Astronauts’ Gut Bacteria Switch to Digesting Protein Within Weeks in Space

If you have ever wondered whether a disrupted routine can change what your gut bacteria are actually doing, a new study of 52 astronauts is one of the cleanest natural experiments available. Researchers tracked blood chemistry before, during, and after missions on the International Space Station and found a specific, repeatable shift in gut bacterial metabolism, one that showed up within weeks of launch and was consistent enough to sort space-flown blood samples from Earth samples with striking accuracy. For anyone already trying to figure out whether their own gut is behind a health complaint, it is a useful reminder that gut bacteria can change their behavior fast, in response to the body's environment, not only to what is on the plate.

Key takeaways:

• Blood tests from 52 astronauts show gut bacteria shift from fermenting fiber toward fermenting protein within weeks of reaching space, misclassifying only 2.6% of in-flight samples.
• The shift showed up shortly after launch and faded within a few days of landing, with no evidence it worsened the longer astronauts stayed in orbit.
• The study measured blood chemistry only. It did not sequence the gut microbiome and did not measure intestinal transit time, so the researchers' idea that slower gut transit explains the shift is a proposed explanation, not a proven one.
• The compounds involved are the same ones studied in kidney disease and everyday gut health, and researchers propose (without yet testing) that more fiber could help astronauts on long missions.

Gut Bacteria Shift From Fermenting Fiber to Protein in Astronauts' Blood

A study of 52 astronauts found that spaceflight shifts gut bacterial metabolism from fermenting fiber toward fermenting protein (proteolysis), a change visible in blood within weeks of launch. The research, led by La Barbera and colleagues at the University of Copenhagen with NASA co-authors, was published in Nature Communications in June 2026. Using a technique called liquid chromatography high-resolution mass spectrometry (LC-HRMS, a method that identifies and measures thousands of small molecules in a blood sample at once), the team found that around 40 circulating compounds changed significantly during spaceflight.

The clearest signal came from a cluster of molecules that gut bacteria produce when they break down protein instead of fiber: p-cresol sulfate, phenylacetylglutamine, 4-ethylphenol sulfate, and, in a secondary analysis, 3-indoxyl sulfate and phenol sulfate, all of which rose during flight. These are "host-microbial co-metabolites," meaning gut bacteria generate the raw compound and the liver then chemically modifies it (in this case, through a process called sulfation) before it circulates in blood. Meanwhile tyrosine, an amino acid that is a raw material for some of these compounds, fell. Three of these same metabolites also turned up as different in NASA's earlier Twins Study, which compared astronaut Scott Kelly's blood chemistry against his identical twin on the ground during Kelly's year in space, giving the new finding independent, if partial, support.

Why Gut-Health Researchers and Kidney Patients Recognize These Molecules

The metabolites that rose in astronauts' blood are not obscure. p-cresol sulfate, phenylacetylglutamine, and indoxyl sulfate are studied extensively as gut-derived compounds tied to cardiovascular and kidney health in people with chronic kidney disease, where the kidneys struggle to clear them and blood levels climb. That does not mean the astronauts in this study had any kidney impairment. The overlap matters for a different reason: it shows that when gut bacteria shift toward digesting protein rather than fiber, they produce a fairly consistent, well-studied set of byproducts, in astronauts and on Earth alike.

That distinction is relevant to anyone managing IBS, IBD, or general digestive symptoms and looking into their own gut health. Fiber fermentation by gut bacteria tends to produce short-chain fatty acids, generally considered favorable for colon lining health, while protein fermentation produces the phenolic and indolic compounds seen in this study, which some fiber research links to less favorable colon conditions when it dominates. This study did not test colon health outcomes in astronauts. It shows the metabolic signature, not proof of harm.

How Researchers Tracked 52 Astronauts' Chemistry Across Nine Missions

The study drew on 488 plasma samples from 52 astronauts (41 men, 11 women, averaging 48 years old) collected before, during, and after ISS missions lasting 2 to 9 months, flown between 2006 and 2018 and pooled from three earlier NASA studies. Samples broke down as 154 taken pre-flight, 233 in-flight, and 101 post-flight. A statistical model built on 81 of the measured molecules classified whether a sample came from space or Earth with an error rate of just 2.6%, while pre-flight Earth samples alone had a higher 7.1% error rate, which the authors attribute to astronauts' spaceflight training and more variable diets on the ground. A separate statistical model tracking changes over time confirmed 96 features changed significantly after launch, narrowing down to roughly 40 compounds after quality filtering. Notably, the researchers found no major differences in this metabolic shift between men and women, despite the cohort skewing heavily male.

