Making a microbe subway map

It was summer in the city. During the long, hot afternoons, high school scientists darted in and out of New York City’s subway stations. At each one, they pulled out cotton swabs and carefully swiped surfaces. They took samples from subway seats, poles, doors, turnstiles, ticket machines — even garbage cans. The students then put each in a plastic container and labeled it. Afterward, they raced back to grow the microbes from those samples in a laboratory at Rockefeller University in New York City.

These teens were not taking part in an episode of CSI. They were collecting data that would be used to create a new type of subway map. But instead of charting station sites, this project mapped microbes. Two of the students didn’t just collect samples. They also showed that while most of the germs living on the subway poles and turnstiles are harmless, a few types can resist the drugs medicine has devised to kill them.

Microbes surround us. Indeed, they are part of us. There are ten times more microbial cells than human cells in the human body. But scientists have only recently started to investigate our microbiota — the microbes that live on us and throughout our environment. By finding out what kinds of microbes we share spaces with, scientists may one day be able to predict or prepare for disease outbreaks.

 “I live in Long Island [N.Y.], and I’m always taking the subway,” says Ebrahim Afshinnekoo. He is a college student at City University of New York Queens College. While doing research at Weill Cornell Medical College, also in New York City, he began working with PathoMap. It’s the subway-swapping project. At each stop, a group of scientists took a sample from the poles and seats inside a train car. They also took two samples from the station. Those station samples could come from ticket kiosks, benches, turnstiles, stair railings or anything else.

“An old man said we were the strangest thing he’d ever seen on the subway. And he’d lived in New York City for 50 years,” notes Anya Dunaif, 17. She’s a senior at St. Anne’s School in New York City. She was one of seven high school students that helped collect samples for the project. “We had boys ask us if we were part of Mythbusters or if we were looking for criminal fingerprints,” the teen recalls.

Back in the lab, the scientists used a process to ”read” the specific sequence of building blocks occurring in long spans — known as sequences — of the germs’ DNA. Each species’ genes contain sequences unique to them. Isolating those sequences from the swabs could identify which species left their traces behind in the subway.

In all, the scientists identified genes from 1,688 different organisms. This genetic material came from bacteria, archaea (another type of single-celled organism) and viruses. There was also genetic debris left by other species — from cucumbers to subway rats, and of course, people. The researchers published their findings March 3 in the journal Cell Systems.

Anya was most interested in the bacteria. She was doing summer research with Jeanne Garbarino, who directs the Rockefeller University Summer Science Research Program. Anya and another student, Nell Kirchberger, wanted to find out if any of the subway bacteria displayed antibiotic resistance. That’s an ability to survive exposure to the antibiotics designed to kill them.

“I saw the microbiome studies as a chance to be able to provide high school students with a huge breadth of scientific experience,” says Garbarino.

The students swabbed surfaces at four subway stations. Then they stored the cotton in a broth that provides food to keep microbes alive. Once they had the samples in the lab, they wiped the swabs carefully across plates filled with agar. A gelatinous material from algae, agar is used to feed bacteria living in the lab. Some of the subway bacteria grew into colonies on these plates. The students then tested the ability of those germs’ to withstand four different antibiotics.

The drugs quickly killed most of the bacteria. But 28 percent resisted at least one of the medicines. “Antibiotic resistance is something that’s becoming a lot more dangerous,” Anya says. “If people are being exposed to dangerous bacteria it’s important to know.”

Just because the resistant germs are present does not mean that taking the subway will make riders sick. Most of the identified germs do not cause illness. Only low numbers of disease-causing bacteria turned up, so subway riding likely poses few risks for healthy people. Bottom line, Afshinnekoo says: “No New Yorker needs to be worried.”

But after putting together this first picture of what a “normal” city looks like, now “we need a field guide for microbes,” says Jonathan Eisen. “We need to know what to expect in particular places.” Eisen studies microbes and their diversity at the University of California, Davis. He says that knowing what the microbial population looks like under normal conditions would allow scientists to see how the microscopic ecosystem changes in response to climate change or something like a flu outbreak.

Meanwhile, plenty of mystery remains. The scientists could not even identify close to half of the species — 48.3 percent — that had left their DNA behind. But that’s also not a big surprise. Many of the organisms that could have shed DNA — such as cockroaches — have not had their genes sequenced yet. So no one knows what to look for. There also are many types of microbes surrounding us that scientists have never investigated.

Eisen hopes that with studies like this “people will start thinking about how they are surrounded by a world of microbes.” And most of the time, that’s not a bad thing at all.  

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Power Words

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agar A gelatinous material made from certain marine algae used as a material (and food source) in which to grow bacteria.

antibiotic  A germ-killing substance prescribed as a medicine (or sometimes as a feed additive to promote the growth of livestock). It does not work against viruses.

archaeon  (plural archaea) A domain of life that includes single-celled organisms. Although archaea superficially resemble bacteria, they are distinct. Archaea inhabit many harsh environments.

bacterium (plural bacteria)  A single-celled organism. These dwell nearly everywhere on Earth, from the bottom of the sea to inside animals.

DNA  (short for deoxyribonucleic acid) A long, double-stranded and spiral-shaped molecule inside most living cells that carries genetic instructions. In all living things, from plants and animals to microbes, these instructions tell cells which molecules to make.

DNA sequencing  The process of determining the exact order of the paired building blocks — called nucleotides — that form each rung of a ladder-like strand of DNA. There are only four nucleotides: adenine, cytosine, guanine and thymine (which are abbreviated A, C, G and T). And adenine always pairs up with thymine; cytosine always pairs with guanine.

ecosystem  A group of interacting living organisms — including microorganisms, plants and animals — and their physical environment within a particular climate. Examples include tropical reefs, rainforests, alpine meadows and polar tundra.

gene   (adj. genetic) A segment of DNA that codes, or holds instructions, for producing a protein. Offspring inherit genes from their parents. Genes influence how an organism looks and behaves.

journal  (in science) A publication in which scientists share their research findings with the public. Some journals publish papers from all fields of science, technology, engineering and math, while others are specific to a single subject. The best journals are peer-reviewed: They send out all submitted articles to outside experts to be read and critiqued. The goal, here, is to prevent the publication of mistakes, fraud or sloppy work.

microbe  Short for microorganism. (see microorganism)

microbiota  The microorganisms that live in a particular place or geological period.

microorganism  A living thing that is too small to see with the unaided eye, including bacteria, some fungi and many other organisms such as amoebas. Most consist of a single cell.

outbreak   The sudden emergence of disease in a population of people or animals. The term may also be applied to the sudden emergence of devastating natural phenomena, such as earthquakes or tornadoes.

resistance    (as in drug resistance) The reduction in the effectiveness of a drug to cure a disease, usually a microbial infection. (as in disease resistance) The ability of an organism to fight off disease. (as in exercise)  A type of rather sedentary exercise that relies on the contraction of muscles to build strength in localized tissues.

virus  Tiny infectious particles consisting of RNA or DNA surrounded by protein. Viruses can reproduce only by injecting their genetic material into the cells of living creatures. Although scientists frequently refer to viruses as live or dead, in fact no virus is truly alive. It doesn’t eat like animals do, or make its own food the way plants do. It must hijack the cellular machinery of a living cell in order to survive.