Designing an Earth-Like Microbiome in Space Could Improve Astronaut Health

As humanity prepares for extended missions to the Moon, Mars and beyond, scientists are rethinking how space habitats should be designed – not just in terms of technology, but in terms of the microbial ecosystems that support astronaut health.

A new study, led by researchers at the University of California, San Diego (UC San Diego) and the National Aeronautics and Space Administration (NASA), suggests that future space habitats could benefit from intentionally fostering a more Earth-like microbiome. By analyzing over 800 surface samples from the International Space Station (ISS), the researchers found that its highly sterile environment lacks microbial diversity – an imbalance that may contribute to astronaut immune dysfunction.

The study was published in Cell.

A too-sterile space environment

The ISS is a highly controlled, industrialized environment characterized by limited microbial diversity. Designed to ensure astronaut safety, the station maintains stringent cleanliness protocols, resulting in a microbiome predominantly composed of human-associated microbes.

This lack of environmental microbial diversity may, however, have unintended consequences for astronaut health. On Earth, exposure to a wide range of microbes is essential for the proper development and functioning of the human immune system. Overly sanitized environments have been linked to immune dysregulation and a rise in inflammatory conditions. Similarly, astronauts in the sterile environment of the ISS have experienced immune dysfunction, including the reactivation of latent viruses such as Epstein-Barr and varicella-zoster.

The absence of diverse microbial exposure in space could contribute to these immune challenges. Incorporating a broader spectrum of non-pathogenic environmental microbes into the spacecraft environment may help bolster astronauts' immune systems, potentially reducing the incidence of inflammatory responses and other health issues associated with immune dysfunction.

Mapping the microbial landscape of the ISS

The team conducted an extensive study involving the collection of 803 surface samples from various locations within the station – around 100 times more samples than were taken in previous tests. These samples underwent metagenomic sequencing, a technique that analyzes the collective DNA of microbial communities, enabling the identification of a wide array of bacteria and fungi present on the ISS surfaces. The data obtained were utilized to construct a detailed three-dimensional (3D) microbial map of the station, illustrating the distribution and diversity of microorganisms across different modules.

Unsurprisingly, the study revealed a strikingly low level of microbial diversity compared to most built environments on Earth. The ISS microbiome is dominated by human-associated microbes, primarily originating from astronaut skin, rather than the diverse mix of environmental microbes typically found in homes, hospitals and research facilities.

The team also discovered the presence of distinct microbial communities in specific modules, indicating that different areas of the ISS harbor unique microbial populations. The dining and food preparation modules contained higher levels of food-associated microbes, while the toilet and hygiene areas had increased levels of fecal- and urine-associated microbes. This distribution mirrors patterns found in built environments on Earth but with a major difference: the ISS lacks microbes typically found in natural environments, such as soil and water bacteria.

The analysis also detected the widespread presence of disinfectant compounds on surfaces throughout the station, suggesting a pervasive use of cleaning agents. While essential for maintaining hygiene, this may influence the composition and diversity of microbial communities by selectively inhibiting certain species.

“We noticed that the abundance of disinfectant on the surface of the ISS is highly correlated with the microbiome diversity at different locations on the space station,” said co-first author Dr. Nina Zhao, a postdoctoral scientist at UC San Diego.

Using metagenomic sequencing, Zhao and the team were able to construct the most detailed 3D microbial and chemical map of the ISS to date. This dataset provides a baseline for monitoring microbial changes over time, assessing astronaut health risks and informing the design of future space habitats.

Engineering a healthier space habitat

The study suggests that future spacecraft and space stations should move away from being hyper-sterile environments and instead incorporate beneficial microbes that mimic Earth’s natural microbial diversity.

“Future built environments, including space stations, could benefit from intentionally fostering diverse microbial communities that better mimic the natural microbial exposures experienced on Earth, rather than relying on highly sanitized spaces,” said co-first author Dr. Rodolfo Salido, the director of Laboratory Automation at the Knight Lab, UC San Diego.

Rather than viewing microbes solely as a risk to be eliminated, the team argues that astronauts need exposure to a broader range of beneficial bacteria, similar to the way contact with soil microbes on Earth helps regulate human immune function.  By introducing select beneficial microbes, this could help mitigate astronaut immune dysfunction without compromising hygiene.

“There’s a big difference between exposure to healthy soil from gardening versus stewing in our own filth, which is kind of what happens if we're in a strictly enclosed environment with no ongoing input of those healthy sources of microbes from the outside,” said corresponding author Dr. Rob Knight, founding director of the Center for Microbiome Innovation and professor of pediatrics, bioengineering, computer ccience & engineering at the Halıcıoğlu Data Science Institute,UC San Diego.

Research has shown that exposure to a wider array of microbes in childhood can help prevent allergies and autoimmune diseases. If incorporating natural microbial ecosystems can benefit human health on Earth, it stands to reason that space habitats could be designed with the same principle in mind.

“If we really want life to thrive outside Earth, we can't just take a small branch of the tree of life and launch it into space and hope that it will work out. We need to start thinking about what other beneficial companions we should be sending with these astronauts to help them develop ecosystems that will be sustainable and beneficial for all,” said Salido.

The implications of this research extend beyond space travel. Many controlled environments on Earth – such as hospitals, submarines and research stations – face similar challenges when it comes to microbial diversity. Understanding how to balance hygiene with beneficial microbial exposure could lead to healthier indoor environments in a wide range of settings.

Reference: Salido RA, Zhao HN, McDonald D, et al. The International Space Station has a unique and extreme microbial and chemical environment driven by use patterns. Cell. 2025. doi: 10.1016/j.cell.2025.01.039

This article is a rework of a press release issued by Cell Press. Material has been edited for length and content.