An astronaut's microbiome 🧠

5 things spaceflight reveals about your gut

What does an austronaut’s microbiome look like?

What happens to your gut in orbit could teach us a lot about health back on Earth.

These changes matter because your microbiome is closely related to your immune system (with 70% of your immune cells found in your gut).

And microbes are linked to many health issues faced in space.

Like how astronauts can get constipated, get skin flares ups, and their immune defences tend to drop (sometimes reawakening long-dormant viruses like herpes).

So understanding what microbes we carry (and how they change) could affect austronaut’s health in space, especially on long missions - and help us explore how microbes adapt to a new environment.

What we’ll cover today

• How space travel rapidly shifts your microbiome

• Why microbes adapt faster than humans in orbit

• The rise of antibiotic resistance during missions

• How 16 sunrises a day mess with your gut (and mood)

Your microbiome changes in space!

Even short spaceflights can shift your microbiome.

In a study of four astronauts on a 3-day mission, researchers tracked changes across the gut, mouth, nose, and skin microbiomes.

There were fast and dramatic shifts in their microbiomes, especially the skin, where there was a noticeable uptick in viral activity (mostly from phages, which are viruses that infect bacteria).

The researchers think it could be down to changes in hygiene (wet wipes instead of showers), or simply picking up new microbes from the shared, enclosed environment of the spacecraft and close contact with other crew members.

Most of these changes were short-lived and bounced back after landing.

Though some longer-lasting shifts happened in the oral microbiome, with more bacteria often seen with oral plaque, which were also linked to changes in immune cell gene expression. That might matter because it suggests these shifts aren’t just surface-level but may influence how the immune system responds.

It’s a fascinating reminder of how sensitive our microbes are to environmental change - like leaving planet Earth - and how quickly they respond.

The International Space Station has a microbial fingerprint

The International Space Station (ISS) has its own unique mix of microbes (like a microbial fingerprint) and it turns out that living there can actually change the microbes living on and inside astronauts.

Over time, the microbes on the ISS and on the astronauts started to look more alike.

It’s not only that astronauts pick up microbes from the ISS, they also leave their own microbial mark on the station.

The astronauts and the station are effectively “trading” microbes.

A few of the new microbes astronauts picked up in space (mostly skin and nose microbes) were still found in their microbiome months after they came home.

Your microbes may be better at space travel than you

In extreme environments like space, microbes can adapt surprisingly fast.

That’s because they reproduce quickly and have simple biological systems that can rapidly shift in response to stress.

Some of the ways microbes adapt:

• Stronger repair tools: Some microbes boost their DNA repair systems to survive space radiation.

• Going dormant: They can shut down and lie low, pausing growth to ride out harsh conditions.

• Tougher armour: Microbes can become more resistant to antibiotics, heat, UV, and dryness by changing their structure and defences.

These changes happen on a much shorter timescale than human adaptation.

While our immune system might take days or weeks to respond, a microbe can evolve across generations in a matter of hours.

Some bacteria get sneakily more resistant in space

A study of microbiome samples from four astronauts found that spaceflight was linked with changes in antibiotic resistance genes, even though no antibiotics were used.

Some microbes carried more antibiotic resistance genes (stretches of DNA that help them survive antibiotics) suggesting these resistant microbes may have become more common during spaceflight.

One of these genes, which protects microbes against a type of antibiotic called elfamycin, stayed higher than normal even months after the astronauts came back to Earth. Another, linked to resistance against penicillin-type antibiotics, rose during the mission but dropped back down afterward.

This matters because it suggests that being in space - where there’s no gravity, more radiation, and added stress - might change microbes in a way that makes them more resistant to antibiotics, even when no antibiotics are used.

In long-term missions, especially those further from Earth, this could make infections harder to treat and complicate medical planning.

Circadian chaos messes with your microbes

On the ISS, astronauts see 16 sunrises and sunsets a day, not exactly ideal for a stable body clock.

That constant disruption to circadian rhythms affects key hormones like melatonin and cortisol, which help regulate sleep, stress, and immunity.

When these rhythms are out of sync, it can shift the gut microbiome, making the immune system more reactive and increasing inflammation.

These changes may feed into mental health risks via the gut–brain axis - the two-way communication between the gut and the brain.

Some of the same microbial groups that drop in astronauts also appear lower in people with depression. That doesn’t mean one causes the other, but it suggests potentially a shared pathway involving inflammation, microbial metabolites, and brain chemistry.

This is why some researchers are suggesting that protecting the body clock, by simulating a natural day–night cycle, and supporting gut health could be one way to help keep astronauts mentally and physically well on long missions.

If you were designing a space mission, what would you do to help support the microbiome of your crew?

Chat soon,

Emily xx

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