‘The big picture of small things’: mapping the microbes of Australia’s train stations
On 21 June each year, right on the winter solstice here in Australia, molecular biologist Ken McGrath takes to Brisbane’s bustling train stations with a pack of swabs. From Park Road Train Station in Brisbane’s south all the way up to Brisbane’s international airport on the northern outskirts of the city, he collects microbes from the stations’ metal railings and chairs, and seals them away ready to be shipped to New York for DNA sequencing.
The samples Ken has collected over the past three years make up a small part of a large-scale, global map of microorganisms collected from across the world’s subway and train stations. Spanning 60 cities, with more than 900 scientists contributing to the map on an annual basis, the data points to signature microbial profiles for each location, but also a ‘core urban microbiome’ shared by different cities.
Of the 4728 samples taken from around the world, DNA analysis conducted by scientists at the Weill Cornell Medical College in New York City, who are leading the project, found 10,000 previously unknown species of virus and bacteria, which scientists say points to how much undiscovered diversity there is in the world around us. Key takeaways from the global data set were published last week in the journal Cell.
The goal of mapping the world’s microbes started with geneticist Christopher Mason of Weill Cornell Medical College, who’s research on New York’s subways quickly gained traction when the very first interactive microbe map was published in 2015. With talk of the project going global, Ken quickly put his hand up to manage Australia’s input. “I jumped at the chance of being involved in something that’s really looking at the big picture of small things,” he says.
What is a microbiome?
A microbiome is a collection of microbes that live as a community in a particular location. The ‘core urban microbiome’ scientists discovered consists of 31 microbes that showed up in almost every sample taken from the 60 participating cities. Most of these were bacteria living on human skin. Those most common in Brisbane, for example, were Cupriavidus metallidurans, which likes metal surfaces, Bradyrhizobium japonicum, a common plant-associated bacterium and Cutibacterium acnes, a bacterium that feeds on the oil produced by the glands of our skin. Altogether, quite harmless.
As for the 10,000 unidentified species of virus and bacteria, Ken says not to be worried. “What it speaks to is just how much undiscovered diversity there is in the world around us and even the world around us that is seemingly boring, like our daily commute.”
However, Ken says that the map has great potential as a surveillance program of biological threats. “In the years prior to 2020, before Covid became headline news, we already knew this project was monitoring the environment for those kinds of pathogens of disease.
“We were aware that by swabbing the surface of all these train stations from around the world, what we’re actually doing is a temperature check of the globe. We’re asking, ‘Have we got any issues around the corner?’, ‘Is there going to be an outbreak of a super pathogen that’s about to spread around the world?’ That became the database we were creating.”
The microbe map and COVID-19
So can the microbe map be used to detect COVID-19? Not quite. Ken explains, “because we were only analysing the DNA component of the surfaces, we couldn’t see COVID-19. It’s a different kind of virus with RNA as its genome, making it a different type of genetic material.”
Since the outbreak of COVID-19 however, the project team is now collecting RNA in parallel to its DNA collections in some cities. “We would have loved to have been able to do it for Covid,” Ken says. “If we were doing RNA swabs prior to last year and say we had five years of data, we might have seen that it was already around China, Europe and the US prior to 2020 or we may have found something similar that wasn’t quite the same virus, but was a few mutations away from the current Covid virus.
Just falling short time-wise for the Covid outbreak, the microbe map will prove to be a handy tool for future outbreaks, Ken says. “The microbe map is a time machine for looking back at the history of a virus, which could help you understand the future trajectory.”
The map is already cataloguing the presence of antimicrobial resistance genes, which are biological defences used by microbes for survival. “Antimicrobial resistance genes are naturally occurring. They’re just part of the environment and they get picked up by different bugs. In certain situations, like hospitals, they can cause some problems, but it’s not of concern in the general environment typically. Now. that would change if there was an outbreak of something that had picked up a resistance gene. What we’re really doing is just monitoring that background level because that helps us understand why outbreaks happen if they do.”
Going beyond the subway
Ken wants the project to go beyond the world’s subways and train stations, even utilise the potential of citizen scientists.
“On the global sampling day, people could go out and swab their own house or their letterbox and really spread the project beyond the capital cities.
“The more information we have about microbial communities and microbiomes lets us map our planet more accurately, understand it and how we interact with these microbes.” This, Ken says, will allow us to predict changes, including tracing the origin of future outbreaks and predict their future.