Big Data and Bacteria: Mapping the New York Subway’s DNA Posted on : Feb 06 - 2015

Aboard a No. 6 local train in Manhattan, Weill Cornell researcher Christopher Mason patiently rubbed a nylon swab back and forth along a metal handrail, collecting DNA in an effort to identify the bacteria in the New York City subway.

In 18 months of scouring the entire system, he has found germs that can cause bubonic plague uptown, meningitis in midtown, stomach trouble in the financial district and antibiotic-resistant infections throughout the boroughs.

Frequently, he and his team also found bacteria that keep the city livable, by sopping up hazardous chemicals or digesting toxic waste. They could even track the trail of bacteria created by the city’s taste for pizza—identifying microbes associated with cheese and sausage at scores of subway stops.

The big-data project, the first genetic profile of a metropolitan transit system, is in many ways “a mirror of the people themselves who ride the subway,” said Dr. Mason, a geneticist at the Weill Cornell Medical College.

It is also a revealing glimpse into the future of public health.

Across the country, researchers are combining microbiology, genomics and population genetics on a massive scale to identify the micro-organisms in the buildings and confined spaces of entire cities.

Interactive: Mapping the Bacteria in New York’s Subways

Like Ebola or measles—detect bioterrorism attacks and combat the growing antibiotic resistance among microbes, which causes about 1.7 million hospital infections every year.

“We know next to nothing about the ecology of urban environments,” said evolutionary biologist Jonathan Eisen at the University of California at Davis. “How will we know if there is something abnormal if we don’t know what normal is?”

Dr. Mason and his research team gathered DNA from turnstiles, ticket kiosks, railings and benches in a transit system shared by 5.5 million riders every day. They sequenced the genetic material they found at the subway’s 466 open stations—more than 10 billion fragments of biochemical code—and sorted it by supercomputer. They compared the results to genetic databases of known bacteria, viruses and other life-forms to identify these all-but-invisible fellow travelers.

In the process, they uncovered how commuters seed the city subways every day with bacteria from the food they eat, the pets or plants they keep, and their shoes, trash, sneezes and unwashed hands. The team detected signs of 15,152 types of life-forms. Almost half of the DNA belonged to bacteria—most of them harmless; the scientists said the levels of bacteria they detected pose no public-health problem. Data from the PathoMap Project, as Dr. Mason calls it, was published online in the journal Cell Systems on Thursday.

As more and more scientists probe urban microbiology, they are also hoping to find ways to foster beneficial bacteria through building design and to learn how to eliminate construction practices that create living conditions for the germs that make people ill.

This emerging field reflects the growing awareness that the human body swarms with bacteria. Typically, every person is home to about a hundred trillion microbial cells bearing five million different genes, totaling about 5 pounds of micro-organisms per person. Indeed, microbes in and on the body outnumber human cells about 10 to one.

“You are a minority party in the democracy of the body,” Dr. Mason said.

The body’s collection of microbes, called the microbiome, influences health in ways that researchers are only beginning to understand. They may be key to proper digestion, vitamin synthesis and brain function, new research suggests. Changes among the millions of microbes living in the human stomach also may promote obesity, trigger ulcers or affect how well a flu vaccine works.

Broadly speaking, city living leaves its mark on people. That includes the sorts of microbes that collect inside them. A recent comparison of urban and rural residents in Russia found that city dwellers had different sets of stomach microbes than people in the countryside.

ENLARGE

Every person trails a distinctive collection of microbes, by shedding about 1.5 million microscopic skin cells every hour. Bacteria from a person’s body can colonize a hotel room in less than six hours, scientists at the U.S. Department of Energy’s Argonne National Laboratory in Illinois recently discovered.

“A city is like an organism,” said IBM Corp. computational biologist Robert Prill, who is among those at the company investigating ways to better collect and analyze these immense new public-health genome databases. “It has a circulating system consisting of the movement of people.”

In New York City, the Cornell scientists and student volunteers gamely dodged rats and gingerly worked around discarded pregnancy tests, used condoms, puddles of vomit and rotting food to swab surfaces in every subway station. On more than one occasion, suspicious police stopped them and escorted them to the street.

The subway findings might unsettle some people, Dr. Mason acknowledged, but he said they illustrate the remarkable microbial diversity of a healthy city. “I don’t want people to be terrified,” he said. “I want them to be intrigued.”

Large-scale microbe studies, called metagenomics, are made possible by recent advances in low-cost, high-speed gene sequencing machines that for the first time allow researchers to study millions of micro-organisms in the wild that normally can’t be grown in a laboratory. The Sloan Foundation in New York jump-started the field by funding 50 building-genome projects since 2005, although not the PathoMap survey.

How Scientists Wrangled 10 Billion Fragments of Genetic Code

In Oregon, researchers are mapping the ebb and flow of bacteria that inhabit the rooms of a busy classroom building. In Virginia, biologists are analyzing the microbes that live inside a building’s plumbing and drinking water pipes. In Chicago, scientists are documenting the microbial life of a new hospital, to see how bacteria in its offices, operating rooms and patient recovery areas changed as the health-care facility became operational.

Researchers are learning that quirks of building materials, ventilation systems, humidity and interior design affect the kinds of bacteria people encounter indoors.

Depending on the material involved, some surfaces can have thousands of different types of bacteria while others may have only a few hundred, researchers monitoring the new Chicago hospital found. Pathogens responsible for common infections, such as the strep germs that cause an estimated 700 million infections world-wide every year, can survive for months on a dry surface, researchers in Germany reported in September in the journal BMC Infectious Diseases.

Upholstery fabric can make a difference. Drug-resistant staph germs can live for up to a week on materials used for airplane seat pockets, while E. coli can last 96 hours on the covering used for an airliner armrest, researchers at Auburn University said at a meeting of the American Society of Microbiology last year.

Air conditioning matters too. Studies of indoor air quality at shopping centers in Singapore and homes in the United Arab Emirates revealed up to 300 distinct species of airborne bacteria, fungi and viruses carried through ventilation systems.

“Unintentionally, architects and engineers are creating ecosystems without much thought at all as to whether they are healthy or harmful to humans,” said biologist Jessica Green, director of the University of Oregon’s Biology and The Built Environment Center. “Different urban conditions might promote the growth of different microbial ecosystems.”

Researchers at the University of Chicago and the Argonne National Laboratory started installing a network of sensors throughout Chicago’s downtown that, among other things, will sample the air periodically for microbes. They hope to have 500 in place by next year and as many as 5,000 sensors when the monitoring system is completed.  View More