| Author | Danko, David | |
| Author | Bezdan, Daniela | |
| Author | Afshin, Evan E. | |
| Author | Ahsanuddin, Sofia | |
| Author | Bhattacharya, Chandrima | |
| Author | Butler, Daniel J. | |
| Author | Chng, Kern Rei | |
| Author | Donnellan, Daysy | |
| Author | Hecht, Jochen | |
| Author | Jackson, Kathelyn | |
| Author | Kuchin, Katerina | |
| Author | Karasikov, Mikhail | |
| Author | Lyons, Abigail | |
| Author | Mak, Lauren | |
| Author | Meleshko, Dmitry | |
| Author | Mustafa, Harun | |
| Author | Mutai, Beth | |
| Author | Neches, Russell Y. | |
| Author | Ng, Amanda | |
| Author | Nikolayeva, Olga | |
| Author | Nikolayeva, Tatyana | |
| Author | Png, Eileen | |
| Author | Ryon, Krista A. | |
| Author | Sanchez, Jorge L. | |
| Author | Shaaban, Heba | |
| Author | Sierra, Maria A. | |
| Author | Thomas, Dominique | |
| Author | Young, Ben | |
| Author | Abudayyeh, Omar O. | |
| Author | Alicea, Josue | |
| Author | Bhattacharyya, Malay | |
| Author | Blekhman, Ran | |
| Author | Castro-Nallar, Eduardo | |
| Author | Cañas, Ana M. | |
| Author | Chatziefthimiou, Aspassia D. | |
| Author | Crawford, Robert W. | |
| Author | Filippis, Francesca De | |
| Author | Deng, Youping | |
| Author | Desnues, Christelle | |
| Author | Dias Neto, Emmanuel | |
| Author | Dybwad, Marius | |
| Author | Elhaik, Eran | |
| Author | Ercolini, Danilo | |
| Author | Frolova, Alina | |
| Author | Gankin, Dennis | |
| Author | Gootenberg, Jonathan S. | |
| Author | Graf, Alexanda B. | |
| Author | Green, David C. | |
| Author | Hajirasouliha, Iman | |
| Author | Hastings, Jaden J. A. | |
| Author | Hernandez, Mark | |
| Author | Iraola, Gregorio | |
| Author | Jang, Soojin | |
| Author | Kahles, Andre | |
| Author | Kelly, Frank J. | |
| Author | Knights, Kaymisha | |
| Author | Kyrpides, Nikos C. | |
| Author | Labaj, Pawel P. | |
| Author | Lee, Patrick K.H. | |
| Author | Leung, Marcus H.Y. | |
| Author | Ljungdahl, Per O. | |
| Author | Mason-Buck, Gabriella | |
| Author | McGrath, Ken | |
| Author | Meydan, Cem | |
| Author | Mongodin, Emmanuel F. | |
| Author | Moraes, Milton Ozório | |
| Author | Nagarajan, Niranjan | |
| Author | Nieto-Caballer, Marina | |
| Author | Noushmehr, Houtan | |
| Author | Oliveira, Manuela | |
| Author | Ossowski, Stephan | |
| Author | Osuolale, Olayinka O. | |
| Author | Paez-Espino, David | |
| Author | Rascovan, Nicolás | |
| Author | Richard, Hugues | |
| Access date | 2022-02-13T20:58:34Z | |
| Available date | 2022-02-13T20:58:34Z | |
| Document date | 2021 | |
| Citation | DANKO, David et al. A global metagenomic map of urban microbiomes and antimicrobial resistance. Cell. v. 184, n. 13, p. 3376-3393, 24 June 2021. | |
| ISSN | 0092-8674 | |
| URI | https://www.arca.fiocruz.br/handle/icict/51165 | |
| Description | Produção científica do Laboratório de Hanseníase. | pt_BR |
| Sponsorship | We thank these organizations, people, and grants for their support: the Tri-I Program in Computational Biology and Medicine (CBM) funded by NIH grant 1T32GM083937. | |
| Sponsorship | GitHub. | |
| Sponsorship | Philip Blood and the Extreme Science and Engineering Discovery Environment (XSEDE), supported by NSF grant number ACI1548562 and NSF award number ACI-1445606. | |
| Sponsorship | WCM SCU and Epigenomics and Genomics Core Facilities. | |
| Sponsorship | Vallee Foundation. | |
| Sponsorship | WorldQuant Foundation. | |
| Sponsorship | Igor Tulchinsky. | |
| Sponsorship | The Pershing Square Sohn Cancer Research Alliance. | |
| Sponsorship | NASA (NNX14AH50G, NNX17AB26G). | |
| Sponsorship | NIH (R01AI151059, R25EB020393, R21AI129851, R35GM138152, U01DA053941). | |
| Sponsorship | STARR Foundation (I13- 0052). | |
| Sponsorship | LLS (MCL7001-18, LLS 9238-16, LLS-MCL7001-18). | |
| Sponsorship | NSF (1840275). | |
| Sponsorship | Bill and Melinda Gates Foundation (OPP1151054). | |
| Sponsorship | Alfred P. Sloan Foundation (G-2015-13964). | |
| Sponsorship | Swiss National Science Foundation grant number 407540_167331. | |
| Sponsorship | NIH award number UL1TR000457. | |
| Sponsorship | US Department of Energy Joint Genome Institute under contract number DEAC02-05CH11231. | |
| Sponsorship | National Energy Research Scientific Computing Center, supported by the Office of Science of the US Department of Energy. | |
| Sponsorship | Stockholm Health Authority grant SLL 20160933. | |
| Sponsorship | Institut Pasteur Korea. | |
