A global metagenomic map of urban microbiomes and antimicrobial resistance
David Danko(Cornell University), Daniela Bezdan(Cornell University), Evan E. Afshin(Cornell University), Sofia Ahsanuddin(Icahn School of Medicine at Mount Sinai), Chandrima Bhattacharya(Cornell University), Daniel Butler(Cornell University), Kern Rei Chng(Agency for Science, Technology and Research), Daisy Donnellan(Cornell University), Jochen Hecht(Centre for Genomic Regulation), Katelyn Jackson(Cornell University), Katerina Kuchin(Cornell University), Mikhail Karasikov(SIB Swiss Institute of Bioinformatics), Abigail Lyons(Cornell University), Lauren Mak(Cornell University), Dmitry Meleshko(Cornell University), Harun Mustafa(SIB Swiss Institute of Bioinformatics), Beth Mutai(Kenya Medical Research Institute), Russell Y. Neches(Lawrence Berkeley National Laboratory), Amanda Hui Qi Ng(Agency for Science, Technology and Research), Olga Nikolayeva(Institute for Independent Studies Zürich), Tatyana Nikolayeva(Institute for Independent Studies Zürich), Eileen Png(Agency for Science, Technology and Research), Krista Ryon(Cornell University), Jorge L. Sánchez(Cornell University), Heba Shaaban(Cornell University), Maria A. Sierra(Cornell University), Dominique Thomas(Cornell University), Ben Young(Cornell University), Omar O. Abudayyeh(McGovern Institute for Brain Research), Josue Alicea(Cornell University), Malay Bhattacharyya(Indian Statistical Institute), Ran Blekhman(University of Minnesota), Eduardo Castro‐Nallar(Universidad Andrés Bello), A Cañas(Cornell University), Aspassia D. Chatziefthimiou(Cornell University), Robert W. Crawford(California State University, Sacramento), Francesca De Filippis(Federico II University Hospital), Youping Deng(University of Hawaiʻi at Mānoa), Christelle Desnues(Centre National de la Recherche Scientifique), Emmanuel Dias‐Neto(AC Camargo Hospital), Marius Dybwad(Norwegian Defence Research Establishment), Eran Elhaik(Lund University), Danilo Ercolini(Federico II University Hospital), Alina Frolova(National Academy of Sciences of Ukraine), Dennis Gankin(McGovern Institute for Brain Research), Jonathan S. Gootenberg(McGovern Institute for Brain Research), Alexandra B. Graf, David C. Green(King's College London), Iman Hajirasouliha(Cornell University), Jaden J. A. Hastings(Cornell University), Mark Hernandez(University of Colorado Boulder), Gregorio Iraola(Universidad Mayor), Soojin Jang(Institut Pasteur Korea), André Kahles(Universidad del Desarrollo), Frank J. Kelly(King's College London), Kaymisha Knights(Cornell University), Nikos C. Kyrpides(Lawrence Berkeley National Laboratory), Paweł P. Łabaj(Jagiellonian University), Patrick K. H. Lee(City University of Hong Kong), Marcus H. Y. Leung(City University of Hong Kong), Per O. Ljungdahl(Stockholm University), Gabriella Mason-Buck(King's College London), Ken McGrath, Cem Meydan(Cornell University), Emmanuel F. Mongodin(University of Maryland, Baltimore), Milton Ozório Moraes(Fundação Oswaldo Cruz), Niranjan Nagarajan(Agency for Science, Technology and Research), Marina Nieto‐Caballero(University of Colorado Boulder), Houtan Noushmehr(Universidade de Ribeirão Preto), Manuela Oliveira(Universidade do Porto), Stephan Ossowski(Centre for Genomic Regulation), Olayinka Osuolale(Elizade University), Orhan Özcan(Kent Hastanesi), David Páez-Espino(Lawrence Berkeley National