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Public transit is just as gross as you thought and that’s why microbiologists love it

Colorado post-docs and undergrads endure the swabbing of seats and handrails in the name of science, part of a worldwide effort to “map the human biome” and sort good germs from bad.

UC Boulder lab technician Blaire Volbers takes particle samples from the air in a Boulder bus on Thursday, June 24. (Olivia Sun, The Colorado Sun)
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As University of Colorado student Alise Gladbach scrubs a testing swab hard on the stainless steel ticket counter in the RTD transit station near the Pearl Street mall in Boulder, ticket seller Laura Erickson watches from behind a sheet of bulletproof glass. 

Erickson appears safe, but she is not necessarily calm. As Gladbach’s swab turns an immediate and alarming soot color from the microbes she is picking up, Erickson’s eyes grow wider and wider. 

“I thought I had just cleaned that,” Erickson said, sounding far less certain about her workstation upkeep than she was just a few moments before. 

Successfully absorbed into the tip of Gladbach’s now-filthy swab, thousands of individual microbes were shipped in dry ice by evening and processed for their DNA breakdown on supercomputers in New York. Slightly skeeved-out undergraduate students just like her, the world over, spent Thursday collecting swabs from the highest-traffic spots of transit facilities from Boulder to Berlin to Bogota. 

Thursday’s swabbing on and near buses in Boulder, which followed a marathon effort Wednesday on DIA’s A Train and connecting lines, is part of a six-year international effort to detail “the human biome” and see what we can’t see. 

Gross? Absolutely. 

Vital to science? Indubitably. 

“This is mapping the microbiology that we live in every day,” said the leader of the CU team, environmental engineering professor Mark Hernandez. “Wherever you go, you leave a fingerprint and you exhale, whatever you touch, whatever you breathe, and we share that with each other in the urban environment.”


Teams around the world focus on transit because it mixes everyone in an urban area, and adds in travelers from other parts of the world to give a full spectrum of common microbes. The overall project is called MetaSUB, as in subway. 

Discovery happens with every swipe of a passenger railing or candy counter. A consortium of scientists publishing in the Cell journal in May announced finding more than 10,000 bacterial and viral strains in previous years that had never before been identified.

The international team chooses the solstice every year for the 60-city survey, though the Boulder team is not sure why. 

CU Boulder environmental engineering professor Mark Hernandez takes particle samples from a ticket desk at the Downtown Boulder bus station on Thursday, June 24, 2021. About once a year, teams across the world gather samples at public transit areas as part of an international project to research the evolving human biome. The six-year project is overseen by Weill Cornell Medicine in New York. (Olivia Sun, The Colorado Sun)

The tangible repulsion of a particularly grungy swab is shared by full professors, post-docs, graduate assistants and undergrads alike. Hernandez watched Gladbach turn a swab a quick brown on a railing at the Walnut Street entrance, and nodded sympathetically. 

“The worst one was yesterday, taking the samples at the water fountains in the bus station at Union Station,” Gladbach said. 

“And the bathrooms,” Hernandez nodded. “People are bathing themselves in the sink in the bathrooms.” 

The consortium’s work, overseen by geneticists at Weill Cornell Medicine in New York, predates the pandemic, but will now offer even more scientific breakthroughs by reporting on the presence of COVID-19 around the world. 

Or lack thereof. 

The absence of detectable COVID-19 in so many international samples has helped confirm earlier science on the virus: It doesn’t stick long on surfaces in a way that is harmful to most people, and cleaning works. 

Samples are gathered by preparing cotton swabs with a preservative for 15 seconds, then wiped across surfaces for 3 continuous minutes. (Olivia Sun, The Colorado Sun)

The pandemic virus, Hernandez explained, is “a very interpersonal contact, aerosol transfer thing. And that’s why social distancing and masking really works. So you don’t see a lot of” COVID-19 in the samples.

“I mean you have to be in very close proximity,” he said. “And, you know that the air we breathe has thousands of microbes in it and maybe one of those is COVID. There is a normal microbiome that we live and breathe in every day and a very few of those are pathogenic.”

On their gathering trips, the CU Boulder team is constantly reminded that while humans come into contact with thousands of pathogens, there’s no pathogen quite like being human. 

“People ask us if we’re with the CIA,” Hernandez said. “They ask us out on dates. They say, ‘Oh, the university is Big Brother!’ ”


As postdoctoral researcher Odessa Gomez sets up an $8,000 portable, military-grade air sampler, Hernandez describes how they leave it running for half an hour because that’s how long it takes for all the air in a lobby like Boulder’s RTD station to turn over completely. Then he mentions the local dude who stole the $8,000 machine in a previous year and demanded cash to give it back. The ransomware negotiations started higher, but Hernandez talked him down to $50. 

Here’s what the team has learned along the way, internationally and locally: 

  • While many of the microorganisms around the world are common to every city on the globe, there’s just enough variety to give Denver or Boulder a character separate from the others. Western cities, for example, will have a much more powerful signature of microbes that thrive in high, dry climates. The scientists on the international team claim that if you hand them a random shoe, they can swab it and tell you with nearly 90% accuracy what city it had been walking around in. 
Samples are gathered by preparing cotton swabs with a preservative for 15 seconds, then wiped across surfaces for 3 continuous minutes. (Olivia Sun, The Colorado Sun)
  • Cultural and work habits make a huge difference from city to city, nation to nation. Hong Kong swabs have made it clear that locals don’t leave the house if they are sick, a longtime safeguard that has helped some Asian nations adapt better to the pandemic. Cleaning materials work everywhere, but only if the person doing the cleaning is trained and thorough, said Hernandez, who also does studies for cleaning supply companies and hotel chains. Also, scheduling matters: Americans tend to book cleanings when it’s convenient, such as when the bus is parked at the end of the day, instead of when it’s most effective, such as when a commuting car is crammed with potentially ill passengers. 

  • Many of the microbes are too busy grossing each other out to bother with humans. Many of the swabbed viruses are “bacteriophages,” which infect bacteria. Researchers hope that identifying other microbes and how they interact could lead to drug development or other medical breakthroughs. Hernandez said one of the most remarkable things he’s noticed is the widespread nature of antibiotic resistance uncovered by the samples. 

“That’s worrisome,” Hernandez said, watching Gladbach take a public phone off the hook and scrub around and around the mouthpiece with a new swab. “It is not a good thing. But you know we have a saying in Spanish: The more you see the fox, the better you know the fox.” 

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