Microbes in the City: Mapping the Urban Genome

Microbes in the City:
Mapping the Urban Genome

Friday, June 19, 2015

The New York Academy of Sciences

Presented By

Presented by New York University and the New York Academy of Sciences

 

Microbes run the world. The human body and our environment are inhabited by trillions of bacteria and other microbes that carry out the majority of the biochemical activity on the planet. From birth, all of our interactions with the world expose us to different sources of microbes, and, conversely, expose microbes to us. As humans settle into built environments within urban settings, microorganisms both within and around us are changing accordingly. Yet we still understand very little about the complex, interdependent microbial ecosystems found in the built environment. By virtue of recent technological breakthroughs in sensing, sampling, and genetic sequencing of the microbes in our midst, we can quantify and map microbial transmission between humans, urban pests such as cockroaches and pigeons, and the air and surfaces of urban habitats — from kiosks and subways, to soil and sewage.

This conference will bring together scientists, engineers, architects, public health workers, ethicists, and policy makers at the forefront of efforts to map all of the genetic information that makes up the urban genome. This information—a living microbial fingerprint known as a metagenome—is intended to be used to create built environments that consider microbial ecology. The goal is to improve the health and productivity of these environments such that we may be able to design healthier homes and workplaces, identify potential health threats, track and fight disease epidemics, and even chart the environmental impact of major storms.

*Networking Reception and Poster Session to follow.

Registration Pricing

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Member (Student / Postdoc / Resident / Fellow)$30$55$105
Nonmember (Academia)$80$105$155
Nonmember (Corporate)$200$225$275
Nonmember (Non-profit)$80$105$155
Nonmember (Student / Postdoc / Fellow)$45$70$120

NYU faculty and students are eligible to register at Academy member rates. To access this discounted pricing, please select “Nonmember (Academia)” or “Nonmember (Student / Postdoc / Fellow)” and use the codes NYUfaculty and NYUstudent, respectively. Please note that a valid NYU ID must be presented upon check-in at the conference. Those without a valid ID will be billed onsite for the difference between the member and regular rates.


This symposium is made possible with support from

Agenda

* Presentation titles and times are subject to change.


June 19, 2015

8:00 AM

Registration, Breakfast, and Poster Setup

8:45 AM

Welcome Remarks
Jane M. Carlton, PhD, New York University (NYU)
Melanie Brickman Stynes, MSc, PhD, The New York Academy of Sciences

Session I. Microbes, Metagenomes, and Humans

Chairperson: Jane M. Carlton, PhD

9:00 AM

Session 1 Keynote
Genomic Analysis of Microbial Communities: What Have We Learned?
Jo Handelsman, PhD, White House Office of Science and Technology Policy (OSTP)

9:30 AM

Missing Microbes and the (Mis)use of Antibiotics
Martin J. Blaser, MD, New York University Langone Medical Center

9:50 AM

Go Viral: Experiences in Real-time Community-Level Disease Surveillance
Rumi Chunara, PhD, New York University Polytechnic School of Engineering

10:10 AM

Hot Topic Talk Selected from Submitted Abstracts
Mobile Genes in the Human Microbiome are Structured at Global, Regional, and Individual Scales
Ilana Brito, PhD, Massachusetts Institute of Technology (MIT)

10:30 AM

Networking Coffee Break

Session 2. The Urban Metagenome I

Chairperson: Martin J. Blaser, MD

11:00 AM

Session 2 Keynote
The Changing Face of Pathogen Discovery
W. Ian Lipkin, MD, Center for Infection and Immunity, Columbia University

11:30 AM

The Built Environment Microbiome: Health and Disease
Jack Gilbert, PhD, Argonne National Laboratory

11:50 AM

Using Metagenomics to Map Transmission of Species, Strains, and Genes
Eric Alm, PhD, MIT Department of Biological Engineering

12:10 PM

A Seed Project for Mapping Austin’s Microbiomes
Juan P. Maestre, PhD, The University of Texas at Austin

