Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics
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Author
Afshinnekoo, EbrahimMeydan, Cem
Chowdhury, Shanin
Jaroudi, Dyala
Boyer, Collin
Bernstein, Nick
Maritz, Julia M.
Reeves, Darryl
Gandara, Jorge
Chhangawala, Sagar
Ahsanuddin, Sofia
Simmons, Amber
Nessel, Timothy
Sundaresh, Bharathi
Pereira, Elizabeth
Jorgensen, Ellen
Kolokotronis, Sergios-Orestis
Kirchberger, Nell
Garcia, Isaac
Gandara, David
Dhanraj, Sean
Nawrin, Tanzina
Saletore, Yogesh
Alexander, Noah
Vijay, Priyanka
Hénaff, Elizabeth M.
Zumbo, Paul
Walsh, Michael
O’Mullan, Gregory D.
Tighe, Scott
Dudley, Joel T.
Dunaif, Anya
Ennis, Sean
O’Halloran, Eoghan
Magalhaes, Tiago R.
Boone, Braden
Jones, Angela L.
Muth, Theodore R.
Paolantonio, Katie Schneider
Alter, Elizabeth
Schadt, Eric E.
Garbarino, Jeanne
Prill, Robert J.
Carlton, Jane M.
Levy, Shawn
Mason, Christopher E.
Journal title
Cell SystemsDate Published
2015-07Publication Volume
1Publication Issue
1Publication Begin page
72Publication End page
87
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Show full item recordAbstract
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.Citation
Afshinnekoo E, Meydan C, Chowdhury S, Jaroudi D, Boyer C, Bernstein N, Maritz JM, Reeves D, Gandara J, Chhangawala S, Ahsanuddin S, Simmons A, Nessel T, Sundaresh B, Pereira E, Jorgensen E, Kolokotronis SO, Kirchberger N, Garcia I, Gandara D, Dhanraj S, Nawrin T, Saletore Y, Alexander N, Vijay P, Hénaff EM, Zumbo P, Walsh M, O'Mullan GD, Tighe S, Dudley JT, Dunaif A, Ennis S, O'Halloran E, Magalhaes TR, Boone B, Jones AL, Muth TR, Paolantonio KS, Alter E, Schadt EE, Garbarino J, Prill RJ, Carlton JM, Levy S, Mason CE. Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics. Cell Syst. 2015 Jul 29;1(1):72-87. doi: 10.1016/j.cels.2015.01.001. Epub 2015 Mar 3. PMID: 26594662; PMCID: PMC4651444.DOI
10.1016/j.cels.2015.01.001ae974a485f413a2113503eed53cd6c53
10.1016/j.cels.2015.01.001
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- Creative Commons
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