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A global metagenomic map of urban microbiomes and antimicrobial resistance
David Danko, Daniela Bezdan, Evan E. Afshin, Sofia Ahsanuddin, Chandrima Bhattacharya, Daniel Butler, Kern Rei Chng, Daisy Donnellan, Jochen Hecht, Katelyn Jackson, Katerina Kuchin, Mikhail Karasikov, Abigail Lyons, Lauren Mak, Dmitry Meleshko, Harun Mustafa, Beth Mutai, Russell Y. Neches, Amanda Hui Qi Ng, Olga Nikolayeva, Tatyana Nikolayeva, Eileen Png, Krista Ryon, Jorge L. Sánchez, Heba Shaaban, Maria A. Sierra, Dominique Thomas, Ben Young, Omar O. Abudayyeh, Josue Alicea, Malay Bhattacharyya, Ran Blekhman, Eduardo Castro‐Nallar, A Cañas, Aspassia D. Chatziefthimiou, Robert W. Crawford, Francesca De Filippis, Youping Deng, Christelle Desnues, Emmanuel Dias‐Neto, Marius Dybwad, Eran Elhaik, Danilo Ercolini, Alina Frolova, Dennis Gankin, Jonathan S. Gootenberg, Alexandra B. Graf, David C. Green, Iman Hajirasouliha, Jaden J. A. Hastings, Mark Hernandez, Gregorio Iraola, Soojin Jang, André Kahles, Frank J. Kelly, Kaymisha Knights, Nikos C. Kyrpides, Paweł P. Łabaj, Patrick K. H. Lee, Marcus H. Y. Leung, Per O. Ljungdahl, Gabriella Mason-Buck, Ken McGrath, Cem Meydan, Emmanuel F. Mongodin, Milton Ozório Moraes, Niranjan Nagarajan, Marina Nieto‐Caballero, Houtan Noushmehr, Manuela Oliveira, Stephan Ossowski, Olayinka Osuolale, Orhan Özcan, David Páez-Espino, Nicolás Rascovan, Hugues Richard, Gunnar Rätsch, Lynn M. Schriml, Torsten Semmler, Osman Uğur Sezerman, Leming Shi, Tieliu Shi, Rania Siam, Le Huu Song, Haruo Suzuki, Denise Syndercombe Court, Scott Tighe, Xinzhao Tong, Klas I. Udekwu, Juan A. Ugalde, Brandon Valentine, Dimitar Vassilev, Elena Vayndorf, Thirumalaisamy P. Velavan, Jun Wu, María Mercedes Zambrano, Jifeng Zhu, Sibo Zhu, Christopher E. Mason, Marcos Abraao, Amro Adel, Muhammad Afaq, Faisal Alquaddoomi, Ireen Alam, Gabriela E. Albuquerque, Alex Alexiev, K. Mohammed Ali, 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, 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, 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, Irvind Buttar, Jalia Bynoe, Sven Bönigk, Kari O. Bøifot, Hiram Caballero, Dayana Calderón, Angela Cantillo, M. Carbajo Carbajo, Alessandra Carbone, Anais Cardenas, Katerine Carrillo-Castro, Laurie Casalot, S Obredor Castro, Ana V. Castro, Astred Castro, Ana Valeria Castro, Simone Cawthorne, Jonathan Cedillo, Salama Chaker, Jasna Chalangal, Allison Chan, Anastasia I. Chasapi, Starr Chatziefthimiou, Sreya Ray Chaudhuri, Akash Keluth Chavan, Francisco Chavez, Gregory Chem, Michelle Chen, Jenn‐Wei Chen, Ariel Chernomoretz, Allaeddine Chettouh, Daisy Cheung, Diana Chicas, Shirley Chiu, Hira Choudhry, Carl Chrispin, Kianna Ciaramella, Erika Alejandra Cifuentes, Jake Cohen, David A. Coil, Sylvie Collin, Colleen Conger, Romain Conte, Flavia Corsi, Cecilia N. Cossio, Ana Flávia D.V. Costa, Delisia Cuebas, Bruno D’Alessandro, Katherine Dahlhausen, Aaron E. Darling, Pujita Das, Lucinda B. Davenport, Laurent David, Natalie R. Davidson, Gargi Dayama, Stéphane Delmas, Chris Deng, Chloé Dequeker, Alexandre Désert, Monika Devi, Felipe Segato Dezem, Clara N. Dias, Timothy Ryan Donahoe, S. Dorado, LaShonda Dorsey, V. A. Dotsenko, Steven Du, Alexandra Dutan, Naya A. Eady, Jonathan A. Eisen, Miar Elaskandrany, Lennard Epping, Juan Pablo Escalera-Antezana, Iqra Faiz, Luice Fan, Nadine Farhat, Emile Faure, Fazlina Fauzi, Charlie Feigin, Skye Felice, Laís Pereira Ferreira, Gabriel Figueroa, Aubin Fleiss, Denisse Flores, Jhovana L. Velasco Flores, Marcos