12:30 PM

Networking Luncheon and Poster Session

Session 3. The Urban Metagenome II

Chairperson: Jack A. Gilbert, PhD

2:00 PM

Session 3 Keynote
From Microbes to Molecules: Detailing Function in Integrated Multi'omics
Curtis Huttenhower, PhD, Harvard T.H. Chan School of Public Health

2:30 PM

Multi-Kingdom Diversity of Subways and Cities with Metagenomics
Christopher Mason, PhD, Institute for Computational Biomedicine, Weill Cornell Medical College

2:50 PM

Don't Forget the Protists! Characterizing Microbial Eukaryotes in New York City
Jane Carlton, PhD, New York University Center for Genomics and Systems Biology

3:10 PM

Wastewater Effluent Impacts on an Urban River Microbiome
Rachel Poretsky, PhD, University of Illinois at Chicago

3:30 PM

Networking Coffee Break

Session 4. The Future of Urban Metagenomics

Chairperson: Claudio Silva, PhD

4:00 PM

Session 4 Keynote
Pests: Cockroaches, Bed-Bugs, and Urban Entomology
Coby Schal, PhD, North Carolina State University Department of Entomology

4:30 PM

Closing Panel Discussion:

Ethical, Legal and Social Issues of Metagenomics

Moderator: Laurie Garrett, Council on Foreign Relations

Panelists:
Joel Ackelsberg, MD, MPH, NYC Department of Health and Mental Hygiene
Jo Handelsman, PhD, White House Office of Science and Technology Policy
Paula Olsiewski, PhD, Alfred P. Sloan Foundation

5:15 PM

Closing Remarks

5:30 PM

Networking Reception & Poster Session

6:30 PM

End of Day

Speakers

Scientific Organizing Committee

Eric Alm, PhD

Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology

Martin J. Blaser, MD

New York University Langone Medical Center

Martin J. Blaser, M.D., is the Muriel and George Singer Professor of Medicine, Professor of Microbiology, and Director of the Human Microbiome Program at the NYU School of Medicine. He served as Chair of the Department of Medicine at NYU from 2000-2012. A physician and microbiologist, Dr. Blaser is interested in understanding the relationships we have with our persistently colonizing bacteria. His work over the past 30 years focused on human pathogens, including Campylobacter species and Helicobacter pylori, which also are model systems for understanding interactions of residential bacteria with their human hosts. Over the last decade, he has been actively studying the relationship of the human microbiome with health and with such important diseases as asthma, obesity, diabetes, and allergies. Over the course of his career, Dr. Blaser has served as the advisor for a large number of students, post-doctoral fellows, and junior faculty, and he has been actively involved in national scientific and professional organizations. He served as President of the Infectious Diseases Society of America, Chair of the Board of Scientific Counselors of the National Cancer Institute, and Chair of the Advisory Board for Clinical Research of the National Institutes of Health. He currently serves on the Scientific Advisory Board of the Doris Duke Charitable Foundation. He was elected to the Institute of Medicine and the American Academy for Arts and Sciences. He holds 24 U.S. patents relating to his research, and has authored over 520 original articles. Most recently, he wrote “Missing Microbes”, a book targeted to general audiences.

