ABSTRACT
Background: The massive secretion of inflammatory cytokines is associated with the Coronavirus Disease 2019 (COVID-19) severity and poor prognosis, as well as, in long COVID, the pathophysiology seems to be related to immune deregulation. The patient's immune status can influence the response to Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) virus infection, and this immunity is affected by the intestinal microbiota condition (eubiotic or dysbiotic). This study aimed to evaluate the intestinal microbiota of patients infected with SARS-CoV-2 with different clinical manifestations and post-COVID-19 (post-COV) periods, and correlate with the use of antibiotics during the acute disease. Results: According to the beta diversity, we observed significant differences between microbial communities in stool samples from post-COV patients when compared with healthy controls. Additionally, we detected four different clusters when we grouped patients into asymptomatic, mild, moderate, and severe disease. Patients who took antibiotics during the COVID-19 course showed decreased richness of the gut microbiota, even months after the disease resolution. We detected some genera possibly associated with the persistent post-COV dysbiosis, including increased Prevotella, Dialister, Haemophillus, Barnesiella, Desulfovibrio, Bilophila, Alistipes, Parabacteroides and Bacteroides, suggesting the impact of the disease in the gut microbiota. Besides that, we found some genera associated with antibiotic-induced dysbiosis in post-COV patients, including decreased Akkermansia and Bifidobacterium species. Conclusions: Therefore, we hypothesized that persistent dysbiosis and indiscriminate use of antibiotics during the COVID-19 pandemic may be associated with long COVID syndromes, suggesting the involvement of the gut-lung axis. These data suggest that intestinal microbiota modulation may represent a therapeutic approach for long COVID.