Laboratory), Nicolás Rascovan(Centre National de la Recherche Scientifique), Hugues Richard(Robert Koch Institute), Gunnar Rätsch(SIB Swiss Institute of Bioinformatics), Lynn M. Schriml(University of Maryland, Baltimore), Torsten Semmler(Robert Koch Institute), Osman Uğur Sezerman(Kent Hastanesi), Leming Shi(Fudan University), Tieliu Shi(East China Normal University), Rania Siam(American University in Cairo), Le Huu Song(Vietnamese - German Center of Excellence in Medical Research), Haruo Suzuki(Keio University), Denise Syndercombe Court(King's College London), Scott Tighe(University of Vermont), Xinzhao Tong(City University of Hong Kong), Klas I. Udekwu(Stockholm University), Juan A. Ugalde(Universidad del Desarrollo), Brandon Valentine(Cornell University), Dimitar Vassilev(Sofia University "St. Kliment Ohridski"), Elena Vayndorf(University of Alaska Fairbanks), Thirumalaisamy P. Velavan(Duy Tan University), Jun Wu(East China Normal University), María Mercedes Zambrano(CorpoGen (Colombia)), Jifeng Zhu(Cornell University), Sibo Zhu(Fudan University), Christopher E. Mason(Cornell University), Natasha Abdullah, Marcos Abraao, Amro Adel(Centre National de la Recherche Scientifique), Muhammad Afaq, Faisal Alquaddoomi, Ireen Alam, Gabriela E. Albuquerque, Alex Alexiev, K. Mohammed Ali(National Academy of Sciences of Ukraine), Lucia Elena Alvarado-Arnez, Sarh Aly, Jennifer Amachee, María Galli de Amorim, Majelia Ampadu, Muhammad Al-Fath Amran, Nala An, Watson Andrew, Harilanto Andrianjakarivony, Michael Angelov, Verónica Antelo, Catharine Aquino, Álvaro Aranguren‐Ibáñez, Luiza Araujo, Hitler Francois Vasquez Arevalo, J. M. G. Arevalo, Carme Arnan, Lucia Elena Alvarado-Arnez, Fernanda Arredondo, Matthew Arthur, Freddy Asenjo, Thomas Saw Aung, Juliette Auvinet, Nuria Aventin, Sadaf Ayaz, Silva Baburyan, Abd-Manaaf Bakere, Katrin Bakhl, Thais Fernanda Bartelli, Batdelger Erdenetsetseg, François Baudon, Kevin Becher, Carla Bello, Médine Benchouaia, Hannah Benisty, Anne‐Sophie Benoiston, Joseph Benson, Diego Benítez, Juliana Bernardes, Denis Bertrand(King's College London), Silvia Beurmann, Tristan Bitard‐Feildel, Lucie Bittner, Christina Black, Guillaume Blanc, Brittany Blyther, Toni Bode, Julia Boeri, Bazartseren Boldgiv, Kevin Bolzli, Alexia Bordigoni, Ciro Borrelli, Sonia Bouchard, Jean‐Pierre Bouly, Alicia Boyd, Gabriela Pereira Branco, Alessandra Breschi, Björn Brindefalk, Christian Brion, Alan C. Briones, Paulina Buczansla, Catherine Burke, A. Millie Burrell, Alina Butova(National Academy of Sciences of Ukraine), Irvind Buttar, Jalia Bynoe, Sven Bönigk, Kari O. Bøifot, Hiram Caballero(University of Colorado Boulder), Xiao Wen Cai, Dayana Calderón, Angela Cantillo, M. Carbajo Carbajo, Alessandra Carbone, Anais Cardenas, Katerine Carrillo-Castro, Laurie Casalot, S Obredor Castro(Universidad Andrés Bello), Ana V. Castro(Universidad Andrés Bello), Astred Castro(Universidad Andrés Bello), Ana Valeria Castro(Universidad Andrés Bello), Simone Cawthorne, Jonathan Cedillo(McGovern Institute for Brain Research), Salama Chaker, Jasna Chalangal, Allison Chan(Cornell University), Anastasia I. Chasapi, Starr Chatziefthimiou(Cornell University), Sreya Ray Chaudhuri, Akash Keluth Chavan, Francisco Chavez, Gregory Chem, Xiaoqing Chen(Centre for Genomic Regulation), Michelle Chen(Centre for Genomic Regulation), Jenn‐Wei Chen(Centre