Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

Global Genetic Cartography of Urban Metagenomes and Anti-Microbial Resistance

View ORCID ProfileDavid C. Danko, Daniela Bezdan, Ebrahim Afshinnekoo, Sofia Ahsanuddin, Josue Alicea, Chandrima Bhattacharya, Malay Bhattacharyya, Ran Blekhman, Daniel J Butler, Eduardo Castro-Nallar, Ana M Cañas, Aspassia D Chatziefthimiou, Kern Rei Chng, David A Coil, Denise Syndercombe Court, Robert W Crawford, Christelle Desnues, Emmanuel Dias-Neto, Daisy Donnellan, Marius Dybwad, Jonathan A Eisen, Eran Elhaik, Danilo Ercolini, Francesca De Filippis, Alina Frolova, Alexandra B Graf, David C Green, Patrick K H Lee, Jochen Hecht, Mark Hernandez, Soojin Jang, Andre Kahles, Mikhail Karasikov, Kaymisha Knights, Nikos C. Kyrpides, Per Ljungdahl, Abigail Lyons, Gabriella Mason-Buck, Ken McGrath, Emmanuel F Mongodin, Harun Mustafa, Beth Mutai, Niranjan Nagarajan, Russell Y. Neches, Amanda Ng, Marina Nieto-Caballero, Olga Nikolayeva, Tatyana Nikolayeva, Houtan Noushmehr, Manuela Oliveira, Stephan Ossowski, Olayinka O Osuolale, David Paez-Espino, Eileen Png, Nicolas Rascovan, Hugues Richard, Gunnar Rätsch, Jorge L Sanchez, Lynn M Schriml, Heba Shaaban, Leming Shi, Maria A Sierra, Le Huu Song, Haruo Suzuki, Dominique Thomas, Klas I Udekwu, Juan A Ugalde, Brandon Valentine, Dimitar I Vassilev, Elena Vayndorf, Marcus H Y Leung, Ben Young, María M Zambrano, Jifeng Zhu, Sibo Zhu, Paweł P Łabaj, Christopher Mason, The International MetaSUB Consortium
doi: https://doi.org/10.1101/724526
David C. Danko
1Weill Cornell Medicine NY, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for David C. Danko
Daniela Bezdan
1Weill Cornell Medicine NY, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Ebrahim Afshinnekoo
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Sofia Ahsanuddin
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Josue Alicea
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Chandrima Bhattacharya
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Malay Bhattacharyya
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Ran Blekhman
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Daniel J Butler
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Eduardo Castro-Nallar
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Ana M Cañas
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Aspassia D Chatziefthimiou
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Kern Rei Chng
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
David A Coil
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Denise Syndercombe Court
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Robert W Crawford
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Christelle Desnues
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Emmanuel Dias-Neto
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Daisy Donnellan
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Marius Dybwad
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Jonathan A Eisen
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Eran Elhaik
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Danilo Ercolini
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Francesca De Filippis
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Alina Frolova
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Alexandra B Graf
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
David C Green
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Patrick K H Lee
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Jochen Hecht
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Mark Hernandez
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Soojin Jang
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Andre Kahles
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Mikhail Karasikov
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Kaymisha Knights
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Nikos C. Kyrpides
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Per Ljungdahl
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Abigail Lyons
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Gabriella Mason-Buck
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Ken McGrath
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Emmanuel F Mongodin
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Harun Mustafa
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Beth Mutai
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Niranjan Nagarajan
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Russell Y. Neches
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Amanda Ng
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Marina Nieto-Caballero
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Olga Nikolayeva
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Tatyana Nikolayeva
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Houtan Noushmehr
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Manuela Oliveira
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Stephan Ossowski
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Olayinka O Osuolale
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
David Paez-Espino
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Eileen Png
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Nicolas Rascovan
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Hugues Richard
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Gunnar Rätsch
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Jorge L Sanchez
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Lynn M Schriml
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Heba Shaaban
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Leming Shi
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Maria A Sierra
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Le Huu Song
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Haruo Suzuki
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Dominique Thomas
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Klas I Udekwu
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Juan A Ugalde
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Brandon Valentine
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Dimitar I Vassilev
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Elena Vayndorf
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Marcus H Y Leung
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Ben Young
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
María M Zambrano
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Jifeng Zhu
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Sibo Zhu
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Paweł P Łabaj
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Christopher Mason
1Weill Cornell Medicine NY, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: chm2042@med.cornell.edu
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Data/Code
  • Preview PDF
Loading

Abstract

Although studies have shown that urban environments and mass-transit systems have geospa-tially distinct metagenomes, no study has ever systematically studied these dense, human/microbial ecosystems around the world. To address this gap in knowledge, we created a global metagenomic and antimicrobial resistance (AMR) atlas of urban mass transit systems from 58 cities, spanning 3,741 samples and 4,424 taxonomically-defined microorganisms collected for three years. The map provides annotated, geospatial data about microbial strains, functional genetics, antimicrobial resistance, and novel genetic elements, including 10,928 novel predicted viral species. Urban microbiomes often resemble human commensal microbiomes from the skin and airways but contain a consistent “core” of 61 species which are predominantly not human commensal species. These data also show that AMR density across cities varies by several orders of magnitude with many AMRs present on plasmids with cosmopolitan distributions. Conversely, samples may be accurately (91.4%) classified to their city-of-origin using a linear support vector machine over taxa. Together, these results constitute a high-resolution global metagenomic atlas, which enables the discovery of new genetic components of the built human environment, forensic application, and an essential first draft of the global AMR burden of the world’s cities.

