ArticleCell2021
A global metagenomic map of urban microbiomes and antimicrobial resistance.
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In one paragraph
Article in Cell, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 176 papers, 1 of them a synthesis that pooled it.
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176citing papers in PubMed, 1 pooled it
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Who cites it
176 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Potential routes of plastics biotransformation involving novel plastizymes revealed by global multi-omic analysis of plastic associated microbes.Scientific reports · 2024Pooled it
- Indoor green wall affects health-associated commensal skin microbiota and enhances immune regulation: a randomized trial among urban office workers.Scientific reports · 2022Trial
- Urbanization-Associated Microbial Diversity Loss and Its Impact on Elderly Health: Integrating Environmental and Host Microbiome Dynamics.Environmental microbiology · 2026Article
- Bonsai reconstructs tree representations for distortion-free visualization and exploration of high-dimensional data.Nature biotechnology · 2026Article
- Classroom microbiome signatures of pest management associate with reduced asthma symptoms.The Journal of allergy and clinical immunology · 2026Article
- Ocular community state types reveal distinct microbial compositions among microbiomes with implications for trachoma control.bioRxiv : the preprint server for biology · 2026Article
- Diversity and distinctive characteristics of the global RNA virome in urban and peri-urban environments.Nature communications · 2026Article
- Editorial for the Special Issue "The Urban Microbiome".Microorganisms · 2026Article
- Evaluation of targeted Massively Parallel Sequencing methods for forensic metagenomics.Applied microbiology and biotechnology · 2026Article
- Forensic analysis of environmental and skin microbiome differences in college dormitories based on 16 S rRNA.International journal of legal medicine · 2026Article
- Moving from a taxonomic to a functional perspective in global microbiome analysis requires optimizing multiplexing ratios.mSystems · 2026Article
- Shotgun metagenomic dataset of surface microbiomes at a train station in Shinagawa, Tokyo.BMC genomic data · 2026Article
- A global-scale framework for quantifying the gut microbiome's mediating role in environmental and personal determinants of health.Eco-Environment & Health · 2026Article
- Assessing links between dental fluorosis and oral/systemic health via salivary microbiome in Chinese young adults.International dental journal · 2026Article
- Analysis of salivary metabolites and microbial characteristics in patients with dental fluorosis.Clinical oral investigations · 2026Article
- A Genomic Catalog of Migratory Microbiomes from Wild Birds across China's Habitats.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Restoring soil and sediment microbiomes in the Anthropocene.Nature reviews. Microbiology · 2026Review
- Human Contact Frequency as a Dominant Ecological Driver of Fungal Community Assembly and Homogenization in Public Built Environments.Journal of microbiology and biotechnology · 2026Article
- Scalable discovery of spatial multicellular patterns via neighborhood-to-sequence transformation.Communications biology · 2026Article
- Recent Microbial Evolutionary Insights From Metagenomics.Genome biology and evolution · 2026Review
116 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
100 authors.
David DankoWeill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.
Daniela BezdanWeill 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.
Evan E AfshinWeill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.
Sofia AhsanuddinIcahn School of Medicine at Mount Sinai, New York, NY, USA.
Chandrima BhattacharyaWeill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.
Daniel J ButlerWeill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.
Kern Rei ChngGenome Institute of Singapore, A(∗)STAR, Singapore, Singapore.
Daisy DonnellanWeill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.
Jochen HechtCentre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.
Katelyn JacksonWeill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.
Katerina KuchinWeill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.
Mikhail KarasikovETH Zurich, Department of Computer Science, Biomedical Informatics Group, Zurich, Switzerland; University Hospital Zurich, Biomedical Informatics Research, Zurich, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland.
Abigail LyonsWeill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.
Lauren MakWeill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.
Dmitry MeleshkoWeill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.
Harun MustafaETH Zurich, Department of Computer Science, Biomedical Informatics Group, Zurich, Switzerland; University Hospital Zurich, Biomedical Informatics Research, Zurich, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland.
Beth MutaiCentre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain; Kenya Medical Research Institute - Kisumu, Kisumu, Kenya.
Russell Y NechesDepartment of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
Amanda NgGenome Institute of Singapore, A(∗)STAR, Singapore, Singapore.
Olga NikolayevaIndependent Researcher, Zurich, Switzerland.
Tatyana NikolayevaIndependent Researcher, Zurich, Switzerland.
Eileen PngGenome Institute of Singapore, A(∗)STAR, Singapore, Singapore.
Krista A RyonWeill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.
Jorge L SanchezWeill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.
Heba ShaabanWeill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.
Maria A SierraWeill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.
Dominique ThomasWeill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.
Ben YoungWeill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.
Omar O AbudayyehMassachusetts Institute of Technology, McGovern Institute for Brain Research, Cambridge, MA, USA.
