Gut bacteria may decide who gets a fever after vaccination

Fever after vaccination has long been treated as an unpredictable nuisance, a roll of the biological dice that leaves some people reaching for a thermometer and others wondering why their arm is the only part of them that hurts. A new study published in Science suggests that the dice were never random at all. Researchers led by Kelsey Huus found that the composition of the human gut microbiome, the vast community of bacteria residing in the intestines, appears to influence whether a person develops fever and flu-like symptoms after receiving an mRNA vaccine. The work points toward a future in which the microbial and dietary landscape of the body could be deliberately shaped before immunization, blunting uncomfortable side effects without weakening the protective immunity that vaccines are designed to build.

The clinical stakes are considerable. Vaccines remain among the most powerful tools in public health, yet people vary enormously in how their bodies respond to them. Fever and flu-like symptoms are among the most commonly reported adverse reactions, and they are particularly frequent with mRNA vaccines and other formulations that use lipid nanoparticles to deliver their payload. These reactions are generally short-lived, but they are not trivial in their consequences. People who experience a rough forty-eight hours after a first dose are more likely to hesitate before a second, and vaccine hesitancy, once seeded, spreads through communities faster than any pathogen. Understanding who is at risk, and why, has therefore become a genuine research priority.

One puzzling observation framed the new investigation: not everyone who receives the same vaccine develops a fever, and those who do tend to develop one repeatedly, across successive doses. That pattern strongly suggested the existence of stable individual risk factors rather than chance variation. The immune system’s baseline state, shaped over years by genetics, environment, and the microbes it coexists with, seemed a likely place to look. The gut microbiome stood out as a candidate because it is known to tune immune activity throughout the body, priming inflammatory pathways and calibrating how the immune system responds to molecular signals it encounters.

To test this hypothesis, Huus and colleagues assembled a cohort of 171 healthy adults and profiled them with unusual thoroughness. Before and after receiving the mRNA vaccine against SARS-CoV-2, participants provided fecal samples for microbiome sequencing, had their body temperatures monitored, and gave blood samples for the measurement of immune markers circulating in plasma. This longitudinal design allowed the researchers to ask a specific question: did features of the gut ecosystem present before vaccination predict who would mount the inflammatory response that produces fever afterward?

The answer, in short, was yes. Participants who entered the study with greater intestinal inflammation were more likely to develop vaccine-induced fever. So were those whose guts harbored higher levels of flagellin expression, flagellin being the protein that forms the whiplike tails many bacteria use to swim. The key contributors belonged to Lachnospiraceae, a family of common gut bacteria. Flagellin is not merely a structural protein; it is also a molecular pattern that the immune system recognizes through dedicated receptors, activating inflammatory signaling cascades. In effect, certain gut residents were already holding the immune system’s alarm system partially depressed, and the vaccine’s arrival pushed it over the threshold that registers as fever.

The mechanistic picture that emerges is one of priming rather than causation in the simple sense. The vaccine does not create the inflammatory tendency; it reveals it. A gut microbiome rich in flagellin-producing Lachnospiraceae, operating in an environment of low-grade intestinal inflammation, establishes a baseline of immune activation. When the vaccine delivers its antigen and its lipid nanoparticle adjuvant effects, the systemic inflammatory response that follows is stronger in these individuals, strong enough to produce the fever and malaise that many recipients dread. In others, with different microbial profiles, the same vaccine triggers a quieter reaction.

Where does that microbial profile come from? The study’s dietary findings offer a provocative clue. Industrialized diets, the researchers found, appear to promote the inflammatory, fever-associated microbiome. Lower consumption of whole plant foods, along with eating patterns characterized by higher fat intake or greater reliance on processed foods, was associated with microbiome features linked to vaccine fever. Vegetarian diets, by contrast, correlated with microbiome characteristics that contributed to less fever. The fiber-rich substrates that plant foods supply are known to nourish gut bacteria that produce short-chain fatty acids, compounds with broadly anti-inflammatory effects on the intestinal lining, and the new data suggest this well-studied axis extends all the way to how the body tolerates vaccination.

Crucially, the researchers showed that dietary manipulation altered both microbiome composition and the vaccine responses associated with it, demonstrating that the relationship is not a fixed trait but a modifiable one. Even more important is what the study did not find. Flagellin, intestinal inflammation, and diet did not affect antibody responses to the vaccine. The microbiome-driven inflammation amplified side effects without touching the immunity that matters. This separation is the study’s most consequential finding, because it means the inflammatory and protective arms of the vaccine response can, in principle, be decoupled. A person could one day reduce their fever risk without sacrificing one iota of protection against infection.

That possibility is captured in an accompanying Perspective by Bali Pulendran, who writes that diet, microbial ecology, and metabolic state are not immutable, and that people might one day prepare for vaccination as deliberately as the vaccine itself is formulated. The image is striking: pre-vaccination protocols that include dietary adjustments or microbiome-targeted interventions, prescribed with the same care as the dose schedule itself. Such interventions remain speculative, and the study establishes associations and mechanisms in a defined cohort rather than prescribing clinical practice. But the direction of travel is clear, and the tools required, from dietary counseling to microbiome profiling, already exist in some form.

The broader lesson reaches beyond mRNA vaccines and beyond fever. The human body is not a passive container into which medicine is poured; it is an ecosystem whose resident organisms and metabolic state shape every pharmacological and immunological encounter. This study adds vaccination, one of medicine’s most standardized interventions, to the growing list of outcomes that individualize at the level of the microbiome. It also reframes an old complaint. The fever that follows a shot is not the vaccine misfiring, but a conversation between the vaccine and the trillions of microbes that were there first. Learning to conduct that conversation, through diet and microbial stewardship, could make vaccination gentler for millions of people while leaving its protective power fully intact.

Subject of Research: Influence of the human gut microbiome and diet on fever side effects after mRNA vaccination

Article Title: The human gut microbiome shapes vaccine side effects

Article References: The human gut microbiome shapes vaccine side effects. (n.d.). Original publication

Image Credits: AI Generated

DOI: Not provided

Keywords: gut microbiome, vaccine side effects, fever, mRNA vaccines, Lachnospiraceae, flagellin, diet, inflammation, antibody response, vaccine hesitancy, Science journal, immunology