ITMO University researchers in Russia recently looked into the microbiome of the Moscow subway and discovered that the bacterial world of the Russian capital’s subway system might be similar to that of New York’s public transportation. They published their findings (“Co-occurrence patterns of bacteria within microbiome of Moscow subway”) in the Computational and Structural Biotechnology Journal.

With urbanization taking over the world, people are still surrounded by bacteria, but their diversity is now decreased and we are exposed to them to a lower extent. Several years ago, an international group of researchers set out to explore the microbiome of subways, with New York being the first to have its subway microbiome investigated.

“Microbial ecosystems of the built environments have become key mediators of health as people worldwide tend to spend large amount of time indoors. Underexposure to microbes at an early age is linked to increased risks of allergic and autoimmune diseases. Transportation systems are of particular interest, as they are globally the largest space for interactions between city-dwellers,” write the investigators.

“Here we performed the first pilot study of the Moscow subway microbiome by analyzing swabs collected from 5 types of surfaces at 4 stations using high-throughput 16S rRNA gene sequencing. The study was conducted as a part of The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) project. The most abundant microbial taxa comprising the subway microbiome originated from soil and human skin. Microbiome diversity was positively correlated with passenger traffic. No substantial evidence of major human pathogens presence was found. Co-occurrence analysis revealed clusters of microbial genera including combinations of microbes likely originating from different niches. The clusters as well as the most abundant microbes were similar to ones obtained for the published data on New York City subway microbiome.

“Our results suggest that people are the main source and driving force of diversity in subway-associated microbiome. The data form a basis for a wider survey of Moscow subway microbiome to explore its longitudinal dynamics by analyzing an extended set of sample types and stations. Complementation of methods with viability testing, ‘shotgun’ metagenomics, sequencing of bacterial isolates and culturomics will provide insights for public health, biosafety, microbial ecology, and urban design.”

“The researchers analyzed the floors, handrails and carriages, and found a curiously varying microbiome,” explains Alexander V. Tyakht, PhD, the chief technology officer at Knomics (Atlas R&D), and staff member of ITMO University’s Computer Technologies Lab. “An international consortium was later established to study the subway microbiomes all over the world. This project aims to catalogize the diversity and patterns in their microbial ecology, thus creating a base for a more focused analysis of microorganisms inhabiting public spaces.”

Traditionally, to study the microbiome of a certain surface you would need to cultivate samples from it. You have to take a swab sample from the floor, the wall or the handrail and streak a Petri dish with the swab. There, the microbes reproduce, which makes them easier to examine. This method, however, has a significant drawback: without prior knowledge of what kind of bacteria were collected, it is difficult to choose a suitable medium for them to flourish. Moreover, many microorganisms are practically uncultivable. High-throughput DNA sequencing is the method of choice for comprehensive microbiome profiling. This method, initially used in the New York subway system, was later used in other cities within the framework of the project, including Moscow.

After comparing their results with those obtained by the US researchers, the Russian group discovered that the most common types of bacteria in the subway systems of Moscow and New York are identical.

Pseudomonas
Source: Janice Haney Carr, USCDCP/PIXNIO

“Most of the Dietzia, Brevundimonas, Pseudomonas, Arsenicicoccus, Stenotrophomonas and Brevundimonas, which are highly abundant in the Moscow subway, have also been detected during the previous New York project,” says Natalya Klimenko, a bioinformatician at Knomics (Atlas R&D). “Apparently, the subway microbial community structures manifest similar patterns across the globe.”

One other interesting outcome was the identified link between the microbiome diversity and the passenger traffic across the stations. At the same time, the highest diversity was found in places with abundant soil bacteria, while the prevalence of the skin microbiome corresponded to lower diversity. This pattern resonates with the fact that in nature the soil microbiome is richer than that of our bodies.

The researchers also found no significant evidence of pathogenic bacteria: no DNA sequences were reliably detected for any of the ten pathogens that could be robustly detected given the applied method. Nevertheless, the researchers emphasize that this finding doesn’t mean you can now stop washing your hands after a subway journey. Only a handful of samples have been analyzed, and the analytical method cannot detect all known pathogenic bacteria, viruses, fungi or protozoa.

Although this study of the Moscow Subway was only a pilot project, it has already demonstrated that DNA sequencing can be successfully used to map the microbiome of public spaces. A further advanced survey of every station and every type of surface would benefit from a richer repertoire of microbiological methods and collaboration with public health, hygiene, and biosurveillance experts.

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