I often tell people that bacteria are everywhere, because they are. They lurk in almost every niche of the planet, including all the niches in and on our bodies. Some are found in more abundance in certain environments such as fresh water, salt water, on reptiles, in the soil, etc.
So, when a study reported all the myriad microbes found in the NYC subway, I wasn't surprised as it as a perfect Petri dish for many different microbes because many people traverse it, it is littered with discarded food and often has puddles of liquid (which could be rain water on a good day, urine or some other substance on a bad day). Plus, rodents abound.
The controversial part of the study, which detailed many different microbes being present, was the researchers detection of the bacteria that cause plague and anthrax in the subway. Such a finding immediately grabbed headlines. I also didn't find this to be too surprising because it is well known that both Bacillus anthracis and Yersinia pestis are widely distributed in the enviroment--though Y.pestis tends to stay west of the "plague line".
I would caution people--and rats--to not breath too deep a sigh of relief in the subway as, though not at risk for plague or anthrax, the smell of urine might do you in.