Vaccination (BBIBP-CorV vaccine) against the SARS-CoV-2 virus affects the gut microbiome

Several observational studies have confirmed that SARS-CoV-2 might substantially affect the gastrointestinal (GI) systems by replicating in human small intestine enterocytes. Yet, so far, no study has reported on the effect of inactivated SARS-CoV-2 virus vaccines on gut microbiome alterations. In this study, we examined the effect of the BBIBP-CorV vaccine (ChiCTR2000032459, sponsored by the Beijing Institute of Biological Products/Sinopharm) on the gut microbiome. Faecal samples were collected from individuals who received two doses of intramuscular injection of BBIBP-CorV, and matched unvaccinated controls. DNA extracted from faecal samples was subjected to 16S ribosomal RNA sequencing analysis. The composition and biological function of the microbiome between vaccinated and unvaccinated individuals were compared. Compared with unvaccinated controls, vaccinated subjects exhibited significantly reduced bacteria diversity, elevated Firmicutes/Bacteroidetes (F/B) ratio, tend toward Faecalibacterium-predominant enterotype, and altered gut microbial composition and functional potential. Specifically, the intestinal microbiome in vaccine recipients was enriched with Faecalibacterium and Mollicutes and a lower abundance of Prevotella, Enterococcus, Leuconostocaceae, and Weissella. Microbial function prediction by PICRUSt analysis further indicated that KEGG pathways involved in carbohydrate metabolism and transcription were positively associated with vaccine inoculation, whereas capacities in neurodegenerative diseases, cardiovascular diseases, and cancers were negatively affected by vaccines. Our findings revealed that vaccine inoculation was particularly associated with gut microbiome alterations, as was demonstrated by improved composition and functional capacities of gut microbiota.