Gut Microbiome May Impact the Effectiveness of Flu Vaccine

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The microbiota of the digestive system plays a fundamental role in the function of the human immune response. Researchers found that the use of antibiotics, long known to disrupt the gut microbiome and increase inflammation in the body, may impact the effectiveness of vaccinations such as the flu vaccine

Research conducted by Stanford University scientists found that the use of oral antibiotics weakens the health of the gut microbiome, a complex community of trillions of microbial cells found in each individual.[i] This weakening of the microbiome, in turn, weakens the body's immune system and alters the response to influenza (flu) vaccination.

During the study, all participants received the flu vaccination but only half received antibiotics for a five-day period before receiving the vaccination. Those receiving oral antibiotics had reduced levels of gut bacteria, a hindered response to the vaccine and experienced higher levels of inflammation -- findings that were consistent with previous studies.[ii]

Interestingly, researchers believe that this may account for the difference in response to vaccination among older adults, who often have weakened immune responses due to aging.[iii] The results of this study seem to suggest that the one-size-fits-all policy of vaccination for everyone, regardless of age or health, may not be the most effective solution and emphasizes how little is understood about the efficacy of vaccinations in general.

This wasn't the first study to find that a loss of microbiome adversely impacts the effectiveness of vaccination. Additional analysis has found that disrupted microbiomes can impair the responses of immunoglobin A (IgA), a type of antibody responsible for the immune function of mucous membranes, and reduce the efficacy of vaccinations.[iv],[v]

Disrupted Microbiome Impairs Immune System and Vaccination Response

Researchers are increasingly convinced that the health of the gut microbiome shapes the health of the body's immune response and that maintaining the health of your microbiome is key to the prevention of a variety of diseases, as well as the response to vaccination.[vi],[vii]

The complex nature of the bacterial system in your gut continues to impress scientists, but understanding of the importance of keeping these bacteria healthy and active has only scratched the surface. It's clear, however, that deviations from "normal" development of gut bacteria can have a catastrophic impact on your immune system. Examples of such immune-disrupting bacterial deviations include:

These disruptions may lead to a greater risk of inflammatory disease later in life, including Type 1 diabetes, Crohn's disease, inflammatory bowel disease, pulmonary disease, atopy and obesity, as well as a variety of cancers.[ix] Researchers have also discovered a possible link between multiple sclerosis and a disrupted microbiome.[x]

This interplay between a healthy gut microbiome and immune response is often seen in individuals adhering to a high processed-food "Western" diet. This type of diet disrupts the production of autoantibodies, a type of antibody produced by the immune system and a common predictor of autoimmune diseases.[xi],[xii],[xiii],[xiv]

An additional dietary factor that increases the production of autoantibodies is gluten, which is highly prevalent in standard Western diets.[xv] Furthermore, the oral antibiotics found prevalently in Western culture play an adverse role in the well-being of your gut microbiome.

Multiple studies have identified antibiotic treatment as an enhancer of inflammation, concluding that the overuse of antibiotics (especially in high-income countries) could explain the dramatic rise in autoimmune and inflammatory-related diseases.[xvi]

This use of antibiotics induces the relocation of bacteria across the lining of the large intestine, promoting inflammation. According to one study, "bacterial translocation occurred following a single dose of most antibiotics tested, and the predisposition for increased inflammation was only associated with antibiotics inducing bacterial translocation."[xvii]

The mechanisms that impact the efficacy of vaccination are numerous and complex, and scientific understanding of the importance of a healthy gut microbiome is still in its infancy, as is knowledge surrounding the health consequences of our vaccination culture.

The one-size-fits-all method of vaccinating everyone deserves careful further research given the various adverse effects of antibiotics and improper diet on the immune system. For more information about the research surrounding vaccinations, and the possible effects vaccinations have on your body, please visit the vaccination research database.


[i] Cell. 2019 Sep 5;178(6):1313-1328.e13. doi: 10.1016/j.cell.2019.08.010.

[ii] NIH/National Institute of Allergy and Infectious Diseases. "Disrupting the gut microbiome may affect some immune responses to flu vaccination." ScienceDaily. ScienceDaily, 6 September 2019.

[iii] NIH/National Institute of Allergy and Infectious Diseases. "Disrupting the gut microbiome may affect some immune responses to flu vaccination." ScienceDaily. ScienceDaily, 6 September 2019.

[iv] Immunol Lett. 2017 Oct;190:247-256. doi: 10.1016/j.imlet.2017.08.025. Epub 2017 Aug 30.

[v] Front Immunol. 2018; 9: 439.

[vi] Nat Rev Immunol. Author manuscript; available in PMC 2014 Jul 14.

[vii] Gut Microbes. 2012 Jan 1; 3(1): 4-14.

[viii] Nat Rev Immunol. Author manuscript; available in PMC 2014 Jul 14.

[ix] Front Immunol. 2018; 9: 1830.

[x] Front Immunol. 2018; 9: 439.

[xi] J Clin Invest. 2015 Jun 1; 125(6): 2194-2202.

[xii] Nat Clin Pract Rheumatol. Author manuscript; available in PMC 2009 Sep 1.

[xiii] Front Immunol. 2018; 9: 439.

[xiv] J Clin Invest. 2001 Nov 15; 108(10): 1417-1422. doi: 10.1172/JCI14452

[xv] Front Immunol. 2018; 9: 439.

[xvi] Cell. Author manuscript; available in PMC 2015 Mar 27.

[xvii] Gut. Author manuscript; available in PMC 2017 Jul 1.

Disclaimer: This article is not intended to provide medical advice, diagnosis or treatment. Views expressed here do not necessarily reflect those of GreenMedInfo or its staff.
Sayer Ji
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