Persistent Damage to the Gut Microbiome Following Messenger RNA SARS-CoV-2 Vaccine

Introduction: Messenger RNA vaccines for SARS-CoV-2 are widely distributed, yet their effect on the human gut microbiome, especially long-term up to one year, is unknown. The human gut microbiome is an essential determinant of human health. Genus Bifidobacteria decline is associated with inflammatory bowel disease, obesity, neurological disorders, C. diffícile infection and severe COVID-19.1,2,3 Case Description/Methods: We longitudinally recorded the relative abundance of genus Bifidobacteria in 4 subjects before receiving mRNA vaccine (Pfizer or Moderna), approximately one month after vaccine, and 6 to 9 months later. Additional SARS-CoV-2 vaccines were given during that period, totaling 2 to 3 doses. Samples were collected at the timepoints mentioned. There were no diet changes or new medication’s during the entire period and subjects were told to stay on the same regimen throughout the 6 months. Metagenomic next generation sequencing-based methods were applied to samples obtained from fecal collection. DNA was extracted, and the library prepped, enriched and sequenced on an Illumina Nextseq 550 system. Relative abundance of Bifidobacteria decreased after 1 month to in 3 of 4 subjects to: 38%, 258%, 49% and 90% of pre-vaccine levels. After 6-9 months, all Bifidobacteria relative abundance decreased to: 15%, 0%, 35%, and 60% of pre-vaccine levels. This study is IRB approved (Figure 1). Discussion: This is the first study to demonstrate a decrease in relative abundance of genus Bifidobacteria bacteria 6-9 months after SARS-CoV-2 vaccination. All subjects dropped below a 1% relative abundance. Although a small sample, these findings may suggest a potential mechanism for post-vaccination complications; however, no subjects in the study demonstrated significant complications. Gut dysbiosis post mRNA SARS-CoV-2 vaccines could potentially be a future indication for restoration of Bifidobacteria either orally or directly via fecal transplant.Figure 1.: Bifidobacteria relative abundance demonstrates a lasting decline after SARS-CoV-2 mRNA vaccination.