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

Ebrahim Afshinnekoo; Cem Meydan; Shanin Chowdhury; Dyala Jaroudi; Collin Boyer; Nick Bernstein; Julia M. Maritz; Darryl Reeves; Jorge Gandara; Sagar Chhangawala; Sofia Ahsanuddin; Amber Simmons; Timothy Nessel; Bharathi Sundaresh; Elizabeth Pereira; Ellen Jorgensen; Sergios Orestis Kolokotronis; Nell Kirchberger; Isaac Garcia; David Gandara; Sean Dhanraj; Tanzina Nawrin; Yogesh Saletore; Noah Alexander; Priyanka Vijay; Elizabeth M. Hénaff; Paul Zumbo; Michael Walsh; Gregory D. O'Mullan; Scott Tighe; Joel T. Dudley; Anya Dunaif; Sean Ennis; Eoghan O'Halloran; Tiago R. Magalhaes; Braden Boone; Angela L. Jones; Theodore R. Muth; Katie Schneider Paolantonio; Elizabeth Alter; Eric E. Schadt; Jeanne Garbarino; Robert J. Prill; Jane M. Carlton; Shawn Levy; Christopher E. Mason

doi:10.1016/j.cels.2015.01.001

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

Ebrahim Afshinnekoo, Cem Meydan, Shanin Chowdhury, Dyala Jaroudi, Collin Boyer, Nick Bernstein, Julia M. Maritz, Darryl Reeves, Jorge Gandara, Sagar Chhangawala, Sofia Ahsanuddin, Amber Simmons, Timothy Nessel, Bharathi Sundaresh, Elizabeth Pereira, Ellen Jorgensen, Sergios Orestis Kolokotronis, Nell Kirchberger, Isaac Garcia, David GandaraSean Dhanraj, Tanzina Nawrin, Yogesh Saletore, Noah Alexander, Priyanka Vijay, Elizabeth M. Hénaff, Paul Zumbo, Michael Walsh, Gregory D. O'Mullan, Scott Tighe, Joel T. Dudley, Anya Dunaif, Sean Ennis, Eoghan O'Halloran, Tiago R. Magalhaes, Braden Boone, Angela L. Jones, Theodore R. Muth, Katie Schneider Paolantonio, Elizabeth Alter, Eric E. Schadt, Jeanne Garbarino, Robert J. Prill, Jane M. Carlton, Shawn Levy, Christopher E. Mason

Research output: Contribution to journal › Article › peer-review

Abstract

Summary 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 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 match a station's history, such as marine-associated bacteria in a hurricane-flooded station. This baseline metagenomic map of NYC could help long-term disease surveillance, bioterrorism threat mitigation, and health management in the built environment of cities.

Original language	English (US)
Article number	1
Pages (from-to)	72-87
Number of pages	16
Journal	Cell Systems
Volume	1
Issue number	1
DOIs	https://doi.org/10.1016/j.cels.2015.01.001
State	Published - Jul 29 2015

ASJC Scopus subject areas

Pathology and Forensic Medicine
Histology
Cell Biology

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10.1016/j.cels.2015.01.001

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Afshinnekoo, E., Meydan, C., Chowdhury, S., Jaroudi, D., Boyer, C., Bernstein, N., Maritz, J. M., Reeves, D., Gandara, J., Chhangawala, S., Ahsanuddin, S., Simmons, A., Nessel, T., Sundaresh, B., Pereira, E., Jorgensen, E., Kolokotronis, S. O., Kirchberger, N., Garcia, I., ... Mason, C. E. (2015). Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics. Cell Systems, 1(1), 72-87. Article 1. https://doi.org/10.1016/j.cels.2015.01.001

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 2015, 'Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics', Cell Systems, vol. 1, no. 1, 1, pp. 72-87. https://doi.org/10.1016/j.cels.2015.01.001

