As part of its Microbiology of the Built Environment initiative, the Alfred P. Sloan Foundation started funding projects a few years ago that touched on the interaction of microbiology with architecture, buildings or, in the case of Curtis Huttenhower, PhD, an associate professor of computational biology and bioinformatics at the Harvard T.H. Chan School of Public Health, transit.
“When we started, there was almost no work on the transit microbiome,” Huttenhower said. “We were interested since it’s such a hub of human interaction.”
Studying microbial samples taken from various cars and ticketing machine surfaces of the Boston subway system, known as the T, Huttenhower’s team found something interesting: The subway might be just as bacteria-laden as you’d expect. However, the organisms found there are largely from normal human skin and unlikely to cause disease in healthy humans. Their work was published this week in mSystems.
The study found that the levels of microbes affecting antibiotic resistance were “much lower than what you’d find in a normal human gut,” Huttenhower said. “They’re exactly what you’d run into shaking somebody’s hand.”
“We were surprised by how normal a lot of the samples looked,” he added. “Even when we looked closely, there was nothing unusual or dangerous about the microbes we found. It shows that, in the absence something like flu season, all the bugs you run into, even in a crowded environment like the T, look like your normal microbial environment.”
With the full support of the Massachusetts Bay Transportation Authority, which provided a transit officer to accompany the research team on their collection days and provide information sheets to curious patrons, the team gathered nearly 100 microbial samples from train cars and stations on three dates in 2013. Train car samples were collected from the red, orange and green lines of the subway and comprised six surface types: hanging grips; horizontal and vertical poles; seats; seat backs; and walls. Station samples were collected from the touchscreens and sides of ticketing machines. They used 16S amplicon and shotgun metagenomic sequencing to profile the microbial communities found on these surfaces.
Overall, through amplicon sequencing, researchers found surface type was the major driver in variation of microbes, with the highest amount of microbes found on hanging grips, followed by seats or touch screens. All surfaces were dominated by normal human skin microbes, with the bacterial phyla Firmicutes, Proteobacteria, and Actinobacteria each responsible for over 20% of the microbial community. The team found low levels of gut and oral microbes such as Lachnospiraceae, or those from the Veillonella and Prevotella families.
“I didn’t expect the grips to have that much DNA on them, because they’re relatively small and seem to be used less often,” said lead study author Tiffany Hsu, a graduate student at the school. "But porous surfaces can collect microbes more efficiently than something solid like a metal pole.”
Outdoor exposures played a role in microbes seen on ticketing machines, with those located by outdoor stations being rich in Alphaproteobacteria while those located indoors having more Acinetobacter and those located underground having increased Corynebacterium and microbes from the Tissierellaceae family.
The team performed shotgun metagenomic sequencing, a more in-depth look at the microbes, on 24 mass transit samples, including 15 from the train cars and nine from stations. This testing found the most abundant species of bacteria seen across all samples to be the skin bacteria Propionibacterium acnes.
Little variation was seen between the train lines or stations serving different demographics. In addition, researchers found minimal numbers of genes associated with antibiotic resistance.
“This indicates that the real pathogenic potential detected in the Boston subway is very low,” Huttenhower said. “One of the things we’ve learned is it’s actually pretty difficult to get a group of bugs to stably transfer from one person to another, and learning that was part of the goal of this study.”
More work is needed to understand whether the microbes found are just lying dormant or actively growing, and under what circumstances they can be transferred from one individual to another, the authors said. A follow-up study will look at whether the microbes identified on the subway system are from living or dead organisms.
-- Karen Blum