Josue AliceaWeill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.
Malay BhattacharyyaMachine Intelligence Unit, Indian Statistical Institute, Kolkata, India; Centre for Artificial Intelligence and Machine Learning, Indian Statistical Institute, Kolkata, India.
Ran BlekhmanUniversity of Minnesota, Minneapolis, MN, USA.
Eduardo Castro-NallarUniversidad Andres Bello, Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Santiago, Chile.
Ana M CañasWeill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.
Aspassia D ChatziefthimiouWeill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.
Robert W CrawfordCalifornia State University, Sacramento, Sacramento, CA, USA.
Francesca De FilippisDepartment 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.
Youping DengUniversity of Hawaii John A. Burns School of Medicine, Honolulu, HI, USA.
Christelle DesnuesAix-Marseille Université, Mediterranean Institute of Oceanology, Université de Toulon, CNRS, IRD, UM 110, Marseille, France.
Emmanuel Dias-NetoMedical Genomics group, A.C.Camargo Cancer Center, São Paulo - SP, Brazil.
Marius DybwadNorwegian Defence Research Establishment FFI, Kjeller, Norway.
Eran ElhaikDepartment of Biology, Lund University, Lund, Sweden.
Danilo ErcoliniDepartment 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.
Alina FrolovaInstitute of Molecular Biology and Genetics of National Academy of Sciences of Ukraine, Kyiv, Ukraine; Kyiv Academic University, Kyiv, Ukraine.
Dennis GankinMassachusetts Institute of Technology, McGovern Institute for Brain Research, Cambridge, MA, USA.
Jonathan S GootenbergMassachusetts Institute of Technology, McGovern Institute for Brain Research, Cambridge, MA, USA.
Alexandra B GrafUniversity of Applied Sciences Vienna, Vienna, Austria.
David C GreenDepartment of Analytical, Environmental and Forensic Sciences, King's College London, London, UK.
Iman HajirasoulihaWeill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.
Jaden J A HastingsWeill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.
Mark HernandezUniversity of Colorado at Boulder, Boulder, CO, USA.
Gregorio IraolaMicrobial Genomics Laboratory, Institut Pasteur de Montevideo, Montevideo, Uruguay; Center for Integrative Biology, Universidad Mayor, Santiago de Chile, Santiago, Chile; Wellcome Sanger Institute, Hinxton, UK.
Soojin JangInstitut Pasteur Korea, Seoul, South Korea.
Andre KahlesETH 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.
Frank J KellyDepartment of Analytical, Environmental and Forensic Sciences, King's College London, London, UK.
Kaymisha KnightsWeill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.
Nikos C KyrpidesDepartment of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
Paweł P ŁabajState Key Laboratory of Genetic Engineering (SKLGE) and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, China; Małopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland; Boku University Viennna, Vienna, Austria.
Patrick K H LeeSchool of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China.
Marcus H Y LeungSchool of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China.
Per O LjungdahlDepartment of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden.
Gabriella Mason-BuckDepartment of Analytical, Environmental and Forensic Sciences, King's College London, London, UK.
Ken McGrathMicroba, 388 Queen St, Brisbane City, QLD 4000, Australia.
Cem MeydanWeill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.
Emmanuel F MongodinUniversity of Maryland School of Medicine, Institute for Genome Sciences, Baltimore, MD, USA.
Milton Ozorio MoraesFundação Oswaldo Cruz, Rio de Janeiro - RJ, Brazil.
Niranjan NagarajanGenome Institute of Singapore, A(∗)STAR, Singapore, Singapore.
Marina Nieto-CaballeroUniversity of Colorado at Boulder, Boulder, CO, USA.
Houtan NoushmehrUniversity of São Paulo, Ribeirão Preto Medical School, Ribeirão Preto - SP, Brazil.
Manuela OliveiraInstituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal.
Stephan OssowskiCentre 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 Tübingen (NCCT), University of Tübingen, Tübingen, Germany.
Olayinka O OsuolaleApplied Environmental Metagenomics and Infectious Diseases Research (AEMIDR), Department of Biological Sciences, Elizade University, Ilara-Mokin, Nigeria.
Orhan ÖzcanAcibadem Mehmet Ali Aydınlar University, Istanbul, Turkey.
David Paez-EspinoDepartment of Energy, Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
Nicolás RascovanMicrobial Paleogenomics Unit, Institut Pasteur, CNRS UMR2000, Paris 75015, France.
Hugues RichardSorbonne University, Faculty of Science, Institute of Biology Paris-Seine, Laboratory of Computational and Quantitative Biology, Paris, France; Robert Koch Institute, Berlin, Germany.
Gunnar RätschETH Zurich, Department of Computer Science, Biomedical Informatics Group, Zurich, Switzerland; University Hospital Zurich, Biomedical Informatics Research, Zurich, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland.
