Abstract Description

The COVID-19 pandemic has highlighted the severe effects of SARS-CoV-2 infection, along with an increasing burden of long-term complications known as Long COVID. Our understanding of how the infection impacts multiple organ systems, including the gastrointestinal tract (GIT), has grown. Although SARS-CoV-2 can manifest in the GIT and change the gut microbiome, few studies have explored the link between Long COVID and the human microbiome, and even fewer have focused on genetically diverse African populations. In this study, we used shotgun metagenomic sequencing to analyze the gut microbiome in South Africans with Long COVID, comparing their profiles with those of healthy controls. Alpha diversity analysis showed no significant difference in overall bacterial diversity between the two groups (p > 0.05, Wilcoxon rank-sum test). In contrast, beta diversity analysis revealed significant differences (p < 0.05, Bray-Curtis dissimilarity). The Bacillota/Bacteroidota ratio was higher in Long COVID patients compared to controls, aligning with previous research. Members of the Prevotella genus, common colonizers in healthy gut microbiomes and especially prevalent in non-Western diets, were lower in Long COVID patients. We found that the beta-lactam resistance pathway was upregulated, indicating increased resistance to penicillin in the gut microbiomes of affected individuals. Our results suggest that Long COVID is linked to specific changes in the gut microbiome of African individuals, differing from patterns seen in other populations. Overall, this work emphasizes the need for further research into microbial markers associated with Long COVID across different geographical locations and expands our understanding of gut dysbiosis in an African context.