CosmosID and MetaSUB Consortium Announce Global Collaboration for Studying Anti-Microbial Resistance and Urban Metagenomics Across 54 Cities

June 21, 2016. Rockville, Maryland and New York City, New York

Today, CosmosID announced a collaboration with Weill Cornell Medicine to support a global study involved in exploration of the microbial community diversity, characterization of  anti-microbial resistance (AMR) genes and the discovery of new biosynthetic gene clusters (BGCs) from cities around the world. CosmosID’s computational tools and curated genome databases will be used for accurate and precise identification of microbial community composition and AMR markers.  CosmosID has analyzed over 20,000 biological samples from various sources that range from human, animal, plant, water, and soil using their database comprising more than 65,000 microbial genomes, including bacteria, viruses, fungi, parasites, and antibiotic resistance and pathogenicity markers.

The global study is a Grand Challenges Explorations winner, an initiative of the Bill & Melinda Gates Foundation that seeks to foster innovation to solve key global health and development problems.  The International MetaSUB Consortium (Metagenomics and Metadesign of Subways and Urban Biomes) will map the unseen genomes and epigenomes of 54 of the world’s cities beginning on June 21, 2016, in what has been called Global City Sampling Day (CSD).  This coordinated sampling day and data collection is also synchronized with the Global Ocean Sampling Day (OSD) Project, thus providing a “genetic snapshot” of the world’s cities and oceans at the same time. 

The MetaSUB Consortium plans a five-year, 54-city study, coordinated across six continents and 32 countries, with planned sampling of high-traffic areas across city subway systems, buses, and parks. Current cities include Buenos Aires, Sydney, Vienna, Ribeirão Preto, Rio Da Janeiro, São Paulo, Santiago, Beijing, Guangzhou, Hong Kong, Shanghai, Bogota, Zagreb, Cairo, Marseille, Paris, Berlin, Hyderabad, New Delhi, Tehran, Rome, Sendai, Tokyo, Mexico City, Auckland City, Ilorin, Lagos, Oslo, Lisbon, Porto, Doha, Moscow, Singapore, Johannesburg, Seoul, Barcelona, Stockholm, Zurich, Izmir, Sheffield, Montevideo, Baltimore, Boston, Chicago, Denver, Fairbanks, New York City, Sacramento, San Francisco, Seattle, Washington DC, Sheffield, and London.

The 2016 Olympics in Rio de Janeiro will also feature a measurement of the city’s metagenome response to the “natural experiment” of a global human migration event, when an estimated 1 million people attend the Olympics.  Sampling will occur before, during, and after the 2016 Olympics, and collections for RNA and DNA will be prepared to look also for the presence of any RNA viruses (e.g. Influenza and Zika). In some cities (e.g. NYC, Boston, Montevideo) orthogonal data will be generated from sewer systems and beaches, and also compared to the OSD data. These data, methods, techniques, and analysis results will all be made open to the public and free for all to use.

Participating funding agencies and Foundations include the Alfred P. Sloan Foundation (2015-13964) for the meetings, and for the sample collections the Clinical and Translational Science Center (CTSC), the Irma T. Hirschl and Monique Weill-Caulier Charitable Trusts, the WorldQuant Foundation, the Bert L and N Kuggie Vallee Foundation, and support from the National Institutes of Health (F31GM111053, R01NS076465, and R25EB020393). Industry partners in the project include CosmosID, GISCloud, QIAGEN, Illumina, Promega, and Copan.  The Phase I, GCE Grant entitled “Global Distribution and Epigenetic Stratification of Anti-Microbial Resistance (AMR)”was awarded to Weill Cornell Medicine and Principal Investigator (PI) Christopher Mason, Ph.D.; Co-Investigators in New York City include Eric Schadt, Ph.D. from the Icahn School of Medicine at Mount Sinai and Martin Blaser, M.D., of New York University (NYU), as well as principal investigators around the world. . For more information, please visit or