Lynn M SchrimlUniversity of Maryland School of Medicine, Institute for Genome Sciences, Baltimore, MD, USA.
Torsten SemmlerRobert Koch Institute, Berlin, Germany.
Osman U SezermanAcibadem Mehmet Ali Aydınlar University, Istanbul, Turkey.
Leming ShiCenter for Pharmacogenomics, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China; 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.
Tieliu ShiThe Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China.
Rania SiamUniversity of Medicine and Health Sciences, St. Kitts, West Indies and American University in Cairo, Cairo, Egypt.
Le Huu Song108 Military Central Hospital, Hanoi, Vietnam; Vietnamese-German Center for Medical Research (VG-CARE), Hanoi, Vietnam.
Haruo SuzukiKeio University, Tokyo, Japan.
Denise Syndercombe CourtDepartment of Analytical, Environmental and Forensic Sciences, King's College London, London, UK.
Scott W TigheUniversity of Vermont, Burlington, VT, USA.
Xinzhao TongSchool of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China.
Klas I UdekwuDepartment of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden; SciLife EVP, Department of Aquatic Sciences Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden.
Juan A UgaldeMillennium Initiative for Collaborative Research on Bacterial Resistance, Santiago, Chile; C+, Research Center in Technologies for Society, School of Engineering, Universidad del Desarrollo, Santiago, Chile.
Brandon ValentineWeill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.
Dimitar I VassilevFaculty of Mathematics and Informatics, Sofia University "St. Kliment Ohridski," Sofia, Bulgaria.
Elena M VayndorfInstitute of Arctic Biology, University of Alaska, Fairbanks, Fairbanks, AK, USA.
Thirumalaisamy P VelavanInstitute of Tropical Medicine, Univeristätsklinikum Tübingen, Tübingen, Germany; Faculty of Medicine, Duy Tan University, Da Nang, Vietnam.
Jun WuThe Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China.
María M ZambranoCorporación Corpogen-Research Center, Bogotá, Colombia.
Jifeng ZhuWeill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA.
Sibo ZhuState Key Laboratory of Genetic Engineering (SKLGE) and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, China; Department of Epidemiology, School of Public Health, Fudan University, Shanghai, China.
Christopher E MasonWeill Cornell Medicine, New York, NY, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA; The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA. Electronic address: chm2042@med.cornell.edu.
International MetaSUB Consortium
Funding
Clinical and Translational Science CenterUL1TR000457 · NCATS · WEILL MEDICAL COLL OF CORNELL UNIV · PI IMPERATO-MCGINLEY, JULIANNE L · 2012 to 2016
$46.0MSupplement for MINI point-of-use deviceU01DA053941 · NIDA · UNIVERSITY OF MIAMI CORAL GABLES · PI MASON, CHRISTOPHER EDWARD, SCHURER, STEPHAN C · 2021 to 2022
$5.2MMetagenomic profiling of urinary cell-free DNA to monitor urinary tract infection after kidney transplantationR01AI151059 · NIAID · CORNELL UNIVERSITY · PI DADHANIA, DARSHANA, DE VLAMINCK, IWIJN · 2020 to 2024
$3.4MTri-Institutional Training Program in Computational Biology & MedicineT32GM083937 · NIGMS · WEILL MEDICAL COLL OF CORNELL UNIV · PI CHRISTINI, DAVID J. · 2009 to 2018
$3.1MImproving Metagenomic Analysis with Novel Algorithms and TechnologiesR35GM138152 · NIGMS · WEILL MEDICAL COLL OF CORNELL UNIV · PI Iman Hajirasouliha · 2020 to 2026
$2.5MCommunity Research Education and Engagement for Data Science (CREEDS)R25EB020393 · NIBIB · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI CLAUDIO, LUZ, KOVATCH, PATRICIA · 2015 to 2017
$578kMapping the RNA modification N6-methyladenosine during Zika virus infectionR21AI129851 · NIAID · WEILL MEDICAL COLL OF CORNELL UNIV · PI HORNER, STACY MICHELLE, MASON, CHRISTOPHER EDWARD · 2017 to 2018
$469kMedical Research Council MR/S019669/1NCATS NIH HHS UL1 TR000457NIAID NIH HHS R01 AI151059NIAID NIH HHS R21 AI129851NIBIB NIH HHS R25 EB020393NIDA NIH HHS U01 DA053941NIGMS NIH HHS R35 GM138152NIGMS NIH HHS T32 GM083937
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.
Indexed as
MetagenomicsUrban PopulationBiodiversityDatabases, GeneticDrug Resistance, BacterialHumansMicrobiotaAMRantimicrobial resistanceBGCbuilt Environmentde novo assemblyglobal healthmetagenomemicrobiomeNGSshotgun sequencing
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