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Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics
Afshinnekoo, Ebrahim Meydan, Cem Chowdhury, Shanin Jaroudi, Dyala Boyer, Collin Bernstein, Nick Maritz, Julia M. Reeves, Darryl Gandara, Jorge Chhangawala, Sagar
Afshinnekoo, Ebrahim
Meydan, Cem
Chowdhury, Shanin
Jaroudi, Dyala
Boyer, Collin
Bernstein, Nick
Maritz, Julia M.
Reeves, Darryl
Gandara, Jorge
Chhangawala, Sagar
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Journal Title
Cell Systems
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2015-07
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Publication Volume
1
Publication Issue
1
Publication Begin
72
Publication End
87
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PIIS2405471215000022.pdf
Adobe PDF, 6.34 MB
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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.
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.