The Other Crew: Microbes on the ISS

Are we really alone in space?

One major stressor astronauts encounter during their missions is isolation. But are they really alone in space? The answer is a resounding NO when you consider all the tiny microbes that give them company (not to mention aliens and conspiracy theories). Some of these microbes live inside our own bodies, and some hitchhike along on missions to outer space, adapting to conditions there. This blog explores humanity's longest-known companions, microbes, in space.

Key Takeaways

·       Astronauts are never alone, microbially. They carry a full microbiome, and the ISS itself hosts a distinct microbial community.

·       Spaceflight measurably shifts the human microbiome, with documented changes in skin, gut, and oral bacteria that mostly revert after astronauts return to Earth.

·       Latent viruses (EBV, CMV, VZV) reactivate at higher rates in space than on Earth, driven by stress and immune dysregulation.

·       Some microbes thrive in space, adapting to radiation, surviving on station surfaces, and in some cases becoming more virulent or antibiotic-resistant.

Microbes

Microbes are tiny living organisms invisible to the naked eye. They include bacteria, viruses, and fungi, among others. They exist everywhere around us and within the human body. For every 1 human cell, there are roughly 1.3 bacterial cells, most of which reside in our gut. (Sender et al. 2016) Needless to say, microbes also accompany astronauts during space missions. Most known microbes are harmless or beneficial to us, supporting important functions like digestion and immunity. Some are used to develop medicines, such as penicillin. However, some microbes are pathogenic and cause disease. Among pathogenic microbes, certain viruses can remain latent in the human body for extended periods.

The International Space Station (ISS) is a unique microbial environment. It has closed air circulation, shared surfaces, cleaning protocols, and microgravity. Among these factors, microgravity in particular is hypothesized to alter microbial growth. On Earth, gravity enables convection, a process that allows fluids to mix and helps microbes ensure optimal nutrient exchange with their surroundings. In space, reduced gravity blocks this route and is hypothesized to stress microbes in ways researchers are still characterizing.

Microbes Within Us

The human body is home to diverse microbes, of which bacteria form the major inhabitants. Bacteria reside on our skin, in the nasal and oral cavities, and in the gut. Skin is the largest organ in the body and has the most contact with the ISS environment. As a result, shed skin cells and their associated microbes are a major source of the bacterial community found on the station itself.

A 2019 study of 9 astronauts who spent 6–12 months on the ISS found that the microbial composition of the GI tract, skin, nose, and tongue changes during spaceflight. One key clinical observation among astronauts is the occurrence of skin rashes and hypersensitivity during spaceflight. This could be due to a decrease in skin Gammaproteobacteria. Space also imposes stressors that delay cell proliferation, particularly in the basal layer of the skin, altering skin structure. This could increase exposure to microbes residing in the deeper layers. Moreover, a weakened skin structure can facilitate skin infections by opportunistic bacteria such as Staphylococcus or Streptococcus. Collectively, changes in microbial populations were associated with increased levels of several pro-inflammatory cytokines, including CCL2, IL-8, IL-1β, and CCL4. (Voorhies et al. 2019) 

Another study examined changes in bacterial populations before, during, and after spaceflight in 4 ISS astronauts. The researchers noted changes to microbial composition during spaceflight; however, these returned to normal after the astronauts returned to Earth. Specifically, saliva samples showed the greatest differences in bacterial species abundance, including increases in Prevotella (implicated in periodontal disease) and a decrease in Neisseria (a marker of oral dysbiosis). (Morrison et al. 2021)

Our body is also home to latent viruses - microbes that remain dormant within host cells and don't cause infections unless reactivated later by stress. Examples include herpes simplex virus 1 (HSV-1), Epstein-Barr virus (EBV), cytomegalovirus (CMV), and varicella-zoster virus (VZV). Spaceflight imposes multiple stressors (e.g., space radiation with protons and Fe ions, microgravity, etc) that can reactivate these latent viruses. Additionally, astronauts tend to have weakened immune systems in space, allowing latent microbes to become active and cause infections.

EBV, VZV, and CMV are frequently detected in saliva, urine, and blood samples from astronauts after both short- and long-term missions. These viral levels have been correlated with increased cytokine levels, including IL-1a, IL-8, IL-10, CCL11, IL-13, and IL-4, which are characteristic of a T helper 2 (Th2) shift that targets extracellular pathogens. Effective anti-viral immunity is mediated by a Th1 response that drives cellular immunity, killing virus-infected cells. A shift towards Th2 leaves astronauts less equipped to control viral infections. (Winer et al. 2026)

Microbes that Travel With Us

Apart from microbes that reside within astronauts, there are also microbes, mainly fungi,  that hitch a ride on space shuttles. These fungi remain dormant during launch but activate and reproduce in space stations. For example, in 1988, astronauts in the Russian space station Mir found a fungus that successfully adapted to space, surviving on windows and air conditioners. Such mold, adapted to space conditions, can damage materials and food supplies and complicate health concerns in closed habitats like the ISS.

