Chapter 1: The Fascination with Urban Microbiomes

Chris Mason, a geneticist at Weill Cornell Medicine, became intrigued by the microbial world when he observed his daughter interacting with surfaces on the New York City subway. His curiosity peaked when she licked a pole, prompting him to investigate further. “I was eager to uncover what had transpired,” he noted.

To delve deeper into this microbial ecosystem, Mason initiated a project that involved swabbing various surfaces on the subway to analyze the diversity of microbes inhabiting these public spaces. Following a groundbreaking study in 2015 that unveiled numerous unknown species in New York City, researchers from around the globe reached out to him for collaboration. This led to an extensive investigation across 60 cities, including Baltimore, Bogotá, and Seoul, uncovering thousands of previously unrecognized viruses and bacteria. The findings showcased that each city possesses its own unique microbial “fingerprint.”

According to Adam Roberts, a microbiologist at the Liverpool School of Tropical Medicine, who was not part of the study, this discovery is “remarkable.” While previous research has focused on individual cities or transit systems, this comprehensive study offered insights on a much larger scale, paving the way for future inquiries. “They have done an extraordinary job compiling this data,” he added, suggesting that it will serve as a valuable resource for years to come.

Section 1.1: Methodology of Urban Sampling

Before Mason and his team could create a global overview of transit microbiomes, they had to devise a method for consistent sample collection. They opted to swab benches, turnstiles, and ticket kiosks—common features of transport systems worldwide. “It strikes an ideal balance between DNA extraction efficiency and social comfort,” Mason explains.

Researchers spent three minutes swabbing surfaces, allowing sufficient time to collect DNA without causing discomfort to themselves or onlookers.

Subsection 1.1.1: Surprising Discoveries

The analysis revealed that approximately 45% of the samples comprised microbes not previously classified: nearly 11,000 viruses and 1,302 bacteria were identified for the first time. Among the findings, 31 species appeared in 97% of the samples, forming a “core” urban microbiome. Additionally, 1,145 species were detected in over 70% of the samples. Interestingly, surfaces frequently touched by people, like railings, showed a higher prevalence of bacteria associated with human skin, alongside bacteria common in soil, water, and dust.

Chapter 2: The Implications of Urban Microbial Diversity

Mason's research team also identified less common species, which contributed to the unique microbiome of each city. Their findings enabled them to accurately determine the origin of random samples with 88% precision. For instance, New York City exhibited a notable presence of Carnobacterium inhibens, a lactic acid-producing bacterium that thrives in low temperatures. Mason believes that these distinct urban microbial signatures could potentially serve forensic purposes with further investigation.

Moreover, Noah Fierer, a microbiologist at the University of Colorado, Boulder, emphasized the significance of the accessible data available at metagraph.ethz.ch. This allows other researchers to explore new questions regarding urban microbiology. “Cities host diverse microbial communities,” he noted, questioning the underlying reasons for these variations.

Although concerns about bacteria in urban areas persist, Mason reassures that the microbes found are generally harmless. He noted that antimicrobial resistance genes were found in much lower concentrations in transit samples compared to those collected from human guts or hospitals.

Mason perceives public transportation systems as a remarkable reservoir of biodiversity, offering opportunities for “wonder and enthusiasm.” He believes that the newly identified species could have potential applications in drug development, and that systematic monitoring of urban microbiomes could enhance public health by facilitating early detection of emerging infections.

“Until recently, monitoring urban microbiomes would have seemed like a peculiar and costly endeavor,” Mason stated. However, he now recognizes its immense value. He speculated, “What if we had been monitoring RNA in samples worldwide? We might have detected the pandemic coronavirus earlier.”

The first video titled "How Your City Has Its Own Unique Microbiome" explores the distinct microbial communities present in urban areas and their implications for public health.

The second video titled "This Video May Contain Germaphobic Material" discusses common misconceptions about urban bacteria and their actual risks to human health.