DNA was collected from turnstiles, benches, hand railings, trashcans and kiosks in all of NYC's subway stations.
Increasingly, scientists are coming to believe that the diversity of micro-organisms in the human habitat make a vital contribution to human health. Within the average human can be found 10 times as many microbes as human cells, which process more than a third of the small molecules in the human bloodstream. This microbiome is believed to help in resisting infections, controlling obesity risk and regulating metabolic rates.
However, scientists know little about the microbial communities found in public areas, transport systems, streets and buildings.
In an attempt to map the microbiome of an entire city, researchers from Weill Cornell Medical College in New York, NY, joined with investigators from five other New York City medical centers and spent 17 months collecting - in triplicate - DNA from turnstiles, benches, hand railings, trashcans and kiosks in all of New York City's open subway stations. Nylon swabs were also used to collect samples from the train interiors - seats, doors, poles and handrails.
Using a purpose-built mobile app, the researchers were able to time stamp each sample, tag it using a global positioning system and log the data in real time. Of more than 4,200 DNA samples collected, 1,457 have been sequenced and analyzed so far.
The majority of the DNA harvested across the samples - 48.3% - did not match any known organisms. The researchers say this "underscores the vast wealth of unknown species that are ubiquitous in urban areas."
The study's senior investigator, Dr. Christopher E. Mason, reassures that these unidentifiable microbes are unlikely to be harmful to human health:
"Our data show evidence that most bacteria in these densely populated, highly trafficked transit areas are neutral to human health, and much of it is commonly found on the skin or in the gastrointestinal tract. These bacteria may even be helpful, since they can out-compete any dangerous bacteria."
The most commonly identified organisms were bacteria (46.9%). Viruses were relatively rare (.032%), but as some seasonal viruses are RNA - rather than DNA - viruses, they would not have shown up in this study.
Most of the subway bacteria (57%) have never been linked with disease in humans. However, 31% of the bacteria were considered to be "opportunistic bacteria," which could cause illness in people who have a compromised immune system, and the remaining 12% were considered to "have some evidence of pathogenicity."
The Bronx - followed by Brooklyn, Manhattan and Queens - was found to host the most diverse array of microbes, with Staten Island being the least diverse.
Plague and anthrax samples showed no indication of being alive
Perhaps most intriguingly, the researchers collected two samples containing DNA fragments of Bacillus anthracis (anthrax) and a plasmid associated with Yersinia pestis (Bubonic plague).
These DNA traces were found at very low levels and there was no indication these microbes were alive.
"Despite finding traces of pathogenic microbes, their presence isn't substantial enough to pose a threat to human health," Dr. Mason says. "The presence of these microbes and the lack of reported medical cases is truly a testament to our body's immune system, and our innate ability to continuously adapt to our environment."
Dr. Mason considers the findings of the "PathoMap" study to be generally reassuring and says there is no need for anyone to avoid using the subway system or begin using protective gloves.
"PathoMap also establishes the first baseline data for an entire city, revealing that low levels of pathogens are typical of this environment," he adds. "While this is expected in rural environments, and also present in livestock, we've never seen these levels before in cities. We can now monitor for changes and potential threats to this balanced microbial ecosystem."