Gut Bacteria May Help Explain Who Runs a Fever After a Vaccine

A team led from the Max Planck Institute for Biology Tübingen reports that the bacteria in a person's gut are linked to whether that person runs a fever after an mRNA vaccination. The study, published Oct. 8, 2026, in Science, followed 171 healthy adults through SARS-CoV-2 mRNA vaccination, tracking their stool bacteria, their oral temperature and markers in their blood.

The authors write that fever is a common reaction to vaccination and one that feeds vaccine hesitancy and lowers uptake. They set out to understand why that risk varies so much from one person to the next.

Across the 171 participants, the paper reports that fever risk tracked with low-grade inflammation in the intestine and with how much flagellin their gut microbes were making before the shot. Flagellin is a protein in the tail that a bacterium swims with. People who later ran a fever also carried more of the tailed bacteria that make it, members of a family called Lachnospiraceae. That is an association measured in one group of 171 adults, not a demonstrated cause. Fever risk was also associated with what participants said they ate and with markers of their metabolism.

The causal tests were run outside people. The authors report that microbiomes taken from donors with high fever risk provoked stronger inflammation in human intestinal organoids, small pieces of gut tissue grown in the laboratory, and produced flagellin-dependent vaccine reactions in mice raised without gut bacteria of their own.

The team also found that, in the mice, diet shifted both the bacteria's flagellin output and the strength of the vaccine reaction.

Kelsey E. Huus of the Max Planck Institute for Biology Tübingen and colleagues write that their findings identify the gut microbiome as a driver of vaccine-induced fever, and that strategies aimed at the microbiome could improve vaccine side effects. No such strategy was tested in people here. A commentary on the paper runs in the same issue of Science.