The city is a microbe jungle
02/10/2015 // Specials // Photo: Shutterstock // Video: TakeIt Media

Any place where people live will also abound with microorganisms. Most of these are harmless, but some viruses or bacteria can be dangerous to us. A team of researchers from New York therefore wanted to know more precisely what it is that we surround ourselves with every day. The idea for the PathoMap was born – an interactive map of the microbiome in the metropolis of million people. To this end, the team collected samples from all subway stations in the city and analyzed their genetic makeups. And this led to surprising results.

For microbiologists, the New York subway is a fascinating habitat: 1.7 billion people pass through it every year, and therefore so do countless bacteria, viruses and fungi, which form a complex ecosystem. Understanding this ecosystem more accurately it could one day help to identify health risks early on and thereby prevent major outbreaks. In order to do this, the team around director of studies Christopher Mason from Weill Cornell Medical College in New York went deep into the city’s complex subway system, armed with cotton swabs, and, over a number of months, collected a total of 1,457 swabs from hand rails, stairs and even trash cans. The researchers were fastidious in their work; after all, they were not looking for one particular pathogen, but all detectable microorganisms. What is the “normal distribution” of pathogens? Which DNA is present naturally? Questions that can only be answered with a large-scale genetic analysis.

In the laboratory, the samples were sequenced with the help of QIAGEN technologies, such as the GeneRead Library I Core Kits, and the findings were then mapped in the PathoMap – with some astonishing results. For example, the researchers probably hadn’t expected beforehand that a subway station would still have genetic similarities to a maritime environment two years after flooding because of Hurricane Sandy. The human DNA from each area of the city was found to match the neighborhood’s U.S. Census Data (alleles for human ancestry) and hundreds of species of bacteria and viruses were found across the city.

“The presence of these microbes is proof of the effectiveness of our immune system as well as our inherent ability to continuously adapt to our environment,” comments the head of the study, Christopher Mason, who, by his own account, continues to use the subway and doesn’t see any danger to people’s health. The vast majority of the 637 microorganisms identified are harmless inhabitants of the subway ecosystem, such as lactic acid bacteria, which ferment sauerkraut, but are not dangerous to humans. Only twelve percent of the bacteria found can make people sick. The fact that almost half of the DNA sequences analyzed could not be allocated to any known organism at all also opens up fascinating prospects for research.

There is therefore still plenty for the researchers to explore, if nothing else because more than 2,000 samples are still waiting to be analyzed. The next step has also been decided on: The study is going to be carried out in 16 other cities worldwide. To learn more, please visit or watch the scientific talk by Dr. Mason listed below.

"Genomic Landscapes in Single Cells, Entire Cities, and the International Space Station" from QIAGEN on Vimeo.