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Second-year Medical Student Ebrahim Afshinnekoo: DNA-Mapping the World

Mr. Afshinnekoo collected DNA data from subway stations to study the microbiome and create a molecular portrait of New York City

July 18, 2016

In the summer of 2013, Ebrahim Afshinnekoo spent an extraordinary amount of time riding the rails of the New York City subway system, visiting far-reaching corners of the metropolis once, then twice, then thrice.  Mr. Afshinnekoo was one of a team of five undergraduate interns collecting DNA data from all 468 NYC subway stations and trains to study the microbiome and create a molecular portrait of New York City. 

The self-proclaimed “Swab Squad” collected more than 1,500 DNA samples from benches, turnstiles, railings and seats on trains and stations using nylon swabs for three minutes at each spot. In total there were three swabs collected from each station/train. They were working in the functional genomics lab of Christopher E. Mason, Ph.D., associate professor in Weill Cornell Medicine’s Department of Physiology and Biophysics, working on the PathoMap Project.  The goal of the effort was to “establish a baseline profile across the subway system, identify potential bio-threats, and provide an additional level of data that can be used by the city to create a “smart city;” one that uses high-dimensional data to improve city planning, management, and human health.

The results of the NYC study were published in an article in Cell Systems in July 2015.  

“It was quite the interesting summer internship experience,” says Mr. Afshinnekoo. I had the chance to explore the city in a way I never did before and had the opportunity to have some delicious food along the way. Plus, you can write a whole paper on the social dynamics of swabbing. When we were collecting samples from the Manhattan stations, I received the most questions and curiosity from fellow riders.”

Since that outset, both the project—and Mr. Afshinnekoo’s role on it—have grown exponentially.  Rather than retiring at summer’s end when he returned to his junior year at Macaulay Honors College at Queens College, Mr. Afshinnekoo remained active and engaged, extracting DNA from the samples collected and helping coordinate the study and volunteers. Eventually he became director of the study and, more recently, co-founder of The International Metagenomics and Metadesign of Subways and Urban Biomes (MetaSUB) Consortium.

MetaSUB is a collective of laboratories, microbiologists, bioinformaticians, engineers, architects, designers, geneticists, urban planners and others in approximately 56 cities globally, established to explore the microbiome and metagenomics at the city scale and create a world-wide “DNA map” of mass transit systems and urban biomes around the world.

This June, MetaSUB launched the first Global City Sampling Day, in which teams of scientists across the globe collected samples from their respective transit systems and other public areas. Approximately 6,000 samples have been banked to date. MetaSUB is also launching the Olympiome Project which seeks to look at the dynamics of the microbiome before, during and after massive events like the Olympics, where millions of people from around the world come to one place. The Olympiome study launches this August with the 2016 Olympic Games in Rio de Janeiro and will be compared with the 2020 Olympics in Tokyo. 

“One of my favorite things about MetaSUB is that it is so open to outreach and education, two of my passions,” says Mr. Afshinnekoo. “It is also an incredible time to be a scientist, especially in genetics and genomics. The cost and development of sequencing technology is advancing so rapidly, it is empowering us to explore and sequence the world around us.”

Back at NYMC, Mr. Afshinnekoo, is looking forward to his second year of medical school and to integrating his MetaSUB work with his studies. “Sequencing is changing the medical field. The whole notion of precision medicine is to integrate sequencing results and incorporate any data generated about a patient into the medical treatment and care of that patient. There are more and more areas where data is being integrated such as precision public health, precision wellness, and even precision microbiome. I’m particularly interested in the clinical applications of the microbiome and metagenomics, integrating it with the current approaches in clinical microbiology and pathology. I’m also really interested in going through the microbiology course this fall and adding a column to my notes that says, 'Did we see it in the subway?'