| Sponsorship | NRF Korea grant (NRF-2014K1A4A7A01074645, 2017M3A9G6068246). | |
| Sponsorship | CONICYT Fondecyt Iniciación grants 11140666 and 11160905. | |
| Sponsorship | Millennium Science Initiative of the Ministry of Economy, Development and Tourism. | |
| Sponsorship | Government of Chile. | |
| Sponsorship | Keio University Funds for Individual Research. | |
| Sponsorship | Yamagata prefectural government and the city of Tsuruoka. | |
| Sponsorship | JSPS KAKENHI grant number 20K10436. | |
| Sponsorship | The bilateral AT-UA collaboration fund (WTZ:UA 02/2019; Ministry of Education and Science of Ukraine, UA:M/84-2019, M/126-2020). | |
| Sponsorship | Kyiv Academic Univeristy. | |
| Sponsorship | Ministry of Education and Science of Ukraine project numbers 0118U100290 and 0120U101734. | |
| Sponsorship | Spanish Ministry of Economy and Competitiveness. | |
| Sponsorship | Centro de Excelencia Severo Ochoa 2013–2017. | |
| Sponsorship | CERCA Programme / Generalitat de Catalunya. | |
| Sponsorship | The "la Caixa" Foundation. | |
| Sponsorship | CRG-Novartis-Africa mobility program 2016. | |
| Sponsorship | TMB Director Eladio De Miguel Sainz. | |
| Sponsorship | Research funds from National Cheng Kung University and the Ministry of Science and Technology. | |
| Sponsorship | Taiwan (MOST grant number 106-2321-B-006-016). | |
| Sponsorship | Weill Cornell Clinical and Translational Science Center (CTSC). | |
| Sponsorship | CUNY Hunter College. | |
| Sponsorship | Macaulay Honors College at CUNY. | |
| Sponsorship | City College of the City University of New York. | |
| Sponsorship | Cornell University. | |
| Sponsorship | Columbia University. | |
| Sponsorship | Icahn School of Medicine at Mt. Sinai. | |
| Sponsorship | Rockefeller University. | |
| Sponsorship | New York University (NYU). | |
| Sponsorship | Minciencias (project no. 639677758300). | |
| Sponsorship | CNPq (EDN - 309973/2015-5). | |
| Sponsorship | Open Research Fund of Key Laboratory of Advanced Theory and Application in Statistics and Data Science – MOE, ECNU, the Research Grants Council of Hong Kong through project 11215017, National Key RD Project of China (2018YFE0201603), and Shanghai Municipal Science and Technology Major Project (2017SHZDZX01) (L.S.). | |
| Language | eng | en_US |
| Publisher | Elsevier | |
| Rights | open access | |
| Title | A global metagenomic map of urban microbiomes and antimicrobial resistance | en_US |
| Type | Article | |
| DOI | 10.1016/j.cell.2021.05.002 | |
| 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 high-resolution 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. | en_US |
| Affilliation | Weill Cornell Medicine. New York, NY, USA / The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine. New York, NY, USA. | |
| Affilliation | Weill Cornell Medicine. New York, NY, USA / The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine. New York, NY, USA / University of Tübingen. Institute of Medical Genetics and Applied Genomics. Tübingen, Germany / University of Tübingen. NGS Competence Center Tübingen. Tübingen, Germany. | |
| Affilliation | Weill Cornell Medicine. New York, NY, USA / The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine. New York, NY, USA. | |
| Affilliation | Icahn School of Medicine at Mount Sinai. New York, NY, USA. | |
| Affilliation | Weill Cornell Medicine. New York, NY, USA / The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine. New York, NY, USA. | |
| Affilliation | Weill Cornell Medicine. New York, NY, USA / The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine. New York, NY, USA. | |
| Affilliation | A*STAR Genome Institute of Singapore. Singapore, Singapore. | |
| Affilliation | Weill Cornell Medicine. New York, NY, USA / The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine. New York, NY, USA. | |
| Affilliation | The Barcelona Institute of Science and Technology. Centre for Genomic Regulation. Barcelona, Spain. | |
| Affilliation | Weill Cornell Medicine. New York, NY, USA / The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine. New York, NY, USA. | |
| Affilliation | Weill Cornell Medicine. New York, NY, USA / The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine. New York, NY, USA. | |
| Affilliation | ETH Zurich. Department of Computer Science. Biomedical Informatics Group. Zurich, Switzerland / University Hospital Zurich. Biomedical Informatics Research. Zurich, Switzerland / University Hospital Zurich. Biomedical Informatics Research. Zurich, Switzerland. | |
