A massive new DNA sequencing project on the New York City subway has been completed and the results have just been published. And as many of us would have guessed, there’s a lot of bacteria on the subway, though most of it is harmless. More importantly, is what we don’t know about it.
The PathoMap project, which involved sampling turnstiles, benches, and keypads at 466 stations, found 15,152 life-forms in total, half of which were bacterial. The Wall Street Journal has created a fun, interactive microbial map of the subway out of the data, showing where on the lines the bacteria “associated with” everything from mozzarella cheese to staph infections was found.
But “associated with” is a pretty fuzzy term that runs up against the limits of science. In the past few years, genetic sequencing has become vastly more powerful and cheap, making metagenomic analyses possible. This means we can take all of the DNA in an environmental sample—human, plant, bacteria, cockroach, whatever—and sequencing the hell out of it.
The problem, though, is that our genetic libraries are still incomplete. For example, if I don’t know what the DNA sequences of a cockroach look like, how can I know my DNA sequence belongs to a cockroach? That’s how why half the DNA found in the project matched no known organism.
This is especially true when it comes to bacteria that are being discovered for the first time in these new metagenomic analyses. And what does “associated with,” when it comes to bacteria, really mean? Maybe we found a certain bacterium on cheese once, but maybe we never sampled its true native habitat?
Even the best technologies we have now are ultimately crude tools to grope at a vast, unseen world. It maybe be hard to intuit whether it make sense for Acinetobacter or Enterococcus to be on the subway, but the research team found plenty of non-microbial DNA, too, and a lot of it didn’t make sense. According to the WSJ, human DNA was prevalent, as were beetle and fly DNA. Those make sense. (We actually don’t know about cockroaches because their genome hasn’t been sequenced yet.)
The next most prevalent type of DNA, though, was cucumber. Cucumber? When was the last time you saw someone gnawing on a cucumber on the subway? More likely, the computer program grouped all plant material under cucumber.
And then there were the straight up weird ones, according to the WSJ.
“Initial database searches with subway DNA, for instance, turned up false matches to the Tasmanian devil, the Himalayan yak and the Mediterranean fruit fly—all creatures highly unlikely to be found in a New York transit system.”
That’s why some of the microbial DNA found that sounds alarming—anthrax, for instance—is no reason to be calling Homeland Security just yet.
None of this detracts, of course, from how incredibly interesting urban microbiology really is. The city is an organism, and we’re slowly beginning to understand its microbiome. Studying how bacteria—be they pathogens or scavengers or simply harmless microbes—spread through the urban environment could yield new insights into how a city works.
I’m just impatiently waiting for the future, when we’re beyond the simple cataloguing of microbes, to truly understanding how they live and function together.