@article{259185adb9544a87abb9195d4639d23a,

title = "Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics",

abstract = "Summary 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 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 match a station's history, such as marine-associated bacteria in a hurricane-flooded station. This baseline metagenomic map of NYC could help long-term disease surveillance, bioterrorism threat mitigation, and health management in the built environment of cities.",

author = "Ebrahim Afshinnekoo and Cem Meydan and Shanin Chowdhury and Dyala Jaroudi and Collin Boyer and Nick Bernstein and Maritz, {Julia M.} and Darryl Reeves and Jorge Gandara and Sagar Chhangawala and Sofia Ahsanuddin and Amber Simmons and Timothy Nessel and Bharathi Sundaresh and Elizabeth Pereira and Ellen Jorgensen and Kolokotronis, {Sergios Orestis} and Nell Kirchberger and Isaac Garcia and David Gandara and Sean Dhanraj and Tanzina Nawrin and Yogesh Saletore and Noah Alexander and Priyanka Vijay and H{\'e}naff, {Elizabeth M.} and Paul Zumbo and Michael Walsh and O'Mullan, {Gregory D.} and Scott Tighe and Dudley, {Joel T.} and Anya Dunaif and Sean Ennis and Eoghan O'Halloran and Magalhaes, {Tiago R.} and Braden Boone and Jones, {Angela L.} and Muth, {Theodore R.} and Paolantonio, {Katie Schneider} and Elizabeth Alter and Schadt, {Eric E.} and Jeanne Garbarino and Prill, {Robert J.} and Carlton, {Jane M.} and Shawn Levy and Mason, {Christopher E.}",

note = "Funding Information: We would like to thank Thomas Abdallah from the Metropolitan Transit Authority (MTA) for access to the flooded subway station and general assistance with sample collection in the subways. We also would like to thank the NIH (F31GM111053), the Epigenomcs Core Facility at Weill Cornell Medical College, the Clinical and Translational Sciences Center (CTSC), the Pinkerton Foundation, the Vallee Foundation, Igor Tulchinsky from the WorldQuant Foundation, Marc Van Oene from Illumina, Peer Schatz and Aaron Lizee from Qiagen, and Indiegogo for crowdfunding and crowdsourcing support. This study was partially funded by a New York University Grand Challenge project, “Microorganisms, Sewage, Health and Disease: Mapping the New York City Metagenome.” We also thank Paul Scheid and Jeffrey A. Rosenfeld for contributions to the sample collection protocols and analysis methods. Many students and citizen scientist volunteers helped us in the sample collection across NYC, and we would like to thank and acknowledge anyone who helped with even a single swab. This includes students from Katie Schneider{\textquoteright}s NYU class: Anna Crouch, Isabel Wang, Jeep Roberto, Malinda Moore, Stephanie Viola, and Davis Saltonstall; and Michael Walsh{\textquoteright}s students (seasonal subway and park sampling): Rachel Berger, Sarah-Ann Celestin, Sheaba Daniel, Wen Deng, Janay Scott, Disleiry Benitez, Nadine Blackwood, Racquel Brereton, Pui Ying Chan, Saurabh Dwivedi, Jennifer Fasheun, Bianca Hill, Tania Kashem, Difaa Majrud, Nicole Mastrogiovanni, Vicky Milford, Olutosin Ojugbele, Alexandr Pinkhasov, Anila Thomas, Tejal Patel, Kalpita Abhyankar, Jovanna Linnen, Chludzinski Stacey, Marc Smith, Herman Chen, Patricia Lolo, Akinwale Akinkunmi, Matthew Lee, Dean Perfetti, Marco Stillo, Britanny Thomas, Harrynauth Persaud, and Sofia Oluwole. Also, for the Gowanus samples, we thank Ian Quate and Matthew Seibert from Nelson Byrd Woltz Architecture firm. We would also like to thank Joan Moriarty for assistance with the crowd-funding campaign and Madeleine Mason-Moriarty for inspiring the project. Publisher Copyright: {\textcopyright} 2015 The Authors.",

year = "2015",

month = jul,

day = "29",

doi = "10.1016/j.cels.2015.01.001",

language = "English (US)",

volume = "1",

pages = "72--87",

journal = "Cell Systems",

issn = "2405-4712",

publisher = "Cell Press",

number = "1",

}

TY - JOUR

T1 - Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics

AU - Afshinnekoo, Ebrahim

AU - Meydan, Cem

AU - Chowdhury, Shanin

AU - Jaroudi, Dyala

AU - Boyer, Collin

AU - Bernstein, Nick

AU - Maritz, Julia M.

