What germs are in the subways and where? A first of its kind study created an interactive map to answer that question. But the Health Department is slamming the results. NY1’s Lori Chung spoke with the author of the study and with straphangers.

"I'm always worried about germs so I always carry a mini bottle of Purell at all times,” said one straphanger.

But a new study suggests some microbes in the subway system may actually be doing some of the anti-bacterial work for you.

“We found that the majority of the organisms around us are actually harmless or in some cases even beneficial,” said Dr. Christopher Mason, a Weill Cornell Medical College Geneticist.

Researchers spent more than a year swabbing each subway station, collecting thousands of samples to create what they call a pathomap, to show which germs are in the subways and where.

Dr. Mason says the study is the first of its kind.

“We've seen some bacteria in different species that actually can clean up toxins out of the environment and may even be protecting you to some degree,” said Dr. Mason.

Swabs did detect trace amount of Anthrax and even Bubonic Plague, but Dr. Mason says it’s no cause for concern.

“To put it in context, if you go hiking out west you'll find Anthrax in the soil, you'll find low levels of these same bacteria in normal environments,” he said.

Most of the straphangers we spoke with on the Upper East Side weren’t ready to forgo the hand sanitizer.

"I don't think so, no it's not, it's filthy,” said one rider.

“The less bubonic plague the better I suppose but I know that there's rats in the subway, and we're underground it's a city it's a dirty place,” said another.

The MTA says the report shows the subway is no more dangerous, at least from germs, than the environment above ground.

A Health Department spokesperson went further, saying, "This report is deeply flawed.  The interpretation of the results is misleading, and the researchers failed to offer alternative, much more plausible explanations for their findings, which is a common best practice for scientific papers."

Researchers want to use this info as a baseline for bacteria data and they're moving this to other cities like Tokyo.