Melanie Brickman Stynes, MSc, PhD

The New York Academy of Sciences

Jane Carlton, PhD

New York University Center for Genomics and Systems Biology

Elodie Ghedin, MSc, PhD

New York University

Jack Gilbert, PhD

Argonne National Laboratory

Dr. Jack A Gilbert earned his Ph.D. from Unilever and Nottingham University, UK in 2002, and received his postdoctoral training at Queens University, Canada. He subsequently returned to the UK in 2005 to Plymouth Marine Laboratory at a senior scientist until his move to Argonne National Laboratory and the University of Chicago in 2010. Dr. Gilbert is Group Leader for Microbial Ecology at Argonne National Laboratory, Associate Professor in the Department of Ecology and Evolution and the Department of Surgery at University of Chicago, Associate Director of the Institute of Genomic and Systems Biology, and Senior Scientist at the Marine Biological Laboratory. Dr. Gilbert uses molecular analysis and sequencing tools to test fundamental hypotheses in microbial ecology. He has authored more than peer reviewed 160 publications and book chapters on metagenomics and approaches to ecosystem ecology (www.gilbertlab.com). He is currently working on generating observational and mechanistic models of microbial communities in natural, urban, built and human ecosystems. He is on the board of the Genomic Standards Consortium (www.gensc.org), is an section editor for PLoS ONE and senior editor for the ISME Journal and Environmental Microbiology. Among other projects, he leads the Earth Microbiome Project (www.earthmicrobiome.org), Home Microbiome Project (www.homemicrobiome.com), Hospital Microbiome Project (www.hospitalmicrobiome.com), and co-founded American Gut (www.americangut.org). In 2014 he was recognized on Crain’s Buisness Chicago’s 40 Under 40 List.

Brooke Grindlinger, PhD

The New York Academy of Sciences

Christopher Mason, PhD

Institute for Computational Biomedicine, Weill Cornell Medical College

Aristides A. N. Patrinos, PhD

Center for Urban Science and Progress (CUSP), New York University

Claudio T. Silva, PhD

Center for Data Sciences; Center for Urban Science and Progress (CUSP); Courant Institute of Mathematical Sciences, New York University

Speakers

Joel Ackelsberg, MD, MPH

NYC Department of Health and Mental Hygiene

Dr. Joel Ackelsberg is an infectious disease physician and medical epidemiologist with the NYC Department of Health and Mental Hygiene. He came to the Health Department’s Bureau of Communicable Disease in 2000 to direct its bioterrorism planning efforts. Since then, Dr. Ackelsberg has been closely involved with all NYC efforts to enhance the effective management of incidents involving biological threat agents. He has participated at a leadership level in all Health Department responses to such incidents, including anthrax in 2001 and 2006, SARS, pandemic influenza and Ebola virus disease. He is a member of NYC’s Joint Terrorism Task Force. Dr. Ackelsberg earned his medical and public health degrees from Tufts University in Boston, MA. He completed an internal medicine residency at Temple University Hospital, Philadelphia, PA, and followed that with an infectious disease fellowship at the University Medical Center/Cooper Hospital in Camden, NJ. Before coming to NYC, Dr. Ackelsberg served as an Epidemic Intelligence Service Officer with the Centers for Disease Control and Prevention.

Eric Alm, PhD

Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology

Martin J. Blaser, MD

New York University Langone Medical Center

Martin J. Blaser, M.D., is the Muriel and George Singer Professor of Medicine, Professor of Microbiology, and Director of the Human Microbiome Program at the NYU School of Medicine. He served as Chair of the Department of Medicine at NYU from 2000-2012. A physician and microbiologist, Dr. Blaser is interested in understanding the relationships we have with our persistently colonizing bacteria. His work over the past 30 years focused on human pathogens, including Campylobacter species and Helicobacter pylori, which also are model systems for understanding interactions of residential bacteria with their human hosts. Over the last decade, he has been actively studying the relationship of the human microbiome with health and with such important diseases as asthma, obesity, diabetes, and allergies. Over the course of his career, Dr. Blaser has served as the advisor for a large number of students, post-doctoral fellows, and junior faculty, and he has been actively involved in national scientific and professional organizations. He served as President of the Infectious Diseases Society of America, Chair of the Board of Scientific Counselors of the National Cancer Institute, and Chair of the Advisory Board for Clinical Research of the National Institutes of Health. He currently serves on the Scientific Advisory Board of the Doris Duke Charitable Foundation. He was elected to the Institute of Medicine and the American Academy for Arts and Sciences. He holds 24 U.S. patents relating to his research, and has authored over 520 original articles. Most recently, he wrote “Missing Microbes”, a book targeted to general audiences.

Ilana Brito, PhD

Massachusetts Institute of Technology

Ilana Brito is currently a postdoc in Eric Alm’s lab at MIT where she works on microbial transmission. Ilana went to college at Harvard University, majoring in both Biology and Government, and completed her PhD in genetics at MIT. Ilana received an Earth Institute postdoctoral fellowship from Columbia University to study microbial transmission, both pathogenic and friendly. While at Columbia University, Ilana launched large-scale project to examine the transmission of microbes.

