Just how many germs are on the subway?

If you've ever lived in a dense city with a busy subway like New York or Boston, you probably know enough to be scared of the creatures that inhabit the rumbling underground world.

I'm not talking about the smelly guy who stands just a little too close or the chatty woman who can't seem to stop herself from reading your private emails on your phone, but the microscopic life-forms on every turnstile, handhold and window.

Is this fear legitimate or misplaced?

Scientists have long considered the subway system an environment different from any other, but little is known about this ecosystem.

The mass transit systems of our megacities are considered increasingly important to public health as the human population grows, and so does the threat of antibiotic-resistant super germs, infectious viruses and even biological weapons. This is where many believe early detection of these potentially devastating perils may be possible.

The most infamous study on subway life was published last year about New York. The 18-month project involved mapping the DNA of the bacteria on the system. It claimed bubonic plague and anthrax were among the many pathogens lurking there.

That assertion was challenged by the Centers for Disease Control and Prevention and the state's health department, and a few months after it first came out, the authors issued a “corrected” paper saying that there was in fact “no strong evidence to suggest these organisms are in fact present.”

While the mistake was embarrassing, the rest of the study was considered solid and provided all kinds of important information about subways and, perhaps more importantly, inspired researchers in far-flung places from Stockholm to Hong Kong to do their own studies.

A team from Harvard set out to understand these microbial communities in their backyard of Boston. The Boston T is the country's oldest subway system, dating back to a single streetcar commissioned in 1897. It is now one of the most crowded in the world, providing 238 million trips per year.

Researcher Curtis Huttenhower said he became curious about what was down there after reading about other work being done to analyze bacteria in “built” or human-made spaces. Because these places are made of materials and chemistry that don't exist in nature, the life in those environments is heavily influenced by those microbes that live on humans.

Huttenhower, an associate professor of computational biology and bioinformatics, specializes in the study of the human microbiome — the set of organisms that are all over our bodies, inside and out. In recent years, scientists have come to have a new appreciation for how the balance or imbalance between the good or beneficial bugs and the bad ones affects our health and well-being.

A study last year found that people carry with them a cloud of bacteria that's as unique as a fingerprint and that you leave traces of it everywhere you go. And when you're in close quarters, like when you're packed into a subway car, those clouds crash into each other in unknown ways.

By better understanding the bugs around us as well as those on and inside us, Huttenhower said, we could one day build public spaces to optimize our microbial health.

“I wanted to take a look at the subway because of the link to the human microbiome. It's a place where thousands and thousand of people interact every day and it can be thought of as a conduit or reservoir for human microbes getting from one person to another,” he said.

Researchers spent three days traveling the network, taking swabs from seats, seat backs, walls, vertical and horizontal poles and hanging grips inside 15 train cars, and of touch screens and walls of ticketing machines inside five stations. They did their work in the spring and fall to get a better baseline reading that was less influenced by people being bundled up or the sticky heat of summer. Then they sequenced the DNA on these samples to try to figure out what was in the mix.

Their work, recently published in mSystems, an open access journal of the American Society for Microbiology, is considered to be first comprehensive genetic profile of the lifeforms on a high-volume public transportation system. There were some surprising findings.

First, little variation was seen between the train lines or stations despite the fact that they served different populations. They were also happy to find few bugs associated with antibiotic resistance. But the big news is that researchers found minimal microbes capable of causing disease.

Most of the bacteria came from normal human skin, our mouths, gut (ick) and, um, other places on our bodies. Those include Staphylococcoceae and Corynebacteriaceae, which are probably transferred through touch. There were also Micrococcaceae and Streptococcaceae from the oral cavity that tend to move from place to place through coughing or sneezing. There were low proportions of Lachnospiraceae, Veillonella and Prevotella from the gut. Researchers also found vaginal microbes, which can be transferred through clothing, on some seats.

In terms of non-human-associated life, there was Alphaproteobacteria, which exists mostly on plants, and Sphingomonads from soils and sediments. These were mostly on the outdoor touch screens. No plague, no anthrax or anything like that.

“The vast majority of the bugs you encounter in the subway that is thought of as a germy kind of place you'd encounter shaking someone's hand,” Huttenhower said. “You'd want to wash your hands, but it's not something that's more scary or dangerous.”

Except, he conceded, that it's more like you're shaking thousands of hands a day.

That means the diversity in the bugs is many times greater than, say, your kitchen counter or office door knob, which means there's still a lot more we need to learn about this world and how it influences our health.

Huttenhower said that it was hard to tell which bacteria were deposited, dormant or actively growing. He and his team will go back for more samples in the coming months to look at that question. He also said they plan to conduct research on how the microorganism mix changes during flu season when it's likely that more virulent bugs will show up.

The Harvard study also only involved life on surfaces. Two previous studies, in Hong Kong and New York, involved testing air and found more microbes originating from soil and the environment so it's likely there's a lot more in the Boston subway than this first study reveals.