Recently, our paper published in Cell Systems surveyed DNA of the entire NYC subway system. Specifically, we had fragments of DNA that matched a myriad of species, and some of these species were alive through functional data in cultures.
These data led us to five exciting metagenomic conclusions:
1) Interestingly, 48 percent of the DNA did not match any known species, indicating a wealth of discovery left in metagenomics and genome assembly projects. This was in range with another recent study from urban air metagenomics.
2) A “molecular echo” could be seen from marine-related bacteria in a subway station flooded by Hurricane Sandy, distinct from the Gowanus Canal in Brooklyn, which created a subway version of the “microbiome aura” posited by Jack Gilbert and Ed Yong.
3) As far as we know, this was the first demonstration that human alleles and their predicted ancestry left on surfaces can match the U.S. Census data demographics in a city, which was previously shown across Europe.
4) We measured the rapid pace of metagenomic dynamics over the course of a day on a public surface.
5) We showed that metagenomics profiling can reveal the likely source of antibiotic (tetracycline) resistance.
We were excited about all of these data and their release, and even made a map so you could look up any organism from any kingdom and play with the data, and the Wall Street Journal made a cool map too. But, what we did not appreciate was the avalanche of fear-based responses that came from the press after reporting that a handful of samples (out of almost 1,500) matched fragments of Yersinia pestis (Yp) and Bacallis anthracis (Ba). We only claimed evidence in our paper for the DNA of these species, we specifically noted there was no evidence that they were alive, and even hedged our discussion on Yp and Ba with statements such as “if truly present.” Yet, the casual mention of pathogens in our paper created a public impression that pathogens were present and pervasive in the subway.
Read full, original article: The long road from Data to Wisdom, and from DNA to Pathogen
