germany
Dr. Jane M. Carlton, Professor, Director, Center for Genomics and Systems Biology, New York University, New York City, USA
Dr. Velavan Thirumalaisamy, Professor of Infectious Diseases at the Institute for Tropical Medicine, Universitätsklinikum Tübingen, Tübingen, Germany
10:00-10:25 Coffee and Tea Break
10:25-11:25 City Updates from MetaSUB Hub Laboratories
5-minute lightening round session of international MetaSUB PIs discussing their insights, analyses, computational methods
11:25-12:25 Thematic Session II (panel discussion): Advances in Bioinformatics and Data Visualization
David Danko, PhD Candidate in computational biology at Weill Cornell Medicine
Dr. Pawel Labaj, Assistant Professor at Boku University, Vienna, Austria
Dr. Nicolas Rascovan, Post-Doctoral Fellow at Mediterranee Infection Institute – Aix Marseille University, Marseille, France
Dr. Hugues Richard, Assistant Professor in the Computational and Quantitative Biology Unit at University Pierre et Marie Curie, Paris, France
Dr. Dimitar Vassilev, Associate Professor of Computer Informatics at University of Sofia, Sofia, Bulgaria
Dr. Sung Chul Hwang, Assistant Professor at Institute Pasteur South Korea, Seoul, South Korea
Dr. Eran Elhaik, Professor University of Sheffield, U.K
13:20-14:00 CAMDA MetaSUB Challenge, Assistant Professor at Boku University, Vienna, Austria
14:10-14:40 Coffee and Tea Break
14:40-18:00 Bioinformatics workshop: Data analyses of City Sampling Day 2016 dataset
18:00-12:00 Visit to the Vasa Museum and dinner
Thursday, July 20, 2017 – Stockholm University; open to the public
8:00-9:00 Poster Session (highlighted posters below)
Xinzhao Tong,“Individual factors and conditionally rare taxa shape the skin mycobiome dynamics over seasons”
Dr. Aspa D. Chatziefthmiou, “Microbial community structure and inter-phyla interactions exhibit distinct patterns in desert marine mats
Andre Kahles “Metagenome Representation with Scalable Reference Graphs”
Dr. Gaston Gonnet “The MetaSEW and MetaBEA Projects from Montevideo”
Dr. Eran Elhaik “Investigating the Dynamics of Ancestral Inference from Public Surfaces”
Scott Tighe “Microbial Communities in Antarctica”
9:00-9:20 Coffee and Tea Break
9:20-9:50 Keynote Address by Dr. Leming Shi
Professor of Personalized Genomics, Fudan University, China; PI for MetaSUB Shanghai
9:50-10:50 Thematic Session III (panel discussion): Metagenomics and Microbial Diversity
Scott Tighe, Chair ABRF Metagenomics Group, Group Leader Extreme Microbiome Project, Vermont, USA
Dr. Daniela Bezdan, Research Director of Mason Lab for Integrative Genomics, Weill Cornell Medicine, New York City, USA, New York City, USA
Dr. Aspa D. Chatziefthmiou, Research Scientist at Weill Cornell Medicine Doha and Founder of Richer Environments, Doha, Qatar
Dr. Bharath Prithiviraj, Research Associate, Earth & Environmental Sciences, Advanced Science Research Center, City University of New York, Adjunct Asst. Professor, Dept. of Biology, Brooklyn College, CUNY
10:50-11:15 MetaGenScope Workshop and Tutorial, David Danko
11:15-11:30 Olympiome Updates, Thyago Leal
11:30-12:30 Thematic Session IV (panel discussion): Air and Water Sampling
Dr. Patrick Lee, Assistant Professor in the School of Energy and Environment at the City University of Hong Kong, Hong Kong, China
Dr. Marius Dybwad, Research Scientist at the Norwegian Defense Research Establishment
Dr. Gaston Gonnet, Professor of Computer Science at ETH Zurich and Institut Pasteur Montevideo, Montevideo, Uruguay
12:30-13:30 Lunch break
13:30-13:50 Sponsored Talk by Illumina (technology update)
13:50-14:45 Session V Viral Metagenomics – RNA Extraction and Processing
Emmanuel Dias-Neto, Assistant Professor of Genomics at AC Camargo Cancer Center, Sao Paulo, Brazil
Nicolas Rascovan, Post-Doctoral Fellow at Mediterranee Infection Institute – Aix Marseille University, Marseille, France
14:45-15:00 H2020 Grant Thematic Session
15:00 Closing Remarks and Adjourn
Jane M. Carlton, PhD
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.
Alexandra Graf, PhD
Assistant Professor, FH Campus Wien, Austria
Dr. Alexadra 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 two fields of interest, she obtained her PhD in Bioinformatics at the University of Life Sciences and Natural Resources in Vienna. Her work focused 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.
Leming Shi, PhD
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 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.
Rita Colwell, PhD
Distinguished University Professor, University of Maryland Institute for Advanced Computer Studies, USA
Rita Colwell is a Distinguished University Professor both at 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.
Lars Engstrand, PhD
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 has currently 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 is 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 at Department of Ecology and Genetics, Limnology, Uppsala University, Sweden
Professor of Biology at the Department of Ecology and Genetics and Director for the SciLifeLab Microbial Single Cell Genomics Facility hosted by Uppsala University. Field of research: Aquatic Microbial Ecology, Biogeochemistry, Environmental Genomics and single cell methodology. Ongoing research projects on microbial transformation and cycling of Carbon, Nitrogen, Mercury and associated elements in freshwaters, oceans, and the deep terrestrial biosphere.
My research focus on the role of microorganisms in nature and foremost their ability to transform and redistribute central elements (e.g. carbon, nitrogen, mercury). In my research group we rely 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. We also study predation, symbiosis and other interactions between microorganisms (microbial ecology) and their evolution. We work both exprimentally in the laboratory and in the field (lakes, oceans) and study microorganisms in more exotic environments such as polar ecosystems and the deep terrestrial biosphere. More information about the group: http://www.ieg.uu.se/limnology/research/microbial+ecology/
“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.
Ellen Jorgensen, PhD
Co-founder and Director of Genspace, USA
Dr. Ellen Jorgensen is 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.
Kyle Bibby, PhD
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 in 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.
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