Jane Carlton, PhD

New York University Center for Genomics and Systems Biology

Rumi Chunara, PhD

New York University Polytechnic School of Engineering

Dr. Chunara is an Assistant Professor at NYU, in Engineering and the Global Institute of Public Health. She specializes in building and harnessing information from participatory tools, such as point of care diagnostics, mobile phones and other Internet-enabled sensors and media. Simultaneously, Dr. Chunara develops statistical methodology for using these observational data sources in population-level disease surveillance. Previously Dr. Chunara was an Instructor at Harvard Medical School, the Children’s Hospital Informatics Program and HealthMap. Dr. Chunara completed her PhD at the Harvard-MIT Division of Health, Sciences and Technology, an ScM at MIT in Electrical Engineering and Computer Science and received her Bachelors degree in Electrical Engineering (Honors) from Caltech. Her research has been reported on widely including in NBC.com, CNN.com, the Toronto Star, Al-Jazeera English Online, the Chronicle for Higher Education, New Scientist, SciDev.net, Nature.com and Scientific American. She is a recipient of the MIT Presidential Fellowship and a Caltech Merit Scholarship. Dr. Chunara obtained clinical experiences in Kenya, Pakistan and the United States, and was selected as an MIT Technology Review Top 35 under 35 Innovator in 2014.

Laurie Garrett

Council on Foreign Relations

Laurie Garrett is the senior fellow for global health at the Council on Foreign Relations. She is the only writer to have been awarded all three of the big “Ps” of journalism: the Peabody, the Polk, and the Pulitzer.

Garrett is also the best-selling author of The Coming Plague: Newly Emerging Diseases in a World Out of Balance and Betrayal of Trust: The Collapse of Global Public Health. Her most recent book, I Heard the Sirens Scream: How Americans Responded to the 9/11 and Anthrax Attacks, received the 2011 E-Literature Award for best science writing. Garrett is an expert on global health with a particular focus on newly emerging and re-emerging diseases, bioterrorism, public health, and its effects on foreign policy and national security.

A member of the National Association of Science Writers, Garrett also served as the organization’s president in the mid-1990s. She currently serves on the advisory board for the Hideyo Noguchi Africa Prize, and is a principal member of the Modernizing Foreign Assistance Network (MFAN). She chaired the Scientific Advisory Panel to the United Nations High Level Commission on HIV Prevention in collaboration with UNAIDS.

Jack Gilbert, PhD

Argonne National Laboratory

Dr. Jack A Gilbert earned his Ph.D. from Unilever and Nottingham University, UK in 2002, and received his postdoctoral training at Queens University, Canada. He subsequently returned to the UK in 2005 to Plymouth Marine Laboratory at a senior scientist until his move to Argonne National Laboratory and the University of Chicago in 2010. Dr. Gilbert is Group Leader for Microbial Ecology at Argonne National Laboratory, Associate Professor in the Department of Ecology and Evolution and the Department of Surgery at University of Chicago, Associate Director of the Institute of Genomic and Systems Biology, and Senior Scientist at the Marine Biological Laboratory. Dr. Gilbert uses molecular analysis and sequencing tools to test fundamental hypotheses in microbial ecology. He has authored more than peer reviewed 160 publications and book chapters on metagenomics and approaches to ecosystem ecology (www.gilbertlab.com). He is currently working on generating observational and mechanistic models of microbial communities in natural, urban, built and human ecosystems. He is on the board of the Genomic Standards Consortium (www.gensc.org), is an section editor for PLoS ONE and senior editor for the ISME Journal and Environmental Microbiology. Among other projects, he leads the Earth Microbiome Project (www.earthmicrobiome.org), Home Microbiome Project (www.homemicrobiome.com), Hospital Microbiome Project (www.hospitalmicrobiome.com), and co-founded American Gut (www.americangut.org). In 2014 he was recognized on Crain’s Buisness Chicago’s 40 Under 40 List.

