A recent study looked at the human and bacterial diversity that exists on NYC subways. The study, Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics, (Afshinnekoo, et al. 2015) finds that the subway is teaming with a great diversity of microbes and the cells of humans. Pathogenic organisms are found, but with no cases of reported illnesses in this area, it is surmised that this is just part of the normal urban microbial environment. Bacterial species associated with the skin are present in higher proportions compared to bacterial species associated with the intestinal tract (poop bacteria).
Of course to read the headlines (NY Times, New Republic), it can be unsettling to some that so much 'contamination' present....whether it is human cells, bacteria, or viruses. Heck, there are bacterial species that have not yet been determined.
But as this is life on earth. It is not sterile. We coexist with a lot of microorganisms. For the most part, they are under control. However, there are certain instances, when our immune system is off or we encounter a large dose of a given microorganism (such as when we temperature abuse our food), we get sick. But encountering a diversity of microorganisms is important for our immune systems to develop. So don't worry about the myriad of microorganisms on the subway, embrace the fact that that 'what doesn't kill me, makes me stronger". And wash your hands before dinner.
A few passages from the study: