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A GLOBAL METAGENOMIC MAP OF URBAN MICROBIOMES AND ANTIMICROBIAL RESISTANCE
Author
Danko, David
Bezdan, Daniela
Afshin, Evan E.
Ahsanuddin, Sofia
Bhattacharya, Chandrima
Butler, Daniel J.
Chng, Kern Rei
Donnellan, Daysy
Hecht, Jochen
Jackson, Kathelyn
Kuchin, Katerina
Karasikov, Mikhail
Lyons, Abigail
Mak, Lauren
Meleshko, Dmitry
Mustafa, Harun
Mutai, Beth
Neches, Russell Y.
Ng, Amanda
Nikolayeva, Olga
Nikolayeva, Tatyana
Png, Eileen
Ryon, Krista A.
Sanchez, Jorge L.
Shaaban, Heba
Sierra, Maria A.
Thomas, Dominique
Young, Ben
Abudayyeh, Omar O.
Alicea, Josue
Bhattacharyya, Malay
Blekhman, Ran
Castro-Nallar, Eduardo
Cañas, Ana M.
Chatziefthimiou, Aspassia D.
Crawford, Robert W.
Filippis, Francesca De
Deng, Youping
Desnues, Christelle
Dias Neto, Emmanuel
Dybwad, Marius
Elhaik, Eran
Ercolini, Danilo
Frolova, Alina
Gankin, Dennis
Gootenberg, Jonathan S.
Graf, Alexanda B.
Green, David C.
Hajirasouliha, Iman
Hastings, Jaden J. A.
Hernandez, Mark
Iraola, Gregorio
Jang, Soojin
Kahles, Andre
Kelly, Frank J.
Knights, Kaymisha
Kyrpides, Nikos C.
Labaj, Pawel P.
Lee, Patrick K.H.
Leung, Marcus H.Y.
Ljungdahl, Per O.
Mason-Buck, Gabriella
McGrath, Ken
Meydan, Cem
Mongodin, Emmanuel F.
Moraes, Milton Ozorio
Nagarajan, Niranjan
Nieto-Caballer, Marina
Noushmehr, Houtan
Oliveira, Manuela
Ossowski, Stephan
Osuolale, Olayinka O.
Paez-Espino, David
Rascovan, Nicolás
Richard, Hugues
Bezdan, Daniela
Afshin, Evan E.
Ahsanuddin, Sofia
Bhattacharya, Chandrima
Butler, Daniel J.
Chng, Kern Rei
Donnellan, Daysy
Hecht, Jochen
Jackson, Kathelyn
Kuchin, Katerina
Karasikov, Mikhail
Lyons, Abigail
Mak, Lauren
Meleshko, Dmitry
Mustafa, Harun
Mutai, Beth
Neches, Russell Y.
Ng, Amanda
Nikolayeva, Olga
Nikolayeva, Tatyana
Png, Eileen
Ryon, Krista A.
Sanchez, Jorge L.
Shaaban, Heba
Sierra, Maria A.
Thomas, Dominique
Young, Ben
Abudayyeh, Omar O.
Alicea, Josue
Bhattacharyya, Malay
Blekhman, Ran
Castro-Nallar, Eduardo
Cañas, Ana M.
Chatziefthimiou, Aspassia D.
Crawford, Robert W.
Filippis, Francesca De
Deng, Youping
Desnues, Christelle
Dias Neto, Emmanuel
Dybwad, Marius
Elhaik, Eran
Ercolini, Danilo
Frolova, Alina
Gankin, Dennis
Gootenberg, Jonathan S.
Graf, Alexanda B.
Green, David C.
Hajirasouliha, Iman
Hastings, Jaden J. A.
Hernandez, Mark
Iraola, Gregorio
Jang, Soojin
Kahles, Andre
Kelly, Frank J.
Knights, Kaymisha
Kyrpides, Nikos C.
Labaj, Pawel P.
Lee, Patrick K.H.
Leung, Marcus H.Y.
Ljungdahl, Per O.
Mason-Buck, Gabriella
McGrath, Ken
Meydan, Cem
Mongodin, Emmanuel F.
Moraes, Milton Ozorio
Nagarajan, Niranjan
Nieto-Caballer, Marina
Noushmehr, Houtan
Oliveira, Manuela
Ossowski, Stephan
Osuolale, Olayinka O.
Paez-Espino, David
Rascovan, Nicolás
Richard, Hugues
Affilliation
Weill Cornell Medicine. New York, NY, USA / The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.
