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Cell Syst. 2015 Jul 29;1(1):72-87. Epub 2015 Mar 3.

Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics.

Author information

1
Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA ; School of Earth and Environmental Sciences, City University of New York (CUNY) Queens College, Flushing, NY 11367, USA.
2
Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA.
3
Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA ; CUNY Hunter College, New York, NY 10065, USA.
4
Center for Genomics, New York University, New York, NY 10003, USA.
5
Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA ; Tri-Institutional Program on Computational Biology and Medicine (CBM), New York, NY 10065, USA.
6
Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA ; CUNY Brooklyn College, Department of Biology, Brooklyn, NY 11210, USA.
7
Cornell University, Ithaca, NY 14850, USA.
8
Genspace Community Laboratory, Brooklyn, NY 11238, USA.
9
Department of Biological Sciences, Fordham University, Bronx, NY 10458, USA.
10
CUNY Brooklyn College, Department of Biology, Brooklyn, NY 11210, USA.
11
State University of New York, Downstate, Brooklyn, NY 11203, USA.
12
School of Earth and Environmental Sciences, City University of New York (CUNY) Queens College, Flushing, NY 11367, USA.
13
University of Vermont, Burlington, VT 05405, USA.
14
Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
15
Rockefeller University, New York, NY 10065, USA.
16
Academic Centre on Rare Diseases, School of Medicine and Medical Science, University College Dublin 4, Ireland ; National Centre for Medical Genetics, Our Lady's Children's Hospital, Dublin 12, Ireland.
17
Academic Centre on Rare Diseases, School of Medicine and Medical Science, University College Dublin 4, Ireland.
18
HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA.
19
CUNY York College, Jamaica, NY 11451, USA.
20
Accelerated Discovery Lab, IBM Almaden Research Center, San Jose, CA 95120, USA.
21
Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA ; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA ; The Feil Family Brain and Mind Research Institute, New York, NY 10065, USA.

Abstract

The panoply of microorganisms and other species present in our environment influence human health and disease, especially in cities, but have not been profiled with metagenomics at a city-wide scale. We sequenced DNA from surfaces across the entire New York City (NYC) subway system, the Gowanus Canal, and public parks. Nearly half of the DNA (48%) does not match any known organism; identified organisms spanned 1,688 bacterial, viral, archaeal, and eukaryotic taxa, which were enriched for harmless genera associated with skin (e.g., Acinetobacter). Predicted ancestry of human DNA left on subway surfaces can recapitulate U.S. Census demographic data, and bacterial signatures can reveal a station's history, such as marine-associated bacteria in a hurricane-flooded station. Some evidence of pathogens was found (Bacillus anthracis), but a lack of reported cases in NYC suggests that the pathogens represent a normal, urban microbiome. This baseline metagenomic map of NYC could help long-term disease surveillance, bioterrorism threat mitigation, and health management in the built environment of cities.

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