Jo Handelsman, PhD

White House Office of Science and Technology Policy

Dr. Jo Handelsman is the Associate Director for Science at the White House Office of Science and Technology Policy, appointed by President Obama and confirmed by the Senate in June of 2014. Dr. Handelsman helps to advise President Obama on the implications of science for the Nation, ways in which science can inform U.S. policy, and on Federal efforts in support of scientific research.

Dr. Handelsman is an expert in communication among bacteria that associate with soil, plants, and insects and helped pioneer the field of metagenomics, bridging agricultural and medical services. Handelsman is also recognized for her research on science education and women and minorities in science, and received the Presidential Award for Excellence in Science Mentoring in 2011. Dr. Handelsman also co-chaired the PCAST working group that developed the 2012 report, “Engage to Excel,” which contained recommendations to the President to strengthen STEM education to meet the workforce needs of the next decade in the United States.

Prior to joining OSTP, Dr. Handelsman was the Howard Hughes Medical Institute Professor and Frederick Phineas Rose Professor in the Department of Molecular, Cellular and Developmental Biology at Yale University. She previously served on the University of Wisconsin-Madison faculty as a Professor in Plant Pathology from 1985 to 2009 and as Professor and Chair of the Department of Bacteriology from 2007 to 2009. In 2013, she served as President of the American Society for Microbiology. From 2002 to 2010, Dr. Handelsman was the co-founder and co-director of the Wisconsin Program for Scientific Teaching, the Yale Center for Scientific Teaching, and the National Academies Summer Institute on Undergraduate Education in Biology, programs focused on teaching principles and practices of evidence-based education to current and future faculty at colleges and universities nationwide.

Dr. Handelsman received a B.S. from Cornell University and a Ph.D. in Molecular Biology from the University of Wisconsin-Madison.

Curtis Huttenhower, PhD

Harvard T.H. Chan School of Public Health

Dr. Curtis Huttenhower is an Associate Professor of Computational Biology and Bioinformatics at the Harvard T. H. Chan School of Public Health and an Associate Member at the Broad Institute. He received his Ph.D. from Princeton University, where he also performed his postdoctoral research at the Lewis-Sigler Institute. He was an analysis lead in the NIH Human Microbiome Project and currently co-leads the "HMP2" Center for Characterizing the Gut Microbial Ecosystem in Inflammatory Bowel Disease. His lab focuses on computational methods for functional analysis of microbial communities. This includes systems biology reconstructions integrating metagenomic, metatranscriptomic, and other microbial community 'omics, the human microbiome in autoimmune disease such as IBD, and its potential as a diagnostic tool and point of therapeutic intervention.

W. Ian Lipkin, MD

Center for Infection and Immunity, Columbia University

W. Ian Lipkin, MD, the John Snow Professor of Epidemiology and Professor of Neurology and Pathology at Columbia University is internationally recognized for the development of genetic methods for microbial surveillance and discovery. He directs the Center for Infection and Immunity at Columbia University and the NIH Center for Diagnostics and Discovery, is a Member of the Advisory Committee to the Director of the NIH and Scientific Director of the Joint Research Laboratory for Pathogen Discovery in the Chinese Centers for Disease Control. His contributions include the first use of genetic methods to identify an infectious agent; implication of West Nile virus as the cause of the encephalitis in North America in 1999; invention of MassTag PCR and the first panmicrobial microarray; first use of deep sequencing in pathogen discovery; and molecular characterization of more than 600 viruses. He has been active in translating science to the public through print and digital media and was chief scientific consultant for the Soderbergh film, Contagion. His honors include Pew Scholar in the Biomedical Sciences, Kinyoun Lecturer National Institutes of Health, Oxford University Simonyi lecturer, the Mendel Medal and Bernard Fields lecturer.

