The state of colonic microbiocenosis in hospitalized COVID-19 patients

The COVID-19 pandemic emphasized the importance of the interaction between viral infections and the gut microbiota as an important regulator of homeostasis. Objective. To determine the dependence of the detected changes in the microbiocenosis of the large intestine in hospitalized COVID-19 patients of moderate severity on the viral load of SARS-CoV-2 RNA in smears from the oral/nasopharyngeal mucosa. Patients and methods. Sixty-four patients (37 males, 27 females aged 18 to 75 years) with moderate-to-severe COVID-19 were examined. Standard investigations (BMP17), quantitative analysis of SARS-CoV-2 RNA in nasopharyngeal/ oropharyngeal swabs, in feces and evaluation of intestinal microbiocenosis in dynamics were performed. Results. In patients, regardless of viral load, the level of commensals (Bifidobacterium spp., Bacteroides spp., Faecalibacterium prausnitzii, Akkermansia muciniphila) decreased and the level of opportunistic bacteria (Enterobacter spp., Klebsiella spp., Clostridium difficile) increased. Bifidobacterium spp. deficiency progressed until the period of early reconvalescence, regardless of viral load. Late treatment was accompanied by a decrease in А. muciniphila, leading to an increase in Enterococcus spp. The dependence of А. muciniphila on viral load was revealed. Conclusion. The results of this study showed that a decrease in bacterial diversity in COVID-19 patients independent of viral load contributed to the depletion of bacteria producing short-chain fatty acids and an increase in opportunistic microbes. Key words: bacterial diversity, viral load, microbiome, gut microbiota, COVID-19, SARS-CoV-2