What This Means If You're Researching Your Own Gut Health

This study does not diagnose or treat anything, and it is not evidence that any supplement or diet change is proven to work. What it does show is that gut bacterial metabolism can shift measurably within weeks of a major environmental change, without any change in willpower or willingness to eat differently. If you already suspect a gut issue is behind fatigue, skin problems, or digestive symptoms, this is a concrete illustration of how quickly the balance between fiber-fermenting and protein-fermenting bacteria can move, and why doctors and researchers increasingly look at these specific metabolites, rather than just "good bacteria versus bad bacteria," when trying to understand gut chemistry.

The authors propose that microgravity may slow intestinal transit time (the speed at which food moves through the gut), possibly giving bacteria more time to ferment protein rather than fiber. That is worth underlining as a hypothesis: this study measured blood chemistry only. It did not sequence the astronauts' gut microbiome and did not measure how fast food moved through their intestines, so it cannot confirm that transit time is the cause. If you have chronic constipation or digestive symptoms, this study is a reasonable thing to mention to a doctor as background on why gut transit time and diet matter, not a diagnosis of what is happening in your own case.

The Study's Open Questions and Limitations

The biggest limitation is that this is observational: no diet or supplement was tested, so nothing here proves that changing what astronauts (or anyone else) eats would change the outcome. The metabolite changes were measured in blood only; the researchers never sequenced the gut microbiome itself, so which specific bacteria are doing the fermenting remains inferred, not directly shown. The cohort, while unusually well-tracked over time, is small, highly selected for fitness, and skews male (41 of 52), which limits how far the findings generalize to the broader public. The samples were also pooled from three separate NASA studies spanning 2006 to 2018 with different original protocols. It is a single study, though it converges with the Twins Study on three metabolites. One further correction worth stating plainly: the shift appeared shortly after launch and faded within a few days of landing, and the researchers found no evidence that it deepened or worsened the longer astronauts remained in orbit.

What Researchers Want to Test Next

The authors propose increasing astronauts' intake of slow-fermented carbohydrates, meaning fiber sources that gut bacteria break down gradually, aboard the ISS to see whether it reduces protein fermentation and improves gastrointestinal comfort on long-duration missions. That intervention has not been tested yet; the current study only established the chemical pattern it is meant to address. With NASA and other agencies planning longer missions, including to Mars, a controlled trial of dietary fiber intake in space is a logical next step the paper points toward without having run it.

Common Questions

Does this study prove spaceflight causes astronaut constipation? No. The study measured blood chemistry, not bowel symptoms, and the researchers describe slowed intestinal transit as a possible explanation for the metabolite shift, not something they measured or proved.

Are these findings useful for people on Earth with gut or kidney issues? The specific metabolites, like p-cresol sulfate and phenylacetylglutamine, are studied in kidney disease and general gut health research, but this study only examined astronauts in space; it did not test or validate anything as a clinical marker for the general public.

Does eating more fiber fix this? The authors propose that more slow-fermented carbohydrates could reduce protein fermentation, but that idea was not tested in this study, so it remains a proposed countermeasure rather than a proven fix.

Did the effect get worse the longer astronauts stayed in space? No. The metabolite changes appeared shortly after launch and subsided within a few days of returning to Earth, and the researchers found no sign that the shift deepened over the course of longer missions.

References

1. Giorgia La Barbera, Jan Stanstrup, Sara R. Zwart, Scott M. Smith, Henrik M. Roager, Lars Ove Dragsted (2026). Longitudinal metabolomics profiles reveal increased gut microbial protein fermentation during Spaceflight. Nature Communications. https://doi.org/10.1038/s41467-026-74979-w
2. Francine E. Garrett-Bakelman, Manjula Darshi, Stefan J. Green, et al. (2019). The NASA Twins Study: A multidimensional analysis of a year-long human spaceflight. Science. https://doi.org/10.1126/science.aau8650
3. Gut-derived uremic toxins and cardiovascular health in chronic kidney disease. NIH. https://pmc.ncbi.nlm.nih.gov/articles/PMC12306874/
4. Dietary Fibre Modulates the Gut Microbiota. NIH. https://pmc.ncbi.nlm.nih.gov/articles/PMC8153313/