Footnotes

  • ↵⋆ Listed Alphabetically, Affiliations listed separately

  • https://github.com/MetaSUB/bioinformatics_management

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
Back to top
PreviousNext
Posted August 05, 2019.
Download PDF
Data/Code
Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
Global Genetic Cartography of Urban Metagenomes and Anti-Microbial Resistance
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Global Genetic Cartography of Urban Metagenomes and Anti-Microbial Resistance
David C. Danko, Daniela Bezdan, Ebrahim Afshinnekoo, Sofia Ahsanuddin, Josue Alicea, Chandrima Bhattacharya, Malay Bhattacharyya, Ran Blekhman, Daniel J Butler, Eduardo Castro-Nallar, Ana M Cañas, Aspassia D Chatziefthimiou, Kern Rei Chng, David A Coil, Denise Syndercombe Court, Robert W Crawford, Christelle Desnues, Emmanuel Dias-Neto, Daisy Donnellan, Marius Dybwad, Jonathan A Eisen, Eran Elhaik, Danilo Ercolini, Francesca De Filippis, Alina Frolova, Alexandra B Graf, David C Green, Patrick K H Lee, Jochen Hecht, Mark Hernandez, Soojin Jang, Andre Kahles, Mikhail Karasikov, Kaymisha Knights, Nikos C. Kyrpides, Per Ljungdahl, Abigail Lyons, Gabriella Mason-Buck, Ken McGrath, Emmanuel F Mongodin, Harun Mustafa, Beth Mutai, Niranjan Nagarajan, Russell Y. Neches, Amanda Ng, Marina Nieto-Caballero, Olga Nikolayeva, Tatyana Nikolayeva, Houtan Noushmehr, Manuela Oliveira, Stephan Ossowski, Olayinka O Osuolale, David Paez-Espino, Eileen Png, Nicolas Rascovan, Hugues Richard, Gunnar Rätsch, Jorge L Sanchez, Lynn M Schriml, Heba Shaaban, Leming Shi, Maria A Sierra, Le Huu Song, Haruo Suzuki, Dominique Thomas, Klas I Udekwu, Juan A Ugalde, Brandon Valentine, Dimitar I Vassilev, Elena Vayndorf, Marcus H Y Leung, Ben Young, María M Zambrano, Jifeng Zhu, Sibo Zhu, Paweł P Łabaj, Christopher Mason, The International MetaSUB Consortium
bioRxiv 724526; doi: https://doi.org/10.1101/724526
Digg logo Reddit logo Twitter logo Facebook logo Google logo LinkedIn logo Mendeley logo
Citation Tools
Global Genetic Cartography of Urban Metagenomes and Anti-Microbial Resistance
David C. Danko, Daniela Bezdan, Ebrahim Afshinnekoo, Sofia Ahsanuddin, Josue Alicea, Chandrima Bhattacharya, Malay Bhattacharyya, Ran Blekhman, Daniel J Butler, Eduardo Castro-Nallar, Ana M Cañas, Aspassia D Chatziefthimiou, Kern Rei Chng, David A Coil, Denise Syndercombe Court, Robert W Crawford, Christelle Desnues, Emmanuel Dias-Neto, Daisy Donnellan, Marius Dybwad, Jonathan A Eisen, Eran Elhaik, Danilo Ercolini, Francesca De Filippis, Alina Frolova, Alexandra B Graf, David C Green, Patrick K H Lee, Jochen Hecht, Mark Hernandez, Soojin Jang, Andre Kahles, Mikhail Karasikov, Kaymisha Knights, Nikos C. Kyrpides, Per Ljungdahl, Abigail Lyons, Gabriella Mason-Buck, Ken McGrath, Emmanuel F Mongodin, Harun Mustafa, Beth Mutai, Niranjan Nagarajan, Russell Y. Neches, Amanda Ng, Marina Nieto-Caballero, Olga Nikolayeva, Tatyana Nikolayeva, Houtan Noushmehr, Manuela Oliveira, Stephan Ossowski, Olayinka O Osuolale, David Paez-Espino, Eileen Png, Nicolas Rascovan, Hugues Richard, Gunnar Rätsch, Jorge L Sanchez, Lynn M Schriml, Heba Shaaban, Leming Shi, Maria A Sierra, Le Huu Song, Haruo Suzuki, Dominique Thomas, Klas I Udekwu, Juan A Ugalde, Brandon Valentine, Dimitar I Vassilev, Elena Vayndorf, Marcus H Y Leung, Ben Young, María M Zambrano, Jifeng Zhu, Sibo Zhu, Paweł P Łabaj, Christopher Mason, The International MetaSUB Consortium
bioRxiv 724526; doi: https://doi.org/10.1101/724526

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Microbiology
Subject Areas
All Articles
  • Animal Behavior and Cognition (4115)
  • Biochemistry (8818)
  • Bioengineering (6522)
  • Bioinformatics (23466)
  • Biophysics (11792)
  • Cancer Biology (9212)
  • Cell Biology (13326)
  • Clinical Trials (138)
  • Developmental Biology (7439)
  • Ecology (11413)
  • Epidemiology (2066)
  • Evolutionary Biology (15155)
  • Genetics (10439)
  • Genomics (14045)
  • Immunology (9173)
  • Microbiology (22159)
  • Molecular Biology (8814)
  • Neuroscience (47581)
  • Paleontology (350)
  • Pathology (1429)
  • Pharmacology and Toxicology (2492)
  • Physiology (3731)
  • Plant Biology (8082)
  • Scientific Communication and Education (1437)
  • Synthetic Biology (2221)
  • Systems Biology (6039)
  • Zoology (1253)