Mapping and identifying all the microbes across New York City is no small feat. Just ask Jane Carlton. About three years ago, Carlton, director of the Center for Genomics and Systems Biology, and professor of biology, at New York University and colleagues won an NYU grand challenge grant for their project “Microbes, Sewage, Health and Disease: Mapping the New York City Metagenome.” To date, the investigators have studied microbes on the New York City subway system, on rental bicycles, in soil and raw sewage, and on circulating $1 bills.
In their latest work, published this week in mSphere, the team investigated automated teller machine keypads across the city. The idea was that ATMs are exposed mostly to the fingers of local residents, so they could maybe identify regional microbial signatures. The researchers did find plenty of microbes – mostly from normal human skin, household surfaces or traces of food – but no particular clustering by geography.
“Our results suggest that ATM keypads integrate microbes from different sources, including the human microbiome, foods, and potentially novel environmental organisms adapted to air or surfaces,” Carlton said. “DNA obtained from ATM keypads may therefore provide a record of both human behavior and environmental sources of microbes.”
The investigators in June and July 2014 took swabs of keypads from 66 ATM machines in eight neighborhoods over three New York boroughs: Manhattan, Queens and Brooklyn. Four of the machines were located outdoors. Then, in the lab, they studied samples with 16S amplicon sequencing to identify and compare bacteria and 18S amplicon sequencing to identify parasites, fungi and protists.
The most abundant bacteria found across most samples were normal human skin microbes from the Actinobacteria, Bacteroides, Firmicutes, and Proteobacteria families. Overall, the bacteria samples had low diversity. In the 18S sequencing, investigators found some fungi and low levels of protists.
The most common identified sources of microbes on the keypads were household surfaces such as televisions, restrooms, kitchens and pillows. Researchers found microbes from bony fish and mollusks, and from chicken on some neighborhood ATMs, suggesting that residual DNA from a meal may remain on a person’s hands and be transferred to the ATM keypad upon use.
ATM keypads located in laundromats and stores had the highest number of biomarkers, with the most prominent being Lactobacillales (lactic acid bacteria), which is usually found in decomposing plants or milk products. In samples from Manhattan, researchers observed the biomarker Xeromyces bisporus, a foodborne mold associated with spoiled baked goods. “It seems plausible that this fungus may have been transferred from people who have recently handled baked goods, particularly in a commuter-heavy area such as Midtown Manhattan where there are many nearby convenience stores and cafés selling this type of food product to business workers,” Carlton said.
Researchers found no significant difference in the keypads from ATMs located outdoors versus indoors.
Since each ATM keypad in New York City is most likely utilized by hundreds of people each day (and may come into contact with air, water, and microbes from different urban surfaces), the microbial communities obtained in this study may represent an “average” community that is effectively pooled from vastly different sources, said Maria Gloria Dominguez-Bello, PhD, an associate professor in New York University School of Medicine’s Human Microbiome Program and corresponding author of the study.
The relative lack of diversity among locations could result from periodic cleaning of the machines, which would wipe out some of the microbes, as well as usage of ATMs by tourists, commuters from other locations, etc., the researchers said.
Next, with funding from the Alfred P. Sloan Foundation, they’ll study microbes in the city’s cats, dogs, rats, mice, pigeons and cockroaches.