Each person has a very individual microbiome of intestinal and skin microbes. Apparently, each city is also a special ecosystem in which a unique species spectrum of bacteria, viruses and other microbes develops, as an international team of researchers reports in the journal Cell. This urban microbiome consists on the one hand of a proportion of fewer bacterial species common to all cities studied worldwide, but on the other hand it is supplemented by additional species of microbes, which are different for each city. Ongoing information on how the species spectrum of microbes in a city changes over time could provide early information about infection risks and impending epidemics, according to the authors.
“With the help of your shoes, I could tell you with about 90 percent certainty which city you’re from,” says Christopher Mason of Weill Cornell Medical College in New York, the head of the research project. “Each city has its own ‘molecular echo’ of the microbes typical of it.” Therefore, monitoring of urban microbiomes could not only be of medical and epidemiological importance, but also serve forensic investigations.
For their study, the researchers selected 60 major cities in Europe, North and South America, East Asia, Africa, Australia and Oceania. These included New York, Brisbane, Hong Kong, Tokyo, Kuala Lumpur, Hanoi, Vienna, Oslo and Berlin. At three different times between 2015 and 2017, a total of 4728 smear samples from buses and trains, seats, benches, railings, turnstiles and ticket sales outlets were collected. Using DNA analyses, the scientists identified 4246 known microbial species as well as 748 previously unknown species of bacteria and several thousand unknown virus species.
A group of 31 bacterial species, including staphylococci, pseudomonads and micrococci, was detectable in 97 percent of the samples of all cities. The list of these bacteria differed from the species spectra characteristic of soil bacteria and bacteria of the human body. The most commonly found bacterium in all cities was Cutibacterium acnes (former name: Propionibacterium acnes), a normal skin bacterium, which is also involved in the development of acne. Among the urban microbes were also species of Streptococcus, Klebsiella, Enterobacter and others that are medically relevant as potential infectious agents.
The researchers also examined the bacterial DNA for genes that make the microbes resistant to antibiotics. The frequency with which such resistance genes were detected varied greatly between cities. Which factors are responsible for these differences and for the different germ spectra of the cities has not yet been investigated. The microbiome of a city, which is detected at regular intervals, could help to detect outbreaks of infections and a proliferation of resistant pathogens at an early stage and to quickly take protective measures.