for Genomic Regulation), Ariel Chernomoretz, Allaeddine Chettouh, Daisy Cheung(Cornell University), Diana Chicas, Shirley Chiu, Hira Choudhry, Carl Chrispin, Kianna Ciaramella, Erika Alejandra Cifuentes, Jake Cohen, David A. Coil(Lawrence Berkeley National Laboratory), Sylvie Collin, Colleen Conger, Romain Conte, Flavia Corsi, Cecilia N. Cossio, Ana Flávia D.V. Costa(Cornell University), Delisia Cuebas, Bruno D’Alessandro, Katherine Dahlhausen, Aaron E. Darling, Pujita Das, Lucinda B. Davenport, Laurent David(Lawrence Berkeley National Laboratory), Natalie R. Davidson, Gargi Dayama, Stéphane Delmas, Chris Deng(University of Hawaiʻi at Mānoa), Chloé Dequeker, Alexandre Désert, Monika Devi, Felipe Segato Dezem, Clara N. Dias(AC Camargo Hospital), Timothy Ryan Donahoe, S. Dorado, LaShonda Dorsey, V. A. Dotsenko, Steven Du(Universidad Andrés Bello), Alexandra Dutan, Naya A. Eady, Jonathan A. Eisen(McGovern Institute for Brain Research), Miar Elaskandrany, Lennard Epping, Juan Pablo Escalera-Antezana, Cassie L. Ettinger, Iqra Faiz, Luice Fan, Nadine Farhat, Emile Faure, Fazlina Fauzi, Charlie Feigin, Skye Felice, Laís Pereira Ferreira, Gabriel Figueroa(King's College London), Aubin Fleiss, Denisse Flores, Jhovana L. Velasco Flores, Marcos A. Fonseca, Jonathan Foox(McGovern Institute for Brain Research), Juan Carlos Forero, Aaishah Francis, Kelly French(King's College London), Pablo Fresia, Jacob E. Friedman, Jaime J. Fuentes, Josephine Galipon, Mathilde Garcia, Laura Garcia, Catalina García, Annie Geiger, Samuel M. Gerner, Sonia L. Ghose, Đào Phương Giang, Matías Giménez, Donato Giovannelli, Dedan Githae, Spyridon Gkotzis, Liliana Godoy, Samantha L. Goldman, Gastón H. Gonnet, Juana Gonzalez, Andrea María Moreno González, Camila Gonzalez-Poblete, Andrew Gray, Tranette Gregory, Charlotte Greselle, Sophie Guasco, Juan José Martínez Guerra(Universidad del Desarrollo), Nika Gurianova, Wolfgang Haehr, Sebastien Halary, Felix Hartkopf, Jaden J. A. Hastings(Cornell University), Arya Hawkins-Zafarnia(Cornell University), Nur Hazlin Hazrin-Chong, Eric J. N. Helfrich, Éva Hell(Institute for Independent Studies Zürich), Tamera Henry, Samuel Hernández(University of Colorado Boulder), Pilar Hernández(University of Colorado Boulder), David Hess-Homeier(Lawrence Berkeley National Laboratory), Lauren Hittle, Nghiem Xuan Hoan, Aliaksei Holik, Chiaki Homma, Irene Hoxie, Michael Huber, Elizabeth Humphries, Stephanie Hyland, A. Hässig, Roland Häusler, Nathalie Hüsser, Robert A. Petit(California State University, Sacramento), Badamnyambuu Iderzorig, Mizuki Igarashi, Shaikh B. Iqbal, Shino Ishikawa, Sakura Ishizuka, Sharah Islam, Riham Islam, Kohei Ito, Sota Ito, Takayuki Ito, Tomislav Ivanković, Tomoki Iwashiro, Sarah Jackson(Cornell University), JoAnn Jacobs, Marisano J. James, Marianne Jaubert, Marie-Laure Jerier, Esmeralda Jiminez, Ayantu Jinfessa, Ymke De Jong, Hyun Woo Joo, Guilllaume Jospin, Takema Kajita, Affifah Saadah Ahmad Kassim, Nao Kato, Amrit Kaur, Inderjit Kaur, Fernanda S. G. Kehdy, Vedbar S. Khadka, Shaira Khan, Mahshid Khavari, Michelle Ki(Keio University), Gina Kim, Hyung Jun Kim, Sangwan Kim, Ryan J. King, Kaymisha Knights(Cornell University), Giuseppe KoLoMonaco, Ellen Koag, Nadezhda Kobko-Litskevitch, Maryna Korshevniuk, Michael Kozhar, Jonas Krebs, Nanami Kubota, A. V. Kuklin, Sheelta S. Kumar, Rachel Kwong, Lawrence