Antibiotics May Disrupt Gut Microbiome and Inhibit Immune Responses to Flu Shot


A NIAID-sponsored study found that most participants who received a 5-day course of broad-spectrum antibiotics prior to a season flu shot had reduced levels of gut bacteria.

As influenza season draws near, public health officials are once again recommending vaccination with the seasonal flu shot for all individuals >6 months.

But now, a new study published in Cell, reports that oral antibiotics, which may alter or kill microorganisms in the gut microbiome, can affect immune responses to the seasonal influenza vaccine. The research was funded by the National Institute of Allergy and Infectious Diseases.

For the investigation, a team of researchers examined 33 adult participants. The first group, comprised of 22 participants was studied during the 2014-15 influenza season and the second group, made up of 11 participants, was studied during the 2015-16 influenza season.

According to the investigators, led by scientists at Stanford University, the participants in the first group had high pre-existing immunity to the virus strains contained in the seasonal flu shot of 2014-15; however, the group of 11 participants had low immunity to the virus strain in the 2015-16 vaccine.

Each of the enrolled participants received a seasonal flu shot. To evaluate the role of antibiotics, half of the participants in each group also received a 5-day oral course of a broad-spectrum antibiotic regimen containing neomycin, vancomycin, and metronidazole prior to vaccination.

The participants were required to submit stool and blood samples at various points up to 1 year after vaccination. The investigators analyzed the samples and tracked each participant’s immune response to the vaccine and observed the diversity and number of organisms present in their gut microbiomes.

Just as the study team hypothesized, most participants who received the 5-day course of broad-spectrum antibiotics had reduced levels of gut bacteria.

According to a press release, the study team observed that among the participants during the 2015-16, who had little prior immunity to the vaccine strains, the course of antibiotics hindered immune responses to 1 of the 3 virus strains in the vaccine, which were an H1N1 A/California-specific virus.

The investigators indicate that this finding signals that these participants would be less protected against infection with that strain when compared to those who had not received antibiotics. Furthermore, this finding supports earlier research results from mouse models.

Individuals who took antibiotics prior to receiving the flu shot also experienced changes to their immune system that led to a pro-inflammatory state, which is often seen in older adults who have received influenza vaccines. The investigators hypothesize that this condition is “related to the process by which the microbiome regulates the metabolism of bile acid—with fewer microorganisms, this process is disrupted.”

The study team notes that since human microbiomes change throughout life, further research could explore why older adults have different reactions to influenza vaccines and why they have weaker immune systems overall.

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