Astronauts on the International Space Station often suffer from various immune system dysfunctions, including allergies and skin rashes, even though they go through rigorous screening and are probably among the healthiest people on (or at least near) Earth. “It’s hard to pinpoint the exact causes for a lot of these symptoms, but we believe microbiome disruptions that happen in their bodies and in their environment up there could be playing an important part”, says Rodolfo Salido Benitez, a bioengineering researcher at the University of California, San Diego who co-authored the largest study on the ISS microbiome to date.
After analyzing over 800 samples collected by astronauts in multiple modules of the United States Orbital Segment in the ISS, Benitez and his team concluded the microbial and chemical environment on the station closely resembled the one found at COVID-19 isolation wards during the height of the pandemic. And that may be less than ideal for keeping people healthy.
Swabbing the space decks
Monitoring microbial life on the ISS is an ongoing effort, and studies of this sort have been done before, although at a much smaller scale. “Previous studies used a low number of samples that could not identify all microbial and chemical factors present up there,” said Nina Zhao, a researcher at the UCSD and co-author of the study.
The United States Orbital Segment of the station has eight pressurized modules built by NASA, ESA, and the Japanese space agency JAXA. The goal of the new study was to find out what microbes and chemicals were in each of those modules, how they spread from module to module, where they came from, and how they compare to microbial environments on Earth. To answer these questions, the team supplied the astronauts with hundreds of custom swabs designed to collect samples from various surfaces on the ISS between October 2020 and April 2021. When the samples came back, the team started analyzing the data.
The swabs made for the study had two sides, so an astronaut would sample the same spot on the surface twice. Once on Earth, the swabs were separated, with one side going for DNA sequencing and the other side being used for mass spectrometry analysis to identify chemicals. “We applied some of the methods we use for monitoring extremely clean environments like the spacecraft assembly facility [SAF] that Jet Propulsion Laboratory employs to build the rovers they send to Mars,” Benitez said.
When the results were in, it turned out that microbial diversity on the ISS was in fact similar to SAF—good for Mars rovers, but not nearly as good for humans.
Orbiting COVID ward
The microbial genetic material collected on the ISS covered 6.31 percent of the entire phylogenetic tree. The majority of microbes on the ISS came there on the human skin. Aside from those, the taxa present varied depending on the purpose of the module where the samples were taken. The Unity module, which is often used for food preparation and storage, contained more food-associated microbes. The Tranquility module, which houses the Waste and Hygiene Compartment (otherwise known as “space toilet”), had more microbes from feces and urine. Largely missing were the microbes that live on plants, animals, and in the soil. When the team compared the ISS microbial diversity with places where people usually live on Earth, those 6.31 percent started to look a bit tiny.
To put that in perspective, microbes found in Finnish homes covered up to 12.23 percent of the phylogenetic tree, while rural homes in South America saw the figure bump up to 15.59 percent. That was still bleak in comparison to rainforests or meadows; microbes living there covered up to 28.37 percent of the tree of life.
The lack of diversity could be a problem, given that previous studies linked lowered exposure to diverse microbial environments with increased risk of chronic inflammatory diseases like asthma.
“One of the more similar environments to the ISS was in the isolation dorms on the UCSD campus during the COVID-19 pandemic. All surfaces were continuously sterilized, so that microbial signatures would be erased by the time another person would show up,” Benitez said. So, one of the first solutions to the ISS microbial diversity problem he and his colleagues suggested was that they perhaps should ease up on sterilizing the station so much.
“The extensive use of disinfection chemicals might not be the best approach to maintaining a healthy microbial environment, although there is certainly plenty of research to be conducted,” Benitez said.
Space-faring gardens
He suggested that introducing microbes that are beneficial to human health might be better than constantly struggling to wipe out all microbial life on the station. And while some modules up there do need to be sterilized, keeping some beneficial microbes alive could be achieved by designing future spacecraft in a way that accounts for how the microbes spread.
“We found that microbes in modules with little human activity tend to stay in those modules without spreading. When human activity is high in a module, then the microbes spread to adjacent modules,” Zhao said. She said spacecraft could be designed to put modules with high human activity at one end and the modules with little to no human activity at the opposite end, so the busy modules don’t contaminate the ones that need to remain sterile. “We are of course talking as microbiologists and chemists—perhaps spacecraft engineers have more pressing reasons to put certain modules at certain spots,” Zhao said. “These are just preliminary ideas.”
But what about crewed deep space missions to Mars and other destinations in the Solar System? Should we carefully design the microbial composition beforehand, plant the microbes on the spacecraft and hope this artificial, closed ecosystem will work for years without any interventions from Earth?
“I’d take a more holistic ecosystem approach,” Benitez said. He imagines in the future we could build spacecraft and space stations hosting entire gardens with microbes that would interact with plants, pollinators, and animals to create balanced, self-sustaining ecosystems. “We’d not only need to think about sending the astronauts and the machines they need to function, but also about all other lifeforms we will need to send along with them,” Benitez said
Cell, 2025. DOI: 10.1016/j.cell.2025.01.039