Weill Cornell Medicine. New York, NY, USA / The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA / Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany / NGS Competence Center Tübingen (NCCT), University of Tübingen, Tübingen, Germany.
Weill Cornell Medicine. New York, NY, USA / The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.
Icahn School of Medicine at Mount Sinai. New York, NY, USA.
Weill Cornell Medicine. New York, NY, USA / The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.
Weill Cornell Medicine. New York, NY, USA / The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.
Genome Institute of Singapore, A*STAR.Singapore, Singapore.
Weill Cornell Medicine. New York, NY, USA / The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.
Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology. Barcelona, Spain.
Weill Cornell Medicine. New York, NY, USA / The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.
Weill Cornell Medicine. New York, NY, USA / The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.
ETH Zurich, Department of Computer Science, Biomedical Informatics Group, Zurich, Switzerland / University Hospital Zurich, Biomedical Informatics Research, Zurich, Switzerland / 64University Hospital Zurich, Biomedical Informatics Research, Zurich, Switzerland.
Weill Cornell Medicine. New York, NY, USA / The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.
Weill Cornell Medicine. New York, NY, USA / The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.
Weill Cornell Medicine. New York, NY, USA / The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.
ETH Zurich, Department of Computer Science, Biomedical Informatics Group, Zurich, Switzerland / University Hospital Zurich, Biomedical Informatics Research, Zurich, Switzerland / 64University Hospital Zurich, Biomedical Informatics Research, Zurich, Switzerland.
Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA;
Genome Institute of Singapore, A*STAR. Singapore, Singapore.
Independent Researcher, Zurich, Switzerland;
Independent Researcher, Zurich, Switzerland;
Genome Institute of Singapore, A*STAR. Singapore, Singapore.
Weill Cornell Medicine. New York, NY, USA / The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA..
Weill Cornell Medicine. New York, NY, USA / The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA..
Weill Cornell Medicine. New York, NY, USA / The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA..
Weill Cornell Medicine. New York, NY, USA / The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA..
Weill Cornell Medicine. New York, NY, USA / The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA..
Weill Cornell Medicine. New York, NY, USA / The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA..
Massachusetts Institute of Technology, McGovern Institute for Brain Research, Cambridge, MA, USA.
Weill Cornell Medicine. New York, NY, USA / The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA..
Machine Intelligence Unit, Indian Statistical Institute, Kolkata, India / Centre for Artificial Intelligence and Machine Learning, Indian Statistical Institute, Kolkata, India.
University of Minnesota, Minneapolis, MN, USA.
Universidad Andres Bello, Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Santiago, Chile.
Weill Cornell Medicine. New York, NY, USA / The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.
Weill Cornell Medicine. New York, NY, USA / The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.
California State University, Sacramento, Sacramento, CA, USA.
Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, Naples, Italy / Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy.
University of Hawaii John A. Burns School of Medicine, Honolulu, HI, USA.
Aix-Marseille Université , Mediterranean Institute of Oceanology, Université de Toulon, CNRS, IRD, UM 110, Marseille, France.
Medical Genomics group, A.C.Camargo Cancer Center, São Paulo – SP, Brazil.
Norwegian Defence Research Establishment FFI, Kjeller, Norway.
Department of Biology, Lund University, Lund, Sweden.
Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, Naples, Italy / Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy.
Institute of Molecular Biology and Genetics of National Academy of Sciences of Ukraine, Kyiv, Ukraine / Kyiv Academic University, Kyiv, Ukraine.
Massachusetts Institute of Technology, McGovern Institute for Brain Research, Cambridge, MA, USA.
Massachusetts Institute of Technology, McGovern Institute for Brain Research, Cambridge, MA, USA.
University of Applied Sciences Vienna, Vienna, Austria.
Department of Analytical, Environmental and Forensic Sciences, King’s College London, London, UK.
Weill Cornell Medicine. New York, NY, USA / The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.
Weill Cornell Medicine. New York, NY, USA / The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.
University of Colorado at Boulder, Boulder, CO, USA.
Microbial Genomics Laboratory, Institut Pasteur de Montevideo, Montevideo, Uruguay / Center for Integrative Biology, Universidad Mayor, Santiago de Chile, Santiago,Chile / Wellcome Sanger Institute, Hinxton, UK.
Institut Pasteur Korea. Seoul, South Korea.
ETH Zurich, Department of Computer Science, Biomedical Informatics Group, Zurich, Switzerland / Kyiv Academic University, Kyiv, Ukraine / C+, Research Center in Technologies for Society, School of Engineering, Universidad del Desarrollo, Santiago, Chile.
Department of Analytical, Environmental and Forensic Sciences, King’s College London. London, UK.