N. Kwong, Ingrid Lafontaine, Juliana Lago, Tsoi Ying Lai(Duy Tan University), Élodie Laine, Manolo Laiola, Olha Lakhneko, Isha Lamba(Cornell University), Gerardo de Lamotte, Romain Lannes, Eleonora de Lazzari, Madeline Leahy, Hyunjung Lee(City University of Hong Kong), Yunmi Lee(City University of Hong Kong), Lucy Lee(City University of Hong Kong), Vincent Lemaire, Emily Leong, Marcus H.Y. Leung(City University of Hong Kong), Dagmara Lewandowska, Chenhao Li(East China Normal University), Weijun Liang, Moses Lin(National Academy of Sciences of Ukraine), Priscilla Lisboa, Anna Litskevitch(Agency for Science, Technology and Research), Eric Minwei Liu(East China Normal University), Tracy Liu(East China Normal University), Mayra Arauco Livia, Yui Him Lo(National Academy of Sciences of Ukraine), Sonia Losim, Manon Loubens, Jennifer Lu, Olexandr Lykhenko, Simona Lysakova, Salah Mahmoud, Sara Abdul Majid, Natalka Makogon, Denisse Maldonado, Krizzy Mallari, Tathiane M. Malta, Maliha Mamun, Dimitri Manoir, German Marchandon, Natalia Marciniak, Sonia Marinovic, Brunna Marques, Nicole Mathews, Yuri Matsuzaki, Vincent Matthys, Madelyn May, Elias McComb, Annabelle Meagher, Adiell Melamed, Wayne Menary, Katterinne N. Mendez, Ambar Mendez, Irène Mauricette Mendy, Irene Meng, Ajay Menon, Mark Menor(University of Colorado Boulder), Roy A. Meoded, Nancy Merino, Cem Meydan(Cornell University), Karishma Miah, Mathilde Mignotte, Tanja Miketic, Wilson F. Miranda, Athena Mitsios, Ryusei Miura, Kunihiko Miyake, Maria Moccia, Natasha Mohan, Mohammed Dlshad Mohsin, Karobi Moitra, Mauricio Moldes, Laura Molina, Jennifer Molinet, Orgil-Erdene Molomjamts, Eftar Moniruzzaman, Sookwon Moon, Isabelle de Oliveira Moraes, Mario Moreno, Maritza Mosella, Josef W. Moser, Christopher Mozsary(Cornell University), Amanda L. Muehlbauer, Oasima Muner, Muntaha Munia, Naimah Munim, Maureen Muscat, Tatjana Mustac, Cristina Muñoz, Francesca Nadalin(University of Naples Federico II), Areeg Naeem, Dorottya Nagy-Szakal, Mayuko Nakagawa, Ashanti Narce, Masaki Nasu, Irene González Navarrete, Hiba Naveed, Bryan Nazario, Narasimha Rao Nedunuri, Thomas Neff(Cornell University), Aida Nesimi, Wan Chiew Ng(Cornell University), Synti Ng(Cornell University), Gloria Nguyen, Elsy Ngwa, Agier Nicolas(Centre National de la Recherche Scientifique), Pierre Nicolas(Centre National de la Recherche Scientifique), Abdollahi Nika, Hosna Noorzi, Avigdor Nosrati, Houtan Noushmehr(Universidade de Ribeirão Preto), Diana Noronha Nunes, Kathryn O’Brien, Niamh B. O’Hara, Gabriella Oken(King's College London), Rantimi A. Olawoyin, Javier Quilez Oliete, Kiara Olmeda, Tolulope Oluwadare, Itunu A. Oluwadare, Nils Ordioni, Jenessa Orpilla, Jacqueline Orrego, Melissa Ortega, Princess Osma(Kent Hastanesi), Israel O. Osuolale(Elizade University), Oluwatosin M. Osuolale(Elizade University), M OTA, Francesco Oteri, Yuya Oto(City University of Hong Kong), Rachid Ounit, Christos Ouzounis, Subhamitra Pakrashi, Rachel Paras, Coral Pardo-Este, Youngja Park, Paulina Pastuszek, Suraj Patel, Jananan Pathmanathan, Andrea Patrignani, Manuel Toledano Pérez(Universidade do Porto), Ante Peros, Sabrina Persaud, Anisia Peters, Adam Phillips, Lisbeth Pineda, Melissa Pool Pizzi, Alma Plaku, Alketa Plaku, Brianna Pompa-Hogan, María Gabriela Portilla, Leonardo Posada, Max Priestman, Bharath Prithiviraj, Sambhawa Priya, Phanthira