A. Fonseca, Jonathan Foox, Juan Carlos Forero, Kelly French, 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, Nika Gurianova, Wolfgang Haehr, Sebastien Halary, Felix Hartkopf, Arya Hawkins-Zafarnia, Nur Hazlin Hazrin-Chong, Eric J. N. Helfrich, Éva Hell, Tamera Henry, Samuel Hernández, Pilar Hernández, David Hess-Homeier, 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, Badamnyambuu Iderzorig, Mizuki Igarashi, Shaikh B. Iqbal, Shino Ishikawa, Sakura Ishizuka, Riham Islam, Kohei Ito, Sota Ito, Takayuki Ito, Tomislav Ivanković, Tomoki Iwashiro, Sarah Jackson, 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, Gina Kim, Hyung Jun Kim, Sangwan Kim, Ryan J. King, Giuseppe KoLoMonaco, Ellen Koag, Nadezhda Kobko-Litskevitch, Maryna Korshevniuk, Michael Kozhar, Jonas Krebs, Nanami Kubota, A. V. Kuklin, Rachel Kwong, Lawrence N. Kwong, Ingrid Lafontaine, Juliana Lago, Tsoi Ying Lai, Élodie Laine, Manolo Laiola, Olha Lakhneko, Isha Lamba, Gerardo de Lamotte, Romain Lannes, Eleonora de Lazzari, Madeline Leahy, Hyunjung Lee, Yunmi Lee, Lucy Lee, Vincent Lemaire, Emily Leong, Marcus H.Y. Leung, Dagmara Lewandowska, Chenhao Li, Weijun Liang, Moses Lin, Priscilla Lisboa, Anna Litskevitch, Eric Minwei Liu, Tracy Liu, Mayra Arauco Livia, Yui Him Lo, 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, Roy A. Meoded, Nancy Merino, 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, Amanda L. Muehlbauer, Oasima Muner, Muntaha Munia, Naimah Munim, Maureen Muscat, Tatjana Mustac, Cristina Muñoz, Francesca Nadalin, Areeg Naeem, Dorottya Nagy-Szakal, Mayuko Nakagawa, Ashanti Narce, Masaki Nasu, Irene González Navarrete, Hiba Naveed, Bryan Nazario, Narasimha Rao Nedunuri, Thomas Neff, Aida Nesimi, Wan Chiew Ng, Synti Ng, Gloria Nguyen, Elsy Ngwa, Agier Nicolas, Pierre Nicolas, Abdollahi Nika, Hosna Noorzi, Avigdor Nosrati, Diana Noronha Nunes, Kathryn O’Brien, Niamh B. O’Hara, Gabriella Oken, Rantimi A. Olawoyin, Javier Quilez Oliete, Kiara Olmeda, Tolulope Oluwadare, Itunu A. Oluwadare, Nils Ordioni, Jenessa Orpilla, Jacqueline Orrego, Melissa Ortega, Princess Osma, Israel O. Osuolale, Oluwatosin M. Osuolale, M OTA, Francesco Oteri, Yuya Oto, Rachid Ounit, Christos Ouzounis, Subhamitra Pakrashi, Rachel Paras, Coral Pardo-Este, Youngja Park, Paulina Pastuszek, Suraj Patel, Jananan Pathmanathan, Andrea Patrignani, Manuel Toledano Pérez, 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, Stephen Eduard Boja Ruiz, Kaitlan Russell, Mariia Yu. Rybak, Thaís S. Sabedot, M.R. Sabina, Ikuto Saito, Yoshitaka Saito, Gustavo Adolfo Malca Salas, Cecilia Salazar, Kaung Myat San, Jorge Sánchez, Sanchir Khaliun, Ryan Sankar, Paulo Thiago de Souza Santos, Zulena Saravi, Kai Sasaki, Yuma Sato, Seisuke Sato, Ryo Sato, Kaisei Sato, Nowshin Sayara, Oli Schacher, Anna-Lena M. Schinke, Ralph Schlapbach, Christian Schori, Jason R. Schriml, Felipe Segato, Felipe D. Sepúlveda, Marianna Sampaio Serpa, Paola Flórez de Sessions, Juan C. Severyn, Heba Shaaban, Maheen Shakil, Heba Abdelhamid Shalaby, Aliyah Shari, Hyenah Shim, Hikaru Shirahata, Yuh Shiwa, Ophélie Da Silva, Jordana M. Silva, Gwenola Simon, Shaleni K. Singh, Kasia Sluzek, Rebecca Smith, Eunice So, Núria Andreu Somavilla, Yuya Sonohara, Nuno Rufino de Sousa, Camila Souza, Jason L. Sperry, Nicolas Sprinsky, Stefan G. Stark, Antonietta La Storia, Kiyoshi Suganuma, Hamood Suliman, Jill Sullivan, Arif Asyraf Md Supie, C. Suzuki, Sora Takagi, Fumie Takahara, Naoya Takahashi, Kou Takahashi, Tomoki Takeda, Isabella K. T. M. Takenaka, Soma Tanaka, Yuk Man