Gut Microbiome and Intestinal Inflammation May Hold Key to Post-Vaccine Fever

A study found that many adults who experienced fever after a COVID vaccine had higher levels of bacteria in intestinal samples.

Matt MacKenzie

Oct. 28, 2026

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Key Highlights

Researchers measured gut microbiomes, body temperature, and immune markers in 171 adults before and after mRNA COVID-19 vaccination.
Participants who developed fevers had higher levels of flagellated gut bacteria, including Lachnospiraceae.
Bacterial flagellin may trigger inflammatory pathways that amplify vaccine-related reactions.
A high-fat, highly processed diet may enhance these reactions.
The increased side effects were not associated with weaker antibody responses or reduced vaccine efficacy.

A new study published in Science suggests that a person’s gut microbiome and levels of inflammation in the intestine could be behind post-vaccination fevers. CIDRAP has the news.

Fever can be a factor in vaccine hesitancy, especially for vaccines against flu and COVID. It is a common reaction to a number of different vaccines.

The study was based on 171 adults whose fecal microbiomes, body temperature, and blood-based immune markers were measured before and after receiving mRNA COVID-19 vaccines. A bacteria that lives in the gut called Lachnospiraceae and produces flagellin played an important role in vaccine-related reactions. Participants who had fevers after vaccination had higher levels of flagellated bacteria in their intestinal samples.

Flagellin may activate inflammatory pathways, intensifying vaccine-related reactions. These reactions may be enhanced by a high-fat and highly processed diet. The authors also were sure to note that flagellin and inflammation don’t affect antibody responses to vaccines; increased side effects had no bearing on vaccine efficacy.