Uncovering the Microbial World: Mapping the Microbiome of New York City’s Subway System and Beyond
In a world where microscopic organisms are all around us, it’s easy to overlook the vast diversity of bacteria, fungi, and viruses that coexist with humans in urban environments. But for geneticist Christopher Mason, a simple incident involving his 3-year-old daughter licking a subway pole sparked a curiosity that led to an ambitious project: mapping the microbiome of New York City’s subway system.
Mason, a researcher at Weill Cornell Medicine, launched the project in 2013, sending out a team of students armed with gloves, vials, and sterile Q-tips to sample various surfaces in the subway system. They collected environmental DNA (eDNA), which represents the genetic material shed by humans, animals, and microorganisms as they go about their daily lives. This eDNA provided insights into the unseen biological diversity of the city, revealing over 1,600 different types of microbes, including known pathogens like Bubonic plague and anthrax.
Fast forward to late 2019, when news of a mysterious pneumonia-like disease circulating in China reached Mason and his colleagues. As the disease, now known as Covid-19, began spreading across the globe, the subway swabbers found themselves on the front lines of monitoring its presence in transit systems, hospitals, and even wastewater. Their project took on a new medical focus, with protocols and tools that could be deployed anywhere.
The Covid-19 pandemic has highlighted the need for advanced technologies to detect and monitor pathogens in real-time. The field of eDNA research has seen significant advancements in recent years, allowing scientists to sample from various sources such as soil, water, and even air to survey the presence of thousands of microbial species. Wastewater surveillance has emerged as one of the most effective methods for monitoring population-level virus spikes, providing early detection and containment measures.
Researchers like Erik Karlsson, a virologist at Institut Pasteur du Cambodge, are working towards developing an early warning system for emerging pathogens. By monitoring high-risk areas where humans and animals interact, such as wet markets and forests, scientists aim to identify potentially threatening pathogens before they spill over into humans or cause outbreaks in different animal species.
Studies have shown that over 70 percent of infectious diseases that emerged in the 21st century originated from wildlife. Deforestation, human development, and hunting in remote areas have created hotspots for zoonotic diseases, where animals and humans come into close contact. By surveying large swaths of forest and collecting eDNA samples from animal carcasses and feces, researchers hope to detect the presence of pathogens like Ebola and educate communities to minimize the risk of exposure.
Southeast Asia, with its population growth, deforestation, and expansion of farming, has become another major hotspot for zoonotic diseases. Scientists are using air sampling and portable devices to detect viruses in high-risk areas such as live bird markets. The ability to collect samples remotely and process them on the spot is crucial for rapid response to outbreaks.
Wastewater surveillance has also proven invaluable in tracking disease spikes and identifying new variants of Covid-19. By testing wastewater samples, health officials can pinpoint areas of high viral circulation and advise the public to take necessary precautions. However, privacy concerns and ethical considerations surrounding the use of wastewater data remain a challenge.
Mason’s work in mapping New York City’s microbiome has inspired scientists worldwide to swab their own cities and create a global network known as the MetaSUB consortium. By sequencing microbial DNA and creating a worldwide reference library, researchers hope to identify new pathogens, track antibiotic resistance, and develop a comprehensive disease surveillance system.
The ultimate goal is to have a global disease surveillance system on par with weather forecasting, where microbial data feeds into real-time maps to identify emerging disease patterns and aid response plans. The lessons learned from the Covid-19 pandemic have emphasized the need for proactive pathogen surveillance to prevent future outbreaks and minimize the economic impact of shutdowns.
As Mason puts it, “money spent on pathogen surveillance is much cheaper than a shutdown of the entire economy.” The advancements in eDNA research and the development of new technologies bring us closer to a world where we can detect and respond to emerging pathogens before they become widespread threats.