Juan Maestre, PhD

The University of Texas at Austin

Dr. Maestre earned his Ph.D. from The Autonomous University of Barcelona, Spain in 2009, and received his postdoctoral training at The University of Texas at Austin, in the Civil, Architectural, and Environmental Engineering department. His doctoral training integrated microbiology, air pollution, and biological treatment processes. His postdoctoral training involved research in water treatment and indoor air quality. Dr. Maestre uses molecular biology and sequencing tools in combination with engineering approaches to study the intersection of biological processes and engineered systems.  He has investigated environments ranging from rural homes to commercial buildings. He is co-lead on the “Mapping the UTBIOME” effort to engage the UT community in the collection and analysis of environmental and microbiome samples from across campus and from the surrounding urban area.

Christopher Mason, PhD

Institute for Computational Biomedicine, Weill Cornell Medical College

Christopher E. Mason completed his dual BS in Genetics and Biochemistry from University of Wisconsin-Madison in 2001, his PhD in Genetics from Yale University in 2006, and his post-doctoral training at Yale Medical School, while also holding a fellowship at Yale Law School.

In 2009, Dr. Mason founded his laboratory at Weill Cornell Medical College in the Department of Physiology and Biophysics and at the Institute for Computational Biomedicine, as well as the Tri-Institutional Program on Computational Biology and Medicine, the Weill Cornell Cancer Center, and the Brain and Mind Research Institute.

He has won the Hirschl-Weill-Caulier Career Scientist Award, the Vallee Foundation Young Investigator Award, the Center for Disease Control and Prevention (CDC) Honor Award for Standardization of Clinical Testing, the WorldQuant Foundation Research Scholar Award, and he was named as one of the "Brilliant Ten" Scientists in the world by Popular Science magazine in 2014. His work has been featured on the covers of Nature Biotechnology, Nature Collections, Cell Systems, Neuron, Genome Biology and Evolution, and also on the cover of the Wall Street Journal and The New York Times, as well as over 300 other media outlets around the world.

Paula Olsiewski, PhD

Alfred P. Sloan Foundation

Paula J. Olsiewski, Ph.D. joined the Alfred P. Sloan Foundation as a Program Director in 2000. Dr. Olsiewski created and directs the Foundation’s programs in the Microbiology of the Built Environment and Synthetic Biology, for which grant making was concluded in 2014. Dr. Olsiewski led Sloan’s Biosecurity program until its conclusion in 2010. She also oversees the Foundation’s Civic Initiatives.

Dr. Olsiewski serves on numerous boards. She serves as Chair of the Board of Scientific Counselors Homeland Security Research Subcommittee at the U.S. Environmental Protection Agency and was recently appointed to the board of the Critical Path Institute. She was a member of the MIT Corporation (2003-2009), was President of the MIT Alumni Association (2003-2004), and served on the MIT Initiative on Faculty Race and Diversity Advisory Committee (2008-2009).

Prior to joining the Foundation, Dr. Olsiewski served in many capacities in the biotech and biomedical community. Dr. Olsiewski received a Bachelor of Science in chemistry from Yale and a PhD in biological chemistry from MIT.

Rachel Poretsky, PhD

University of Illinois at Chicago

Rachel Poretsky began her scientific career as a high school student in Brooklyn, which resulted in the only other time presenting research at the New York Academy of Sciences: in 1995 as the recipient of a NYAS high school research award. Since then, she obtained a BS in Biology from Brandeis University and a PhD in Marine Sciences from the University of Georgia. She was a postdoc at Caltech in Geology and Planetary Sciences and at Georgia Tech in Environmental Engineering. She has done pioneering work using metagenomics and metatranscriptomics of microbial communities. Since January 2013 she has been an Assistant Professor in Ecology and Evolutionary Biology at the University of Illinois at Chicago.