| Affilliation | Weill Cornell Medicine. New York, NY, USA / The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine. New York, NY, USA. | |
| Affilliation | Weill Cornell Medicine. New York, NY, USA / The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine. New York, NY, USA. | |
| Affilliation | Weill Cornell Medicine. New York, NY, USA / The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine. New York, NY, USA. | |
| Affilliation | ETH Zurich. Department of Computer Science. Biomedical Informatics Group. Zurich, Switzerland / University Hospital Zurich. Biomedical Informatics Research. Zurich, Switzerland / University Hospital Zurich. Biomedical Informatics Research. Zurich, Switzerland. | |
| Affilliation | Lawrence Berkeley National Laboratory. Joint Genome Institute. Department of Energy. Berkeley, CA, USA. | |
| Affilliation | A*STAR Genome Institute of Singapore. Singapore, Singapore. | |
| Affilliation | Independent Researcher. Zurich, Switzerland. | |
| Affilliation | Independent Researcher. Zurich, Switzerland. | |
| Affilliation | A*STAR Genome Institute of Singapore. Singapore, Singapore. | |
| Affilliation | Weill Cornell Medicine. New York, NY, USA / The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine. New York, NY, USA. | |
| Affilliation | Weill Cornell Medicine. New York, NY, USA / The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine. New York, NY, USA. | |
| Affilliation | Weill Cornell Medicine. New York, NY, USA / The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine. New York, NY, USA. | |
| Affilliation | Weill Cornell Medicine. New York, NY, USA / The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine. New York, NY, USA. | |
| Affilliation | Weill Cornell Medicine. New York, NY, USA / The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine. New York, NY, USA. | |
| Affilliation | Weill Cornell Medicine. New York, NY, USA / The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine. New York, NY, USA. | |
| Affilliation | Massachusetts Institute of Technology. McGovern Institute for Brain Research. Cambridge, MA, USA. | |
| Affilliation | Weill Cornell Medicine. New York, NY, USA / The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine. New York, NY, USA. | |
| Affilliation | Indian Statistical Institute. Machine Intelligence Unit. Kolkata, India / Indian Statistical Institute. Centre for Artificial Intelligence and Machine Learning. Kolkata, India. | |
| Affilliation | University of Minnesota. Minneapolis, MN, USA. | |
| Affilliation | Universidad Andres Bello. Center for Bioinformatics and Integrative Biology. Facultad de Ciencias de la Vida. Santiago, Chile. | |
| Affilliation | Weill Cornell Medicine. New York, NY, USA / The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine. New York, NY, USA. | |
| Affilliation | Weill Cornell Medicine. New York, NY, USA / The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine. New York, NY, USA. | |
| Affilliation | California State University. Sacramento, CA, USA. | |
| Affilliation | University of Naples Federico II. Division of Microbiology. Department of Agricultural Sciences. Naples, Italy / University of Naples Federico II. Task Force on Microbiome Studies. Naples, Italy. | |
| Affilliation | University of Hawaii John A. Burns School of Medicine. Honolulu, HI, USA. | |
| Affilliation | Université de Toulon. Aix-Marseille Université. Mediterranean Institute of Oceanology. Marseille, France. | |
| Affilliation | A. C. Camargo Cancer Center. Medical Genomics Group. São Paulo, SP, Brasil. | |
| Affilliation | Norwegian Defence Research Establishment FFI. Kjeller, Norway. | |
| Affilliation | Lund University. Department of Biology. Lund, Sweden. | |
| Affilliation | University of Naples Federico II. Division of Microbiology. Department of Agricultural Sciences. Naples, Italy / University of Naples Federico II. Task Force on Microbiome Studies. Naples, Italy. | |
| Affilliation | National Academy of Sciences of Ukraine. Institute of Molecular Biology and Genetics. Kyiv, Ukraine / Kyiv Academic University. Kyiv, Ukraine. | |
| Affilliation | Massachusetts Institute of Technology. McGovern Institute for Brain Research, Cambridge, MA, USA. | |
| Affilliation | Massachusetts Institute of Technology. McGovern Institute for Brain Research, Cambridge, MA, USA. | |
