After push back from the Centers for Disease Control and Prevention and the New York City Department of Health and Mental Hygiene, the researchers have added a correction to their study. Their data collection was just fine -- so they're not retracting their study -- but they admit that their interpretations may have been a bit speculative in nature, and that the media's interpretation of those interpretations got a little out of control.
In summary: No, the subway probably doesn't have anthrax on it. And you're probably not going to get the plague on your morning commute.
"We now state that although all our metagenomic analysis tools identified reads with similarity to B. anthracis [anthrax] and Y. pestis [plague] sequences, there is minimal coverage to the backbone genome of these organisms, and there is no strong evidence to suggest these organisms are in fact present, and no evidence of pathogenicity," the correction states.
Scientific watchdog site Retraction Watch pulled some of the key corrections out in a recent blog post. Essentially, the authors have now toned down some of the speculative language they used throughout the study, making it more clear that the fragments of DNA they found might not be from the dangerous microbes to which they bear similarities.
As Columbia University's Ian Lipkin told National Geographic back in February, "The genetic footprints they report are not specific for the agents that cause anthrax or plague; they are also found in other common bacteria that are not associated with disease."
A close reading of the study made this issue clear even before the correction was issued. Among non-microbial DNA detected, for example, cucumber was the most common. Unless New Yorkers have been dumping their salads onto the tracks en mass, that's an indication that the computer program the study used -- which matched found DNA fragments to known organisms -- was probably making some pretty rough guesses. In another example, the system "found" DNA from Mediterranean fruit fly, which is such a troublesome pest that we'd know it if it had made it to the big city. (It hasn't.)
The truth is, most microorganisms in the world have yet to be "discovered." There are tons upon tons of bacteria that we know next to nothing about. A Q-tip swabbed inside a belly button would produce mysterious bacteria, too. And if you tried to match those unknown organisms -- and partial fragments of their DNA -- up to things already in the system, you might start to think there was some pretty unorthodox stuff going on in your navel.