Abstract
SUMMARYThe panoply of microorganisms and other species present in our environment influence human health and disease, especially in cities, but have not been profiled with metagenomics at a city-wide scale. We sequenced DNA from surfaces across the entire New York City (NYC) subway system, the Gowanus Canal, and public parks. Nearly half of the DNA (48%) does not match any known organism; identified organisms spanned 1,688 bacterial, viral, archaeal, and eukaryotic taxa, which were enriched for harmless genera associated with skin (e.g., Acinetobacter). Predicted ancestry of human DNA left on subway surfaces can recapitulate U.S. Census demographic data, and bacterial signatures can reveal a station’s history, such as marine-associated bacteria in a hurricane-flooded station. Some evidence of pathogens was found (Bacillus anthracis), but a lack of reported cases in NYC suggests that the pathogens represent a normal, urban microbiome. This baseline metagenomic map of NYC could help long-term disease surveillance, bioterrorism threat mitigation, and health management in the built environment of cities.
Highlights
The microbiome represents the diversity of the microorganisms present in an environment, and the human microbiome has been increasingly recognized as an integral component of human health and disease (Peterson et al, 2009)
Each sample was geotagged with longitude and latitude coordinates via global positioning system (GPS), time-stamped, and photo-documented, and collection fields were completed for data entry and included the swabbing time, the scientist performing the collection, and collection notes (Figure 1B)
This protocol enabled a built-in sample confirmation, wherein we could confirm that the sample ID of the swab in the laboratory matched the ID in the photo taken during the collection
Summary
The microbiome represents the diversity of the microorganisms present in an environment, and the human microbiome has been increasingly recognized as an integral component of human health and disease (Peterson et al, 2009). The subway of NYC is the largest mass-transit system in the world (by station count), spreading over 252 miles and used by 1.7 billion people per year (APTA Ridership Report, 2014) This vast urban ecosystem is a precious resource that requires monitoring to sustain and secure it against acts of bioterrorism, environmental disruptions, or disease outbreaks. We sought to characterize the NYC metagenome by surveying the genetic material of the microorganisms and other DNA present in, around, and below NYC, with a focus on the highly trafficked subways and public areas We envision this as a first step toward identifying potential bio-threats, protecting the health of New Yorkers, and providing a new layer of baseline molecular data that can be used by the city to create a ‘‘smart city,’’ i.e., one that uses highdimensional data to improve city planning, management of the mass-transit built environment, and human health
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