A city is not only unique in its architecture, geography, or history, but also in its microbiome, which denotes microorganisms in a particular environment. This was discovered by a metagenomic study conducted at a global level and recently published in the Cell.
The study conducted genome sequencing of samples collected from public transit systems including subways, buses, trains, trams, and hospitals in 60 cities around the world. The research team identified new viruses and bacteria and found that each of the cities has a unique fingerprint of the microbial world within it.
Christopher Mason, the corresponding author of the study had previously researched on this topic, but that was limited to New York city only. Back in 2015, Mason and his team published a study where it was found that there exist previously unknown species of microbes in New York city. Now, in the latest study, this process was expanded and data was collected at a global level.
However, it was a challenge to conduct such a study at a global level. Mason and his collaborators needed to figure out how to collect samples consistently. Finally, they settled on swabbing objects that are commonly found in transit systems everywhere, such as benches, ticket kiosks, turnstiles etc. The scientists involved in the project swabbed the surfaces for about three minutes, which is enough time to collect sufficient DNA. They also became cautious that the time of swabbing does not linger much to avoid discomfort for the bystanders. Mason commented on their process saying, “It’s the perfect balance between DNA yield and social discomfort.”
The researchers took back the samples to the lab and they analysed the DNA samples collected by swabbing objects in the transit system. What they found is a matter of excitement — 45% of the DNA did not match with any known species; nearly 11,000 viruses and 1,300 bacteria were new to them. This is indeed a matter of excitement.
The research also revealed that there is a set of 31 species of microbes that are present in about 97% of the samples collected from different cities across the world. The researchers termed this as the core of urban microbiome. Further, it was found that about 1,145 species were present in more than 70% of the samples. Surfaces that people touch, such as railings, were found to contain bacteria associated with human skin in comparison to surfaces like windows. Bacteria were often found in soil, water, air and dust.
However, the research also revealed that there exists microbe species that are not widespread, but rather specific to cities. This set of species forms the unique ‘fingerprint’ of a city. This helped the researchers to predict which random sample comes from which city, that too with an accuracy of over 88%, as reported in the Cell. For example, the team found Carnobacterium inhibens, a bacterium that produces lactic acid and is tolerant to low temperatures, is prevalent in New York City.
The implication of the research can be very useful for forensics with more finding in future about more such fingerprint microbiome in cities all over the world. Moreover, few new questions also open up with the findings, such as why do different cities have a unique fingerprint of microorganisms to begin with?
The map of cities and their microbiomes can be found here.