Coby Schal, PhD

North Carolina State University Department of Entomology

Dr. Coby Schal is Blanton Whitmire Distinguished Professor of Entomology at North Carolina State University. He has a B.S. in Biology from SUNY Albany, a Ph.D. in Entomology from the University of Kansas–Lawrence, and postdoctoral training in chemical ecology at the University of Massachusetts–Amherst. Between 1984 and 1993, he was Assistant and then Associate Professor of Entomology at Rutgers University. Schal’s research group takes an integrative approach to challenging questions in fundamental insect biology and urban entomology, including cockroach and bed bug pheromones, roles of microbes in mediating insect behavior, electrophysiological and molecular basis of sugar-aversion in cockroaches, and cockroach-produced allergens (their biology, intervention strategies to mitigate their pervasiveness in the indoor environment, and studies on the impacts of environmental interventions on health outcomes in asthmatic children). Schal’s research has been funded by EPA, HUD, NIH, NSF, USDA, and Foundations and he has published over 250 refereed papers. He teaches a graduate course in Insect Behavior, and graduate seminars in Urban Entomology and Chemical Ecology. Schal is Fellow of AAAS and the Entomological Society of America, and recipient of the Silverstein-Simeone Award from the International Society for Chemical Ecology and the Holladay Medal (NCSU’s highest faculty award).

Abstracts

Missing Microbes and the Mis(use) of Antibiotics
Martin J. Blaser, MD, New York University School of Medicine, New York, New York, United States

Antibiotic use in the United States is staggering. CDC data indicate that, in 2010 and in 2011, more than 250 million courses were prescribed for USA outpatients. This translates into more than 830 courses/1000 persons, or five courses for every six persons. This has been going on for years, and prescribing practices by physicians vary substantially; the overuse of antibiotics has been recognized by professional organizations for years, based on concerns about antibiotic resistance. Yet an estimated 70+% of all of the antibiotics used in the USA are employed on the farm, chiefly as growth promoters for livestock. Surveys have shown antibiotic residua in meats, milk, and in some cities in their tap water as a result of these practices. Despite the extent of this widespread exposure to trace antibiotic levels, whether or not it is consequential has not been studied. Recent epidemiologic studies have consistently shown associations between early-life exposures to prescription antibiotics and later onset of increased adiposity or obesity. Experimental exposures of mice in my laboratory to early-life antibiotics have shown significant changes in the intestinal microbiota, with changes in intestinal wall and hepatic gene expression, suppression of immune cell populations and effectors, and changes in body morphology. Together these epidemiologic and experimental studies point toward substantial consequences to early-life antibiotic use that had not been previously appreciated.  Confirmation of these findings should lead to public health strategies to stem losses in microbial biodiversity and to restore lost microbes.
 

GoViral: Experiences in Real-time Community-Level Disease Surveillance
Rumi Chunara, PhD, New York University Polytechnic School of Engineering, New York, New York, United States

A real-time picture of human infections is a vital component of the urban genome. Particularly in heterogeneous urban environments, it is useful to have a sense of local community disease prevalence, which can affect an individual’s disease risk in an actionable manner. Traditional healthcare-based surveillance information is robust, however data captured through these systems involves lengthy collection and dissemination cycles, high cost, inherent biases due to healthcare seeking behavior and thus suffers from limits in speed and imprecise resolution. Internet and mobile connectivity offer the opportunity for more rapid, local and scalable quantitative intelligence on disease dynamics. GoViral combines Internet-based participatory surveillance with advanced molecular methods for high sensitivity and specificity viral identification. This platform enables us to test multiple questions regarding: the specimen types that individuals can generate on their own, willingness to participate in a timely manner, viral stability, and the information that individuals would find useful communicated to them about their own infections and those circulating near them. To-date the project has focused on acute respiratory infections, and over 600 people have participated in Massachusetts and New York. Preliminary findings from GoViral indicate that diagnostic specimens can be generated by the public, oral specimens are comparable and preferable to nasal specimens for the identification of upper respiratory pathogens, and individuals desire to see real-time community prevalence. Thus GoViral generates community data that together with existing surveillance information can advance epidemiological knowledge and generate actionable information to improve public health behaviors and community disease prevalence.
 

The Changing Face of Pathogen Discovery and Surveillance
W. Ian Lipkin, MD, Mailman School of Public Health and College of Physicians and Surgeons, Columbia University, New York, New York, United States

The field of microbial diagnostics has burgeoned with the advent of high throughput sequencing platforms and bioinformatics programs that enable rapid identification and molecular characterization of known and novel agents, investments in global microbial surveillance that includes wildlife and domestic animals as well as humans, and recognition that viruses may be implicated in chronic as well as acute diseases. Here we review methods for microbial surveillance and discovery, strategies and pitfalls in linking discoveries to disease and point to opportunities for improvements, and the use of social media and medical informatics that will further advance clinical medicine and public health.
 