Tang, Emilio Tarcitano, Andrea Tassinari, Mahdi Taye, Alexis Terrero, Eunice Thambiraja, Antonin Thiébaut, Sade Thomas, Andrew Maltez Thomas, Yuto Togashi, Takumi Togashi, A. Tomaselli, Masaru Tomita, Itsuki Tomita, 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, Laura Vann, Fabienne Velter, Valeria Ventorino, Patricia Vera-Wolf, Riccardo Vicedomini, Michael A. Suarez-Villamil, Sierra Vincent, Renee Vivancos-Koopman, Andrew Wan, Cindy X. Wang, Tomoro Warashina, Ayuki Watanabe, Samuel Weekes, Johannes Werner, David A. Westfall, 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, O.M. Yemets, Tetiana V. Yeskova, Shusei Yoshikawa, Laraib Zafar, Yang Zhang, Shu Zhang, Amy Zhang, Yuanting Zheng, Stanislav Zubenko
Bibliographic record
VenueCell · 2021
Typearticle
Languageen
FieldBiochemistry, Genetics and Molecular Biology
TopicGut microbiota and health
Canadian institutionsnot available
FundersClinical and Translational Science Center, Weill Cornell Medical CollegeNational Institute of Biomedical Imaging and BioengineeringNational Institute of Allergy and Infectious DiseasesNational Institute on Drug AbuseNational Center for Advancing Translational SciencesMedical Research CouncilWeill Cornell Medical CollegeHunter CollegeOffice of ScienceMinistry of Education and Science of UkraineYork UniversityMinistry of Education, IndiaJapan Society for the Promotion of ScienceJoint Genome InstituteKeio UniversityConselho Nacional de Desenvolvimento Científico e TecnológicoNational Cheng Kung UniversityMinisterio de Economía y CompetitividadGeneralitat de CatalunyaNational Institutes of HealthSchweizerischer Nationalfonds zur Förderung der Wissenschaftlichen ForschungWorldQuant FoundationNational Energy Research Scientific Computing CenterCity University of New YorkVallee FoundationAlfred P. Sloan FoundationNational Science FoundationBill and Melinda Gates FoundationEast China Normal UniversityNational Aeronautics and Space AdministrationNational Institute of General Medical SciencesCentres de Recerca de CatalunyaU.S. Department of EnergyPershing Square Sohn Cancer Research Alliance
KeywordsMetagenomicsBiologyGeospatial analysisMicrobiomeAntibiotic resistanceMicrobial geneticsComputational biologyEcologyGeneticsGeneBacteriaCartographyGeography
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.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
metaresearch head score (Codex)0.000
metaresearch head score (Gemma)0.000
Version: metacan-v3-hybrid-931329e0061cValidation status: machine_predicted_unvalidated
Candidate categoriesnone
Consensus categoriesnone
DomainCandidate signal: none · Consensus signal: none
Study designCandidate signal: Observational · Consensus signal: Observational
GenreCandidate signal: Empirical · Consensus signal: Empirical
Teacher disagreement score0.005
Threshold uncertainty score0.011
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.004 | 0.005 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.000 | 0.001 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.003 | 0.001 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
Opus teacher head0.005
GPT teacher head0.222
Teacher spread0.217 · how far apart the two teachers sit on this one work
Validation status
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
The models applied no category: nothing in the taxonomy fit this work.
Study designObservational
Domainnot available
GenreEmpirical
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".
Quick stats
Citations382
Published2021
Admission routes1
Has abstractyes