S227 Messenger RNA SARS-CoV-2 Vaccines Affect the Gut Microbiome : Official journal of the American College of Gastroenterology | ACG

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S227 Messenger RNA SARS-CoV-2 Vaccines Affect the Gut Microbiome

Hazan, Sabine MD1; Dave, Sonya PhD2; Barrows, Brad DO1; Borody, Thomas J. MD, PhD, DSc, FACG3

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The American Journal of Gastroenterology 117(10S):p e162, October 2022. | DOI: 10.14309/01.ajg.0000857548.07509.09
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Messenger RNA vaccines for preventing SARS-CoV-2 infection are widely used yet their effect on the gut microbiome is not known. Low bifidobacteria levels have been linked with severe SARS-CoV-2 infection, inflammatory bowel disease, Clostridioides diffícile infection, obesity and aging. Preliminary case reports suggest fecal microbiota transplant could cure SARS-CoV-2 infection (1). A study by Bozkurt et al. showed that SARS-CoV-2 patients taking bifidiobacteria-containing probiotics had lower COVID-related hospitalization times (2).


34 subjects had stool collection prior to vaccination and one month post vaccination to evaluate the relative abundance of bifidobacteria in the gut. DNA was extracted, library was prepped, and enrichment and sequencing were done using metagenomic next generation sequencing.


Relative abundance of genus bifidobacteria significantly decreased to about half of original value after vaccination (P = 0.0065 via Wilcoxon signed rank test). Prior to vaccination, median (interquartile range) values of relative abundance for genus bifidobacteria were 1.13% (0.0016% to 2.52%) and after vaccination were 0.64% (0.0015% to 2.48%).


Bifidobacteria, included in the $1 billion industry of probiotics, has been shown to be critical in inflammatory diseases, severe COVID-19, obesity, and the aging process. Our results, although preliminary suggest that SARS COV-2 mRNA vaccine decreases levels of bifidobacteria (P = 0.0065). Future studies will be needed to characterize the time course of this decrease in bifidobacteria abundance, its impact on human health, and whether or not similar findings are seen with other vaccines (Figure).

Figure 1.:
Bifidobacterium relative abundance decreases ( P = 0.0065) in subjects (n=34) after vaccination compared to before vaccination in the same subjects. Bars plot median; error bars plot interquartile range


1. Biliński J, Winter K, Jasiński M, et al. Rapid resolution of COVID-19 after faecal microbiota transplantation. Gut. 2022;71(1):230-232. doi:10.1136/gutjnl-2021-325010
2. Bozkurt HS, Ö Bilen. Oral booster probiotic bifidobacteria in SARS-COV-2 patients. Int J Immunopathol Pharmacol. 2021;35:20587384211059677 doi:10.1177/20587384211059677
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