Editors' ChoiceMicrobiology

Seq and the city

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Science Translational Medicine  25 Feb 2015:
Vol. 7, Issue 276, pp. 276ec35
DOI: 10.1126/scitranslmed.aaa5547

As 1.7 billion riders pass through New York City’s 466 subway stations every year, they leave a little bit of themselves behind but also take something of their environment with them. Although poets and authors have long contemplated this exchange on a metaphysical level, Afshinnekoo et al. now provide actual genetic evidence. In doing so, they offer a glimpse into the highly dynamic and varied genetic ecology of the largest mass transit system in the world.

The authors obtained 1457 swabs from 484 locations, including all 466 open subway stations. This included station turnstiles and kiosks as well as train doors, handrails, and seats. DNA was extracted and sequenced, resulting in 10.4 billion reads that were then aligned to known sequences. Notably, 48% of reads did not match to a known organism. Although some of these unfamiliar sequences will represent species not previously identified, most will likely reflect organisms with genomes yet to be sequenced and cataloged. For example, the Mediterranean fruit fly and mountain pine beetle were among the most abundant eukaryotic species identified; however, the authors note that cockroaches are not yet in the NCBI database.

The authors also analyzed human DNA allele frequency. In doing so, they found station-specific demographics that were remarkably similar to census demographic data. However, it was bacteria that constituted the largest category (47% of all reads), followed by eukaryotes (0.8%), viruses (0.03%), and archaea (0.003%). Pseudomonas stutzeri was the most frequently identified bacterial species, followed by Stenotrophomonas maltophilia and Enterobacter cloacae. The identified viruses were largely phages that mirrored the prevalence of their target bacteria. Of potential clinical relevance, the authors identified several antibiotic-resistant genes as well as bioterror pathogens including Bacillus anthracis and Yersinia pestis. Among several other findings, the authors also document temporal shifts in bacterial ecology at one station over the course of a day. They observed a striking dynamism whereby only 5 to10% of taxa persisted over that time.

The methods and setting described by Afshinnekoo et al. have been described before. Rather, it is the scope of their efforts that sets this analysis apart. By sampling every New York City subway station, the authors present a broad snapshot of the city’s genetic profile. That sampling was largely limited to subway stations and typically occurred at only one time per station. However, sampling and testing of additional locations is ongoing and promises a more comprehensive and deeper understanding of the city’s highly dynamic and varied genetic footprint.

E. Afshinnekoo et al., Geospatial resolution of human and bacterial diversity with city-scale metagenomics. Cell Systems 10.1016/j.cels.2015.01.001 (2015). [Full Text]

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