Mass-transit systems represent unique urban biomes, microbiomes, and metagenomes. These subterranean and above-ground structures are ubiquitous and the interactions between passengers and the subway surfaces define perhaps one of the world’s largest, high-traffic, and universal built environments. Also, these subway surfaces define the daily commute for millions of people every single day and billions of people each year. The microbiome constitutes an important element of our environment: bacterial cells in and on our bodies outnumber human cells by a 10:1 ratio, contribute as much as 36% of the active molecules present in the human bloodstream, and serve as a key mediator of human health. Yet, how humans may interact with (or acquire) new species of bacteria depends on the environment they are exposed to, the types of surfaces they touch, and the physical dynamics of their environment. This is especially true in dense, built environments such as cities, wherein the majority of the world’s population (54%) currently live.


In summer 2013, the Mason lab began a project called PathoMap, with a goal to profile the New York City metagenome in, around, and below NYC on mass-transit areas of the built environment, focusing on the subway. They sought to establish baseline profiles across the subway system, identify potential bio-threats, and provide an additional level of data that can be used by the city to create a “smart city;” i.e., one that uses high- dimensional data to improve city planning, management, and human health. Notably, nearly half of the DNA sequenced (48%) did not match any known organism, underscoring the vast wealth of likely unknown organisms that surround passengers every day. Nevertheless, the absence of diagnosed cases of these diseases in NYC helps dispel the common belief that a subway station needs to be “clean” and have no bacteria; rather, the station’s surfaces need only harbor non-dangerous levels of bacteria, and contain a healthy mixture of many species. However, NYC is not the only city in the world that could benefit from a systematic, longitudinal metagenomic profile of its subway system vis-à-vis the architecture. Although NYC subway has the most stations, it ranks 7th in the world in term of the number of riders per year. A wide variety of population density, length, and climate types define the busiest subways of the world, ranging from cold (Moscow) to temperate (New York City, Paris), to sub-tropical (Mexico City) and tropical (São Paulo).


To address this gap in our knowledge of the built environment, we have created an international consortium of laboratories to establish a world-wide “DNA map” of microbiomes in mass transit systems.


List of cities represented in the consortium:

North America

New York City, USA

Chicago, USA
San Francisco, USA
Sacramento, USA
Boston, USA
Washington DC, USA
Baltimore, USA
Fairbanks, USA
Denver, USA
Mexico City, Mexico

South America

Buenos Aires, Argentina
São Paulo, Brazil
Ribeiro Preto, Brazil
Rio de Janeiro, Brazil
Bogota, Colombia
Santiago, Chile
Montevideo, Uruguay

Lima, Peru








Auckland, New Zealand


Singapore, Singapore
Sendai, Japan
Beijing, China
Seoul, South Korea
Shanghai, China
Tokyo, Japan
Guangzhou, China
Hong Kong, China
Hyderabad, India

Taipei and Tainan, Taiwan

New Delhi, India
Doha, Qatar
Tehran, Iran
Izmir, Turkey

Thessalonica, Greece

Hanoi, Vietnam

Kuala Lumpur, Malaysia



Cairo, Egypt
Johannesburg, South Africa
Ilorin, Nigeria


Rome, Italy

Trenton, Italy
Oslo, Norway
Sheffield, UK
Lisbon, Portugal
Porto, Portugal
Paris, France
Marseilles, France
Barcelona, Spain
Vienna, Austria
Berlin, Germany

Dusseldorf, Germany
Stockholm, Sweden
Moscow, Russia

Novosibirsk, Russia
Zagreb, Croatia
London, UK

Kiev, Ukraine

Zurich, Switzerland

To read more about our hub cities, visit our city profiles.