| Affilliation | University of Applied Sciences Vienna. Vienna, Austria. | |
| Affilliation | King's College London. Department of Analytical, Environmental and Forensic Sciences. London, UK. | |
| Affilliation | Weill Cornell Medicine. New York, NY, USA / The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine. New York, NY, USA. | |
| Affilliation | Weill Cornell Medicine. New York, NY, USA / The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine. New York, NY, USA. | |
| Affilliation | University of Colorado at Boulder. Boulder, CO, USA. | |
| Affilliation | Institut Pasteur de Montevideo. Microbial Genomics Laboratory. Montevideo, Uruguay / Universidad Mayor. Center for Integrative Biology. Santiago de Chile, Santiago, Chile / Wellcome Sanger Institute. Hinxton, UK. | |
| Affilliation | Institut Pasteur Korea. Seoul, South Korea. | |
| Affilliation | ETH Zurich. Department of Computer Science. Biomedical Informatics Group. Zurich, Switzerland / Kyiv Academic University. Kyiv, Ukraine / Universidad del Desarrollo. School of Engineering. Research Center in Technologies for Society. C+. Santiago, Chile. | |
| Affilliation | King's College London. Department of Analytical, Environmental and Forensic Sciences. London, UK. | |
| Affilliation | Weill Cornell Medicine. New York, NY, USA / The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine. New York, NY, USA. | |
| Affilliation | Lawrence Berkeley National Laboratory. Joint Genome Institute. Department of Energy. Berkeley, CA, USA. | |
| Affilliation | Fudan University. Human Phenome Institute. School of Life Sciences. State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology. Shanghai, China / Jagiellonian University. Małopolska Centre of Biotechnology. Kraków, Poland / Boku University Viennna. Vienna, Austria. | |
| Affilliation | City University of Hong Kong. School of Energy and Environment. Hong Kong SAR, China. | |
| Affilliation | City University of Hong Kong. School of Energy and Environment. Hong Kong SAR, China. | |
| Affilliation | Stockholm University. The Wenner-Gren Institute. Department of Molecular Biosciences. Stockholm, Sweden. | |
| Affilliation | King's College London. Department of Analytical, Environmental and Forensic Sciences. London, UK. | |
| Affilliation | Microba. Brisbane City, Australia. | |
| Affilliation | Weill Cornell Medicine. New York, NY, USA / The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine. New York, NY, USA. | |
| Affilliation | University of Maryland School of Medicine. Institute for Genome Sciences. Baltimore, MD, USA. | |
| Affilliation | Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Hanseníase. Rio de Janeiro, RJ, Brasil. | |
| Affilliation | A*STAR Genome Institute of Singapore. Singapore; Singapore. | |
| Affilliation | University of Colorado at Boulder. Boulder, CO, USA. | |
| Affilliation | Universidade de São Paulo. Escola de Medicina de Ribeirão Preto. Ribeirão Preto, SP, Brasil. | |
| Affilliation | Universidade do Porto. Instituto de Patologia e Imunologia Molecular. Porto, Portugal. | |
| Affilliation | The Barcelona Institute of Science and Technology. Centre for Genomic Regulation. Barcelona, Spain / University of Tübingen. Institute of Medical Genetics and Applied Genomics. Tübingen, Germany / University of Tübingen. NGS Competence Center Tübingen. Tübingen, Germany. | |
| Affilliation | Elizade University. Department of Biological Sciences. Applied Environmental Metagenomics and Infectious Diseases Research. Ilara-Mokin, Nigeria. | |
| Affilliation | Acibadem Mehmet Ali Aydınlar Universit. Istanbul, Turkey. | |
| Affilliation | Lawrence Berkeley National Laboratory. Joint Genome Institute. Department of Energy. Berkeley, CA, USA. | |
| Affilliation | Institut Pasteur. Microbial Paleogenomics Unit. Paris, France. | |
| Affilliation | Sorbonne University. Faculty of Science. Institute of Biology Paris-Seine. Laboratory of Computational and Quantitative Biology. Paris, France / Robert Koch Institute. Berlin, Germany. | |
| Subject | Built Environment | en_US |
| Subject | Metagenome | en_US |
| Subject | Global health | en_US |
| Subject | Antimicrobial resistance | en_US |
| Subject | Microbiome | en_US |
| Subject | NGS | en_US |
| Subject | Shotgun sequencing | en_US |
| Subject | De novo assembly | en_US |
| Subject | BGC | en_US |
| Subject | AMR | en_US |
| e-ISSN | 1097-4172 | |
| xmlui.metadata.dc.subject.ods | 03 Saúde e Bem-Estar | |
