iScience (Nov 2022)
A history of the MetaSUB consortium: Tracking urban microbes around the globe
- Krista A. Ryon,
- Braden T. Tierney,
- Alina Frolova,
- Andre Kahles,
- Christelle Desnues,
- Christos Ouzounis,
- Cynthis Gibas,
- Daniela Bezdan,
- Youping Deng,
- Ding He,
- Emmanuel Dias-Neto,
- Eran Elhaik,
- Evan Afshin,
- George Grills,
- Gregorio Iraola,
- Haruo Suzuki,
- Johannes Werner,
- Klas Udekwu,
- Lynn Schriml,
- Malay Bhattacharyya,
- Manuela Oliveira,
- Maria Mercedes Zambrano,
- Nur Hazlin Hazrin-Chong,
- Olayinka Osuolale,
- Paweł P. Łabaj,
- Prisca Tiasse,
- Sampath Rapuri,
- Silvia Borras,
- Sofya Pozdniakova,
- Tieliu Shi,
- Ugur Sezerman,
- Xavier Rodo,
- Zehra Hazal Sezer,
- Christopher E. Mason
Affiliations
- Krista A. Ryon
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY USA; Weill Cornell Medicine, New York, NY, USA
- Braden T. Tierney
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY USA; Weill Cornell Medicine, New York, NY, USA
- Alina Frolova
- Institute of Molecular Biology and Genetics of NASU, Kyiv, Ukraine; Kyiv Academic University, Kyiv, Ukraine
- Andre Kahles
- ETH Zurich, Zurich, Switzerland
- Christelle Desnues
- Mediterranean Institute of Oceanography, 163 Avenue de Luminy Bâtiment Méditerranée, 13288, Marseille Cedex 9, France
- Christos Ouzounis
- Aristotle University of Thessalonica & CERTH, Thessaloniki, Greece
- Cynthis Gibas
- University of North Carolina, Charlotte, NC, USA
- Daniela Bezdan
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany; GermanyNGS Competence Center Tübingen (NCCT), University of Tübingen, Tübingen, Germany; yuri GmbH, Meckenbeuren, Germany
- Youping Deng
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96813, USA
- Ding He
- University of Copenhagen, Copenhagen, Denmark
- Emmanuel Dias-Neto
- AC Camargo Cancer Center, Sao Paulo, Brazil
- Eran Elhaik
- Lund University, Lund, Sweden
- Evan Afshin
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- George Grills
- University of Miami, Miami, FL, USA
- Gregorio Iraola
- Institut Pasteur de Montevideo, Mataojo 2020, Montevideo, 11400, Uruguay
- Haruo Suzuki
- Keio University, Tokyo, Japan
- Johannes Werner
- High Performance and Cloud Computing Group, Zentrum für Datenverarbeitung (ZDV), Eberhard Karls University of Tübingen, Tübingen, Germany
- Klas Udekwu
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
- Lynn Schriml
- University of Maryland School of Medicine, University of Maryland, Baltimore, MD, USA
- Malay Bhattacharyya
- Indian Statistical Institute, Kolkata, India
- Manuela Oliveira
- University of Porto, Porto, Portugal
- Maria Mercedes Zambrano
- Corporación Corpogen, Bogotá, Columbia
- Nur Hazlin Hazrin-Chong
- Universiti Kebangsaan Malaysia, Bangi, Malaysia
- Olayinka Osuolale
- Elizade University, Ilara-Mokin, Nigeria
- Paweł P. Łabaj
- MCB Jagiellonian University, Kraków, Poland
- Prisca Tiasse
- MCB Jagiellonian University, Kraków, Poland
- Sampath Rapuri
- The Community Lab; Los Alamos Makers, Los Alamos, NM 87544, USA
- Silvia Borras
- Barcelona Institute for Global Health, Rosselló, 132, 708036 Barcelona, Spain
- Sofya Pozdniakova
- Barcelona Institute for Global Health, Rosselló, 132, 708036 Barcelona, Spain
- Tieliu Shi
- East China Normal University, Zhongshan Rd (N), 3663, 200050 Shanghai, Putuo, China
- Ugur Sezerman
- Department of Biostatistics, Acibadem University, Istanbul, Turkey
- Xavier Rodo
- Barcelona Institute for Global Health, Rosselló, 132, 708036 Barcelona, Spain
- Zehra Hazal Sezer
- University of Tübingen, Tübingen, Germany
- Christopher E. Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA; WorldQuant Initiative for Quantitative Prediction, New York, NY, USA; Corresponding author
- Journal volume & issue
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Vol. 25,
no. 11
p. 104993
Abstract
Summary: The MetaSUB Consortium, founded in 2015, is a global consortium with an interdisciplinary team of clinicians, scientists, bioinformaticians, engineers, and designers, with members from more than 100 countries across the globe. This network has continually collected samples from urban and rural sites including subways and transit systems, sewage systems, hospitals, and other environmental sampling. These collections have been ongoing since 2015 and have continued when possible, even throughout the COVID-19 pandemic. The consortium has optimized their workflow for the collection, isolation, and sequencing of DNA and RNA collected from these various sites and processing them for metagenomics analysis, including the identification of SARS-CoV-2 and its variants. Here, the Consortium describes its foundations, and its ongoing work to expand on this network and to focus its scope on the mapping, annotation, and prediction of emerging pathogens, mapping microbial evolution and antibiotic resistance, and the discovery of novel organisms and biosynthetic gene clusters.
