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Labs & diagnostics · health · gut · Emerging
Gut Bacteria Pattern Linked To Fever Risk After mRNA Vaccination In Adults
171 healthy adults studiedFecal microbes tracked over timeFlagellin protein flaggedDiet modified mouse reactions
Researchers publishing in Science on October 8, 2026 found that the mix of bacteria living in a person's gut before vaccination was linked to whether they developed a fever after getting an mRNA vaccine.
Scientists longitudinally tracked fecal microbes, oral temperature, and blood markers of immune activity in 171 healthy adults who received SARS-CoV-2 mRNA vaccines. Fever risk was linked to three things measured before the shot: low-grade intestinal inflammation, a higher abundance of flagellated Lachnospiraceae bacteria, and increased expression of flagellin, a protein found on the tail-like structures these bacteria use to move. People who reported certain diet patterns and had particular metabolic markers were also more likely to run a fever after vaccination.
To test whether the gut bacteria themselves were driving the reaction, researchers transferred microbiomes from high-fever and low-fever donors into human intestinal organoids, which are lab-grown clusters of gut tissue, and into germ-free mice. Microbiomes from fever-prone donors were linked to stronger inflammation in the organoids and to fever-like vaccine reactions in the mice, an effect the authors report depended on flagellin. The flagellin pattern in the microbiome and the strength of the mouse vaccine reaction could both be changed by altering diet.
Flagellin is a protein bacteria use to build their flagella, the whip-like tails that let them move. The immune system has sensors built specifically to detect flagellin because it signals the presence of live, motile bacteria, so more flagellin exposure means more immune alarm bells going off, which can translate into a stronger inflammatory reaction, including fever, when the immune system is also responding to a vaccine.
These findings identify the gut microbiome as a driver of vaccine-induced fever, suggesting that microbiome-targeting strategies could modulate immune tone and improve vaccine side effects.
Data Panel
- Who
- 171 healthy adults receiving SARS-CoV-2 mRNA vaccines; age and sex breakdown not reported
- Design
- Longitudinal observational study tracking fecal microbiota, oral temperature, and blood immune markers, paired with human intestinal organoid and gnotobiotic mouse experiments
- Dose
- Not applicable; standard mRNA vaccine dosing, no study-administered dose reported
- Primary result
- Fever risk was linked to prevaccine low-grade intestinal inflammation, higher abundance of flagellated Lachnospiraceae bacteria, and increased flagellin expression; exact percentages not reported in the abstract
- Secondary
- Microbiomes from fever-high donors were linked to stronger inflammation in human intestinal organoids and to flagellin-dependent vaccine reactions in germ-free mice; diet changes modified both the flagellin phenotype and the mouse vaccine reaction; size not reported
- Funding / conflicts
- Funding and conflicts not reported in the abstract.
This is a human observational study combined with lab-dish and mouse experiments; it shows a link between gut bacteria patterns and fever risk, not proof that the bacteria alone cause fever in people. The abstract does not report average age, sex breakdown, exact fever rates, or funding and conflict disclosures.
Dr. Axe's Take
This fits what I believe about the gut being command central for how the immune system behaves, including how hard it reacts to a vaccine. A gut already simmering with low-grade inflammation and carrying more flagellin-producing bacteria looks primed to overreact once a vaccine arrives. The diet link makes sense too, since what you eat shapes which bacteria thrive and how much flagellin they produce. My recommendation for anyone getting vaccinated: spend the weeks beforehand eating gut-supportive foods, fiber-rich vegetables and fermented foods like sauerkraut and kefir, while cutting processed food and added sugar that feed inflammatory bacteria. A calmer gut generally means a calmer immune response.
— Dr. Axe