title: Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics.
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.
authors.affiliation: 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.
authors.forename: Ebrahim
authors.initials: E
authors.lastname: Afshinnekoo
authors.affiliation: 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.
authors.forename: Cem
authors.initials: C
authors.lastname: Meydan
authors.affiliation: 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.
authors.forename: Shanin
authors.initials: S
authors.lastname: Chowdhury
authors.affiliation: 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.
authors.forename: Dyala
authors.initials: D
authors.lastname: Jaroudi
authors.affiliation: 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.
authors.forename: Collin
authors.initials: C
authors.lastname: Boyer
authors.affiliation: 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.
authors.forename: Nick
authors.initials: N
authors.lastname: Bernstein
authors.affiliation: Center for Genomics, New York University, New York, NY 10003, USA.
authors.forename: Julia M
authors.initials: JM
authors.lastname: Maritz
authors.affiliation: 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.
authors.forename: Darryl
authors.initials: D
authors.lastname: Reeves
authors.affiliation: 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.
authors.forename: Jorge
authors.initials: J
authors.lastname: Gandara
authors.affiliation: 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.
authors.forename: Sagar
authors.initials: S
authors.lastname: Chhangawala
authors.affiliation: 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.
authors.forename: Sofia
authors.initials: S
authors.lastname: Ahsanuddin
authors.affiliation: 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.
authors.forename: Amber
authors.initials: A
authors.lastname: Simmons
authors.affiliation: Cornell University, Ithaca, NY 14850, USA.
authors.forename: Timothy
authors.initials: T
authors.lastname: Nessel
authors.affiliation: Cornell University, Ithaca, NY 14850, USA.
authors.forename: Bharathi
authors.initials: B
authors.lastname: Sundaresh
authors.affiliation: Cornell University, Ithaca, NY 14850, USA.
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Pereira
authors.affiliation: Genspace Community Laboratory, Brooklyn, NY 11238, USA.
authors.forename: Ellen
authors.initials: E
authors.lastname: Jorgensen
authors.affiliation: Department of Biological Sciences, Fordham University, Bronx, NY 10458, USA.
authors.forename: Sergios-Orestis
authors.initials: SO
authors.lastname: Kolokotronis
authors.affiliation: 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.
authors.forename: Nell
authors.initials: N
authors.lastname: Kirchberger
authors.affiliation: 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.
authors.forename: Isaac
authors.initials: I
authors.lastname: Garcia
authors.affiliation: 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.
authors.forename: David
authors.initials: D
authors.lastname: Gandara
authors.affiliation: CUNY Brooklyn College, Department of Biology, Brooklyn, NY 11210, USA.
authors.forename: Sean
authors.initials: S
authors.lastname: Dhanraj
authors.affiliation: CUNY Brooklyn College, Department of Biology, Brooklyn, NY 11210, USA.
authors.forename: Tanzina
authors.initials: T
authors.lastname: Nawrin
authors.affiliation: 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.
authors.forename: Yogesh
authors.initials: Y
authors.lastname: Saletore
authors.affiliation: 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.
authors.forename: Noah
authors.initials: N
authors.lastname: Alexander
authors.affiliation: 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.
authors.forename: Priyanka
authors.initials: P
authors.lastname: Vijay
authors.affiliation: 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.
authors.forename: Elizabeth M
authors.initials: EM
authors.lastname: Hénaff
authors.affiliation: 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.
authors.forename: Paul
authors.initials: P
authors.lastname: Zumbo
authors.affiliation: State University of New York, Downstate, Brooklyn, NY 11203, USA.
authors.forename: Michael
authors.initials: M
authors.lastname: Walsh
authors.affiliation: School of Earth and Environmental Sciences, City University of New York (CUNY) Queens College, Flushing, NY 11367, USA.
authors.forename: Gregory D
authors.initials: GD
authors.lastname: O'Mullan
authors.affiliation: University of Vermont, Burlington, VT 05405, USA.
authors.forename: Scott
authors.initials: S
authors.lastname: Tighe
authors.affiliation: Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
authors.forename: Joel T
authors.initials: JT
authors.lastname: Dudley
authors.affiliation: Rockefeller University, New York, NY 10065, USA.
authors.forename: Anya
authors.initials: A
authors.lastname: Dunaif
authors.affiliation: 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.
authors.forename: Sean
authors.initials: S
authors.lastname: Ennis
authors.affiliation: Academic Centre on Rare Diseases, School of Medicine and Medical Science, University College Dublin 4, Ireland.
authors.forename: Eoghan
authors.initials: E
authors.lastname: O'Halloran
authors.affiliation: 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.
authors.forename: Tiago R
authors.initials: TR
authors.lastname: Magalhaes
authors.affiliation: HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA.
authors.forename: Braden
authors.initials: B
authors.lastname: Boone
authors.affiliation: HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA.
authors.forename: Angela L
authors.initials: AL
authors.lastname: Jones
authors.affiliation: CUNY Brooklyn College, Department of Biology, Brooklyn, NY 11210, USA.
authors.forename: Theodore R
authors.initials: TR
authors.lastname: Muth
authors.affiliation: Center for Genomics, New York University, New York, NY 10003, USA.
authors.forename: Katie Schneider
authors.initials: KS
authors.lastname: Paolantonio
authors.affiliation: CUNY York College, Jamaica, NY 11451, USA.
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Alter
authors.affiliation: Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
authors.forename: Eric E
authors.initials: EE
authors.lastname: Schadt
authors.affiliation: Rockefeller University, New York, NY 10065, USA.
authors.forename: Jeanne
authors.initials: J
authors.lastname: Garbarino
authors.affiliation: Accelerated Discovery Lab, IBM Almaden Research Center, San Jose, CA 95120, USA.
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Prill
authors.affiliation: Center for Genomics, New York University, New York, NY 10003, USA.
authors.forename: Jane M
authors.initials: JM
authors.lastname: Carlton
authors.affiliation: HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA.
authors.forename: Shawn
authors.initials: S
authors.lastname: Levy
authors.affiliation: 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.
authors.forename: Christopher E
authors.initials: CE
authors.lastname: Mason