Human Gut and respiratory Microbiome 16S Raw sequence reads. Human Gut Microbiome - 16S rRNA

Background and aims: Research into the association between the microbiome and SARS-CoV-2 infection and acute respiratory distress syndrome remains unclear. Here we examined the dynamics of the gut and respiratory microbiomes in severe COVID-19 cases in need of mechanical ventilation in the intensive care unit (ICU).Methods: We recruited 76 critically ill patients (48 with COVID-19 and 32 without COVID-19) and 17 healthy controls (HCs) and monitored them for up to 4 weeks. We analyzed the bacterial and fungal taxonomic profiles and loads of 232 gut and respiratory samples and measured blood levels of Interleukin 6, IgG and IgM from ICU-COV(+) patients.Results: At ICU admission, bacterial composition and load in gut and respiratory samples were altered in critically ill patients compared to HCs. Six bacterial species could discriminate ICU-COV(+) from ICU-COV(-) cases. During their time in the ICU, all patients experienced increased bacterial and fungal loads, decreased bacterial richness, and progressive changes in bacterial and fungal taxonomic profiles. ICU-COV(+) cases were associated with a depletion of Streptoccocus and Saccharomyces and an enrichment of Pseudomonas in the respiratory tract while the GI tract was enriched in Enterococcus. Respiratory bacterial signatures, associated with disease severity and inflammation markers, were predictive of death, and a fecal dysbiosis score negatively associated with PaO2/FiO2 ratio could be used as an indicator for ICU admission.Conclusion: Gut and respiratory microbiome dysbiosis and bacterial signatures associated with critical illness emerge as biomarkers of COVID-19 severity and predictors of clinical outcome.