Weill Cornell Medicine. New York, NY, USA / The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.
Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory. Berkeley, CA, USA.
State Key Laboratory of Genetic Engineering (SKLGE) and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, China / Ma1opolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland / Boku University Viennna, Vienna, Austria.
School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China.
School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China.
Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden.
Department of Analytical, Environmental and Forensic Sciences, King’s College London. London, UK.
Microba, 388 Queen St, Brisbane City, QLD 4000,. Australia.
Weill Cornell Medicine. New York, NY, USA / The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.
University of Maryland School of Medicine, Institute for Genome Sciences. Baltimore, MD, USA.
Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Rio de Janeiro, RJ, Brasil.
Genome Institute of Singapore, A*STAR, Singapore; Singapore;
University of Colorado at Boulder. Boulder, CO, USA.
Universidade de São Paulo. Escola de Medicina de Ribeirão Preto. Ribeirão Preto, SP, Brasil.
Universidade do Porto. Instituto de Patologia e Imunologia Molecular; Porto, Portugal.
Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain / Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany / NGS Competence Center Tu¨ bingen (NCCT), University of Tübingen, Tübingen, Germany.
Applied Environmental Metagenomics and Infectious Diseases Research (AEMIDR), Department of Biological Sciences, Elizade University, Ilara-Mokin, Nigeria.
Acibadem Mehmet Ali Aydınlar Universit. Istanbul, Turkey.
Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory. Berkeley, CA, USA.
Microbial Paleogenomics Unit, Institut Pasteur. CNRS UMR2000, Paris 75015, France.
Sorbonne University, Faculty of Science, Institute of Biology Paris-Seine, Laboratory of Computational and Quantitative Biology, Paris, France / Robert Koch Institute,. Berlin, Germany.
Weill Cornell Medicine. New York, NY, USA / The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA / Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany / NGS Competence Center Tübingen (NCCT), University of Tübingen, Tübingen, Germany.
Weill Cornell Medicine. New York, NY, USA / The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.
Icahn School of Medicine at Mount Sinai. New York, NY, USA.
Weill Cornell Medicine. New York, NY, USA / The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.
Weill Cornell Medicine. New York, NY, USA / The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.
Genome Institute of Singapore, A*STAR.Singapore, Singapore.
Weill Cornell Medicine. New York, NY, USA / The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.
Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology. Barcelona, Spain.
Weill Cornell Medicine. New York, NY, USA / The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.
Weill Cornell Medicine. New York, NY, USA / The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.
ETH Zurich, Department of Computer Science, Biomedical Informatics Group, Zurich, Switzerland / University Hospital Zurich, Biomedical Informatics Research, Zurich, Switzerland / 64University Hospital Zurich, Biomedical Informatics Research, Zurich, Switzerland.
Weill Cornell Medicine. New York, NY, USA / The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.
Weill Cornell Medicine. New York, NY, USA / The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.
Weill Cornell Medicine. New York, NY, USA / The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.
ETH Zurich, Department of Computer Science, Biomedical Informatics Group, Zurich, Switzerland / University Hospital Zurich, Biomedical Informatics Research, Zurich, Switzerland / 64University Hospital Zurich, Biomedical Informatics Research, Zurich, Switzerland.
Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA;
Genome Institute of Singapore, A*STAR. Singapore, Singapore.
Independent Researcher, Zurich, Switzerland;
Independent Researcher, Zurich, Switzerland;
Genome Institute of Singapore, A*STAR. Singapore, Singapore.
Weill Cornell Medicine. New York, NY, USA / The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA..
Weill Cornell Medicine. New York, NY, USA / The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA..
Weill Cornell Medicine. New York, NY, USA / The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA..
Weill Cornell Medicine. New York, NY, USA / The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA..
Weill Cornell Medicine. New York, NY, USA / The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA..
Weill Cornell Medicine. New York, NY, USA / The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA..
Massachusetts Institute of Technology, McGovern Institute for Brain Research, Cambridge, MA, USA.
Weill Cornell Medicine. New York, NY, USA / The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA..
Machine Intelligence Unit, Indian Statistical Institute, Kolkata, India / Centre for Artificial Intelligence and Machine Learning, Indian Statistical Institute, Kolkata, India.
University of Minnesota, Minneapolis, MN, USA.
Universidad Andres Bello, Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Santiago, Chile.
Weill Cornell Medicine. New York, NY, USA / The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.
Weill Cornell Medicine. New York, NY, USA / The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.
California State University, Sacramento, Sacramento, CA, USA.
Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, Naples, Italy / Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy.
University of Hawaii John A. Burns School of Medicine, Honolulu, HI, USA.
Aix-Marseille Université , Mediterranean Institute of Oceanology, Université de Toulon, CNRS, IRD, UM 110, Marseille, France.
Medical Genomics group, A.C.Camargo Cancer Center, São Paulo – SP, Brazil.
Norwegian Defence Research Establishment FFI, Kjeller, Norway.
Department of Biology, Lund University, Lund, Sweden.
Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, Naples, Italy / Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy.
Institute of Molecular Biology and Genetics of National Academy of Sciences of Ukraine, Kyiv, Ukraine / Kyiv Academic University, Kyiv, Ukraine.
Massachusetts Institute of Technology, McGovern Institute for Brain Research, Cambridge, MA, USA.
Massachusetts Institute of Technology, McGovern Institute for Brain Research, Cambridge, MA, USA.
University of Applied Sciences Vienna, Vienna, Austria.
Department of Analytical, Environmental and Forensic Sciences, King’s College London, London, UK.
Weill Cornell Medicine. New York, NY, USA / The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.
Weill Cornell Medicine. New York, NY, USA / The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.
University of Colorado at Boulder, Boulder, CO, USA.
Microbial Genomics Laboratory, Institut Pasteur de Montevideo, Montevideo, Uruguay / Center for Integrative Biology, Universidad Mayor, Santiago de Chile, Santiago,Chile / Wellcome Sanger Institute, Hinxton, UK.
Institut Pasteur Korea. Seoul, South Korea.
ETH Zurich, Department of Computer Science, Biomedical Informatics Group, Zurich, Switzerland / Kyiv Academic University, Kyiv, Ukraine / C+, Research Center in Technologies for Society, School of Engineering, Universidad del Desarrollo, Santiago, Chile.
Department of Analytical, Environmental and Forensic Sciences, King’s College London. London, UK.
Weill Cornell Medicine. New York, NY, USA / The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.
Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory. Berkeley, CA, USA.
State Key Laboratory of Genetic Engineering (SKLGE) and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, China / Ma1opolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland / Boku University Viennna, Vienna, Austria.
School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China.
School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China.
Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden.
Department of Analytical, Environmental and Forensic Sciences, King’s College London. London, UK.
Microba, 388 Queen St, Brisbane City, QLD 4000,. Australia.
Weill Cornell Medicine. New York, NY, USA / The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.
University of Maryland School of Medicine, Institute for Genome Sciences. Baltimore, MD, USA.
Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Rio de Janeiro, RJ, Brasil.
Genome Institute of Singapore, A*STAR, Singapore; Singapore;
University of Colorado at Boulder. Boulder, CO, USA.
Universidade de São Paulo. Escola de Medicina de Ribeirão Preto. Ribeirão Preto, SP, Brasil.
Universidade do Porto. Instituto de Patologia e Imunologia Molecular; Porto, Portugal.
Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain / Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany / NGS Competence Center Tu¨ bingen (NCCT), University of Tübingen, Tübingen, Germany.
Applied Environmental Metagenomics and Infectious Diseases Research (AEMIDR), Department of Biological Sciences, Elizade University, Ilara-Mokin, Nigeria.
Acibadem Mehmet Ali Aydınlar Universit. Istanbul, Turkey.
Department of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory. Berkeley, CA, USA.
Microbial Paleogenomics Unit, Institut Pasteur. CNRS UMR2000, Paris 75015, France.
Sorbonne University, Faculty of Science, Institute of Biology Paris-Seine, Laboratory of Computational and Quantitative Biology, Paris, France / Robert Koch Institute,. Berlin, Germany.
Abstract
We present a global atlas of 4,728 metagenomic samples from mass-transit systems in 60 cities over 3 years,
representing the first systematic, worldwide catalog of the urban microbial ecosystem. This atlas provides an
annotated, geospatial profile of microbial strains, functional characteristics, antimicrobial resistance (AMR)
markers, and genetic elements, including 10,928 viruses, 1,302 bacteria, 2 archaea, and 838,532 CRISPR arrays
not found in reference databases. We identified 4,246 known species of urban microorganisms and a
consistent set of 31 species found in 97% of samples that were distinct from human commensal organisms.
Profiles of AMR genes varied widely in type and density across cities. Cities showed distinct microbial taxonomic
signatures that were driven by climate and geographic differences. These results constitute a highresolution
global metagenomic atlas that enables discovery of organisms and genes, highlights potential
public health and forensic applications, and provides a culture-independent view of AMR burden in cities.
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