The Built Environment Microbiome: Health and Disease
Jack A. Gilbert, PhD, Argonne National Laboratory, Argonne, Illinois, United States

Little is known about how microbial (e.g., bacteria, Archaea and fungi) organisms are transmitted around built infrastructure. Here we will discuss our continued exploration of the home and hospital microbiome. The Home Microbiome Project has identified forensic level capabilities for tracking microbial and host interaction in the building space. The Hospital Microbiome Project is characterizing the microbial taxonomic and functional composition of surface-, air-, water-, and human-associated communities to monitor changes in community structure following the introduction of patients and hospital staff. The goal of the hospital study is to determine the influence of numerous factors on the rate and nature of microbial community succession in these hospitals including:  human population demographics; how these demographics interface with a space; and the building materials, environmental conditions, and building operational characteristics used to create and maintain that space. A total of 10,000 samples were collected using sterile swabs from patients, staff, rooms, common areas, water, and air filters over 365 time points prior to and following the official opening of the hospital. Absolute microbial abundance (plate counts and qPCR) and building environmental measurements (ventilation rates, temperature, relative humidity, light intensity, and human occupancy) were combined with relative taxonomic and functional gene abundance via amplicon sequencing (16S/ITS) and shotgun metagenomics. The microbial assemblage trends towards increased diversity with the introduction of patients and staff, and an increased human microbiome presence. A total of 70,000 bacterial taxa that call the hospital home are exploiting novel transmission routes that may influence building design and operation.
 

From Microbes to Molecules: Detailing Function in Integrated Multi'omics
Curtis Huttenhower, PhD, Harvard T.H. Chan School of Public Health

Sequencing-based studies of microbial communities have become a powerful tool for surveying whole-community ecology, but their mechanistic interpretation remains challenging both computationally and biologically. Moreover, multiple high-throughput functional profiling technologies, including metabolomics and transcriptomics, are now mature and cost-effective enough to apply across both temporal and spatial gradients to relate the human microbiome to its built environment. I will discuss recent bioinformatic approaches to data integration during microbial community studies and their application to functional profiling and downstream epidemiological analysis. These include integration of metatranscriptomic and metabolomic profiles in a strain- and pathway-specific manner in multiple environments ranging from the human gut to subways and environmental dust. I will conclude with highlights of ongoing work applying these models to metagenomics, metatranscriptomics, and metabolomic profiles of the gut during inflammatory bowel disease as part of the NIH Integrative Human Microbiome Project.
 

Pests: Cockroaches, Bed-Bugs, and Urban Entomology
Coby Schal, PhD, North Carolina State University, Raleigh, North Carolina, United States

Insects that live in our homes (a.k.a., pests!) evolved incredible adaptations to cope with the built environment and to deal with their enemies — you and I! Two major pests, the German cockroach (Blattella germanica) and the bed bug (Cimex lectularius), have become specialized commensals of human-built structures and populations of both species are rarely found elsewhere in nature. Under favorable conditions, both species can expand to extremely high densities, reaching thousands of individuals per home. A large body of literature details the impacts of cockroaches on health, concentrating on their etiological role in allergic disease and asthma and their potential to carry and vector microbial pathogens to humans. Nothing is known, however, on the role of the home microbiome in shaping the insect-associated microbial community, and conversely, the impacts of the massive organic excrements, shed cuticles, and dead bodies that cockroaches and bed bugs leave behind on shaping the density and diversity of the home microbiome. This presentation will highlight major gaps in our understanding of the interactions between us and these two species that often share our homes. It will identify unique features of these interactions that can serve as terrific model systems for further explorations of the evolution of synanthropy in the anthropogenic biome.
Supported in part by HUD grant NCHHU-0017-13 and Alfred P. Sloan Foundation grant G-2013-5-35 MBE.
 

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