Pugdeethosal, Catherine E. Pugh, Benjamin Pulatov, Angelika Pupiec, Kyrylo Pyrshev, Tao Qing, Saher Rahiel, Savlatjon Rahmatulloev, Kannan Rajendran, Aneisa Ramcharan, Adan Ramirez-Rojas, Shahryar Rana, Prashanthi Ratnanandan, Timothy D. Read, Hubert Rehrauer, Renee Richer, Alexis Rivera, Michelle Rivera, Alessandro Robertiello, Courtney Robinson, Paula Nicole Viteri Rodriguez, Nayra Aguilar Rojas, Paul Roldán, A. B. Del Rosario, Sandra Roth, Maria Ruiz(CorpoGen (Colombia)), Stephen Eduard Boja Ruiz, Kaitlan Russell(Lawrence Berkeley National Laboratory), Mariia Yu. Rybak, Thaís S. Sabedot, M.R. Sabina, Ikuto Saito, Yoshitaka Saito, Gustavo Adolfo Malca Salas, Cecilia Salazar, Kaung Myat San(Cornell University), Jorge Sánchez(Cornell University), Sanchir Khaliun, Ryan Sankar, Paulo Thiago de Souza Santos, Zulena Saravi, Kai Sasaki, Yuma Sato, Masaki Sato, Seisuke Sato, Ryo Sato(Cornell University), Kaisei Sato, Nowshin Sayara, Steffen Schaaf, Oli Schacher(Universidade do Porto), Anna-Lena M. Schinke, Ralph Schlapbach, Christian Schori, Jason R. Schriml(University of Maryland, Baltimore), Felipe Segato, Felipe D. Sepúlveda, Marianna Sampaio Serpa, Paola Flórez de Sessions, Juan C. Severyn, Heba Shaaban(Cornell University), Maheen Shakil, Heba Abdelhamid Shalaby, Aliyah Shari, Hyenah Shim, Hikaru Shirahata, Yuh Shiwa, Rania Siam(American University in Cairo), Ophélie Da Silva, Jordana M. Silva, Gwenola Simon, Shaleni K. Singh, Kasia Sluzek, Rebecca Smith, Eunice So(Cornell University), Núria Andreu Somavilla, Yuya Sonohara, Nuno Rufino de Sousa, Camila Souza, Jason L. Sperry, Nicolas Sprinsky(Centre National de la Recherche Scientifique), Stefan G. Stark, Antonietta La Storia, Kiyoshi Suganuma, Hamood Suliman, Jill Sullivan, Arif Asyraf Md Supie, C. Suzuki(Keio University), Sora Takagi, Fumie Takahara, Naoya Takahashi, Kou Takahashi, Tomoki Takeda, Isabella K. T. M. Takenaka, Soma Tanaka, Anyi Tang, Yuk Man Tang, Emilio Tarcitano, Andrea Tassinari, Mahdi Taye, Alexis Terrero, Eunice Thambiraja, Antonin Thiébaut, Sade Thomas(Cornell University), Andrew Maltez Thomas(Cornell University), Yuto Togashi, Takumi Togashi, A. Tomaselli(Agency for Science, Technology and Research), Masaru Tomita, Itsuki Tomita, Xinzhao Tong(City University of Hong Kong), Oliver Toth, Nora C. Toussaint, Jennifer M. Tran, Catalina Truong, Stefan I. Tsonev, Kazutoshi Tsuda, Takafumi Tsurumaki, Michelle Tuz, Yelyzaveta Tymoshenko, Carmen Urgiles, Mariko Usui, Sophie Vacant, Brandon Valentine(Cornell University), Laura Vann, Fabienne Velter, Valeria Ventorino, Patricia Vera-Wolf, Riccardo Vicedomini, Michael A. Suarez-Villamil, Sierra Vincent(Cornell University), Renee Vivancos-Koopman, Andrew Wan, Cindy X. Wang, Tomoro Warashina, Ayuki Watanabe, Samuel Weekes, Johannes Werner, David A. Westfall(Lawrence Berkeley National Laboratory), Lothar H. Wieler, Michelle D. Williams, Silver A. Wolf, Brian Wong, Yan Ling Wong, Tyler Wong, Rasheena Wright, Tina Wunderlin, Ryota Yamanaka, Jingcheng Yang, Hirokazu Yano, George C. Yeh(McGovern Institute for Brain Research), O.M. Yemets, Tetiana V. Yeskova, Shusei Yoshikawa, Laraib Zafar, Yang Zhang, Shu Zhang, Amy Zhang(Duy Tan University), Yuanting Zheng, Stanislav Zubenko
Cited by 379Open Access
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.
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