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Metagenomic Study Offers Glimpse of NYC Subway System Microbes

NYC subway

NEW YORK (GenomeWeb) – In a study published online today in Cell Systems, researchers from Weill Cornell Medical College and elsewhere provided a look at the diverse microbial communities present in the New York City subway system.

The team did metagenomic sequencing on multiple samples from nearly 500 New York subway sites as well as samples collected in the city's public parks and the Gowanus Canal. The resulting microbial community collection — a so-called "PathoMap" of the city — revealed mostly innocuous bacteria, archaea, and viruses, including an over-representation of harmless bacterial genera previously associated with human skin.

"Our data show evidence that most bacteria in these densely populated, highly trafficked transit areas are neutral to human health, and much of it is commonly found on the skin or in the gastrointestinal tract," senior author Christopher Mason, a physiology, biophysics, and computational biomedicine researcher at Weill Cornell Medical College, said in a statement.

"These bacteria may even be helpful," Mason added, "since they can out-compete any dangerous bacteria."

But some samples contained sequences that were more concerning: around 12 percent of the taxa appeared to match potential pathogens such as the plague culprit Yersinia pestis and the anthrax agent Bacillus anthracis. And more than a quarter of the samples housed sequences associated with drug-resistance genes from more run-of-the-mill microbes.

Nevertheless, Mason emphasized that the anthrax and plague bugs were detected at levels that are expected to be far too low to negatively impact human health. "They are … likely just the co-habitants of any shared urban infrastructure and city," he said, noting that "[t]he presence of these microbes and the lack of reported medical cases is truly a testament to our body's immune system, and our innate ability to continuously adapt to our environment."

As GenomeWeb reported in 2013, PathoMap is aimed at understanding the microbial communities present in public spaces in NYC—particularly those associated with the city's highly trafficked transit system — with the goal of ramping up to do more routine microbe monitoring of such sites.

In their current study, members of the PathoMap team reported on findings for 1,457 samples collected at NYC Metropolitan Transit Authority sites, public parks, and a dozen Gowanus Canal locations.

These included swabs representing a variety of subway-related surfaces — from turnstiles and Metro Card kiosks to benches, handrails, poles, and train seats — at open subway stations in all five boroughs. One station closed due to flooding after Hurricane Sandy was also tested.

After generating metagenomic sequence data on the samples with Illumina HiSeq 2500 instruments, the researchers used MegaBLAST-based sequence alignments and the MEGAN algorithm to predict microbial members present in each sample.

The analysis uncovered organisms from nearly 1,700 bacterial, viral, archaeal, and eukaryptic taxa, the team reported, with mostly harmless bacteria turning up most frequently. Nearly half of the sequences generated came from still-to-be identified organisms.

Microbial community composition and diversity varied by train and between boroughs, the researchers noted. For instance, they determined that bacterial diversity was highest in the Bronx and relatively low in Staten Island, with the other boroughs falling in between.

From the low levels of human DNA that contaminated their samples, meanwhile, the investigators got a broad look at the ancestry in individuals using the trains in each neighborhood — patterns that more or less matched demographic data from the US Census.

Similar microbiome studies are reportedly underway in other large cities from across the US.

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