AU - Reeves, Darryl

AU - Gandara, Jorge

AU - Chhangawala, Sagar

AU - Ahsanuddin, Sofia

AU - Simmons, Amber

AU - Nessel, Timothy

AU - Sundaresh, Bharathi

AU - Pereira, Elizabeth

AU - Jorgensen, Ellen

AU - Kolokotronis, Sergios Orestis

AU - Kirchberger, Nell

AU - Garcia, Isaac

AU - Gandara, David

AU - Dhanraj, Sean

AU - Nawrin, Tanzina

AU - Saletore, Yogesh

AU - Alexander, Noah

AU - Vijay, Priyanka

AU - Hénaff, Elizabeth M.

AU - Zumbo, Paul

AU - Walsh, Michael

AU - O'Mullan, Gregory D.

AU - Tighe, Scott

AU - Dudley, Joel T.

AU - Dunaif, Anya

AU - Ennis, Sean

AU - O'Halloran, Eoghan

AU - Magalhaes, Tiago R.

AU - Boone, Braden

AU - Jones, Angela L.

AU - Muth, Theodore R.

AU - Paolantonio, Katie Schneider

AU - Alter, Elizabeth

AU - Schadt, Eric E.

AU - Garbarino, Jeanne

AU - Prill, Robert J.

AU - Carlton, Jane M.

AU - Levy, Shawn

AU - Mason, Christopher E.

N1 - Funding Information: We would like to thank Thomas Abdallah from the Metropolitan Transit Authority (MTA) for access to the flooded subway station and general assistance with sample collection in the subways. We also would like to thank the NIH (F31GM111053), the Epigenomcs Core Facility at Weill Cornell Medical College, the Clinical and Translational Sciences Center (CTSC), the Pinkerton Foundation, the Vallee Foundation, Igor Tulchinsky from the WorldQuant Foundation, Marc Van Oene from Illumina, Peer Schatz and Aaron Lizee from Qiagen, and Indiegogo for crowdfunding and crowdsourcing support. This study was partially funded by a New York University Grand Challenge project, “Microorganisms, Sewage, Health and Disease: Mapping the New York City Metagenome.” We also thank Paul Scheid and Jeffrey A. Rosenfeld for contributions to the sample collection protocols and analysis methods. Many students and citizen scientist volunteers helped us in the sample collection across NYC, and we would like to thank and acknowledge anyone who helped with even a single swab. This includes students from Katie Schneider’s NYU class: Anna Crouch, Isabel Wang, Jeep Roberto, Malinda Moore, Stephanie Viola, and Davis Saltonstall; and Michael Walsh’s students (seasonal subway and park sampling): Rachel Berger, Sarah-Ann Celestin, Sheaba Daniel, Wen Deng, Janay Scott, Disleiry Benitez, Nadine Blackwood, Racquel Brereton, Pui Ying Chan, Saurabh Dwivedi, Jennifer Fasheun, Bianca Hill, Tania Kashem, Difaa Majrud, Nicole Mastrogiovanni, Vicky Milford, Olutosin Ojugbele, Alexandr Pinkhasov, Anila Thomas, Tejal Patel, Kalpita Abhyankar, Jovanna Linnen, Chludzinski Stacey, Marc Smith, Herman Chen, Patricia Lolo, Akinwale Akinkunmi, Matthew Lee, Dean Perfetti, Marco Stillo, Britanny Thomas, Harrynauth Persaud, and Sofia Oluwole. Also, for the Gowanus samples, we thank Ian Quate and Matthew Seibert from Nelson Byrd Woltz Architecture firm. We would also like to thank Joan Moriarty for assistance with the crowd-funding campaign and Madeleine Mason-Moriarty for inspiring the project. Publisher Copyright: © 2015 The Authors.

PY - 2015/7/29

Y1 - 2015/7/29

N2 - Summary 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 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 match a station's history, such as marine-associated bacteria in a hurricane-flooded station. This baseline metagenomic map of NYC could help long-term disease surveillance, bioterrorism threat mitigation, and health management in the built environment of cities.

AB - Summary 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 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 match a station's history, such as marine-associated bacteria in a hurricane-flooded station. 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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DO - 10.1016/j.cels.2015.01.001

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JO - Cell Systems

JF - Cell Systems

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ER -

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

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