A 2-year experiment in open space near the ISS revealed that microbes like bacteria, fungi, and archaea (single-celled organisms distinct from bacteria) can adapt to outer space. These included spore-forming bacteria of Bacillus subtilis species, fungi of Aureobasidium pullulans species, and archaea of Methanosarcina mazei S-6^T species. (Deshevaya et al. 2024)

In a separate study, an ISS isolate of the fungus Penicillium rubens was found to select for traits that increased its radiation resistance and altered its growth dynamics in response to microgravity exposure. (Schiele et al. 2025) 

Bacteria collected from various sites on the ISS, including exercise devices and toilets, particularly Enterobacter strains, developed resistance to multiple drugs. (Singh et al. 2018) In a separate study, spaceflight-grown Salmonella typhimurium (a common cause of food poisoning) was more virulent than those grown on Earth, suggesting that the spaceflight environment induces molecular changes in bacterial cells. (Wilson et al. 2007)

Studies like these are key to helping astronauts fight potential infections in future space missions. They also underscore the importance of considering the contaminating space with Earth-bugs with previously unknown features.

Conclusions

So, are astronauts alone in space? Not even close. They travel with trillions of microbial companions. Some of them are helpful, some are opportunistic, and some are quietly evolving in ways we're still working out.

Microbiome changes are not always harmful. But in a closed spacecraft environment with immune dysregulation, limited medical resources, and long mission durations, even harmless microbes need to be closely studied.

References

Deshevaya, Elena A., Svetlana V. Fialkina, Elena V. Shubralova, et al. 2024. “Survival of Microorganisms during Two-Year Exposure in Outer Space near the ISS.” Scientific Reports 14 (January): 334. https://doi.org/10.1038/s41598-023-49525-z.

Morrison, Michael D., James B. Thissen, Fathi Karouia, et al. 2021. “Investigation of Spaceflight Induced Changes to Astronaut Microbiomes.” Frontiers in Microbiology 12 (June): 659179. https://doi.org/10.3389/fmicb.2021.659179.

Schiele, Alessa, Stella Marie Timofeev, Afonso Mota, and Marta Cortesão. 2025. “Fungus Penicillium Rubens Isolated from the International Space Station (ISS) Shows Faster Colony Growth and Better Spore Resistance to Cosmic Radiation than Type Strain.” International Journal of Astrobiology 24 (January): e13. https://doi.org/10.1017/S147355042510013X.

Sender, Ron, Shai Fuchs, and Ron Milo. 2016. “Revised Estimates for the Number of Human and Bacteria Cells in the Body.” PLOS Biology 14 (8): e1002533. https://doi.org/10.1371/journal.pbio.1002533.

Singh, Nitin K., Daniela Bezdan, Aleksandra Checinska Sielaff, Kevin Wheeler, Christopher E. Mason, and Kasthuri Venkateswaran. 2018. “Multi-Drug Resistant Enterobacter Bugandensis Species Isolated from the International Space Station and Comparative Genomic Analyses with Human Pathogenic Strains.” BMC Microbiology 18 (1): 175. https://doi.org/10.1186/s12866-018-1325-2.

Voorhies, Alexander A., C. Mark Ott, Satish Mehta, et al. 2019. “Study of the Impact of Long-Duration Space Missions at the International Space Station on the Astronaut Microbiome.” Scientific Reports 9 (1): 9911. https://doi.org/10.1038/s41598-019-46303-8.

Wilson, J. W., C. M. Ott, K. Höner zu Bentrup, et al. 2007. “Space Flight Alters Bacterial Gene Expression and Virulence and Reveals a Role for Global Regulator Hfq.” Proceedings of the National Academy of Sciences 104 (41): 16299–304. https://doi.org/10.1073/pnas.0707155104.

Winer, Daniel A., Huixun Du, JangKeun Kim, et al. 2026. “Astroimmunology: The Effects of Spaceflight and Its Associated Stressors on the Immune System.” Nature Reviews Immunology 26 (3): 189–212. https://doi.org/10.1038/s41577-025-01226-6.