High abundance of butyrate-producing bacteria in the naso-oropharynx of SARS-CoV-2-infected persons in an African population: implications for low disease severity

Abstract

Abstract Background: Microbiome dysbiosis is associated with various diseases, including COVID-19. The association of the oral microbiome with SARS-CoV-2 infections and disease progression has been documented in European, Asian, and American populations but not in Africa. Methods: We conducted a study in Ghana to evaluate and compare the naso-oropharyngeal microbiome in SARS-CoV-2-infected and noninfected persons before and after vaccination. 16S rDNA was sequenced and analysed from DNA extracted from the naso-oropharyngeal swabs of consenting participants. Results: Alpha diversity was high among pre-vaccinated virus-positive individuals (Shannon: p< 0.0001) but reduced among vaccinated persons. Contrary to other reports, differences in viral loads did not significantly affect alpha diversity. Pre-vaccinated SARS-CoV-2-positive and -negative individuals had little yet significant microbial compositional dissimilarity (PERMANOVA: R2=0.14, p= 0.001) but not when some individuals were vaccinated (PERMANOVA: R2=0.013, p= 0.49). Consistent with other studies, Prevotella and Atopobium were abundant in pre-vaccinated virus-positive persons (adjusted p value <0.05). Butyrate-producing microbes, including members of Lachnospiraceae and Fusobacterium sp., were in relatively high abundances in infected individuals. As biomarkers associated with the infection (log10LDA> 4.0), they suggest probable protective pathophysiological processes that would prevent severe disease outcomes in this population. Anaerovoracaceae was increased in infected vaccinated persons, further implicating Firmicutes in protective immunity against COVID-19. Conclusion: Our results necessitate further studies to confirm the integral role of Firmicutes in immune responses and disease progression. We also recommend expansion of microbiome–disease association studies across Africa to identify possible bacterial-mediated therapeutics for emerging infections.