Assessment of upper respiratory and gut bacterial microbiomes during COVID-19 infection in adults potential aerodigestive transmission

SARS-CoV-2 is the viral pathogen responsible COVID-19. Although SARS-CoV-2 primarily targets the lung, the gastrointestinal tract is a major focus of SARS-CoV-2. Connections and interactions have been found between the microbiome of the gut and respiratory system in the context of viral infections via what has been referred to as the gut-lung axis with potential aerodigestive communication in health and disease. The aim of this research, was to explore the relationship between the microbiomes of the upper respiratory and GI tracts in patients with COVID-19 and to examine Extraesophageal reflux, a mechanism which could contribute to dysregulated communication between the GI and respiratory tract, which we have described in COVID-19.97 patients who had a laboratory diagnosis of COVID-19 infection, and 50 age matched controls were recruited. Stool, saliva and sputum were acquired from participants. ELISA Pepsin tests and Reflux Symptom Index scores were conducted for EOR assessment. DNA sequencing of the V4 region of the 16S rRNA gene was performed for microbiome analysisNo differences were observed between the fecal microbiome alpha and Shannon diversity indices. However, a distinct microbial composition was observed in COVID-19 patients compared to controls.The respiratory microbiota from individuals with COVID-19 demonstrated a statistically significant reduction in Shannon diversity and bacterial richness, with a general fall in the prevalence of organisms from a typical healthy respiratory microbiome. Furthermore, bacterial richness of both stool and sputum samples was significantly lower among COVID-19 patients admitted to ICU. A significantly higher RSI score and salivary pepsin level were detected among those with COVID-19.Our data indicate that COVID 19 infection is associated with a dysregulation of both the gut and lung microbiome, with a more marked perturbation in the lung, which was especially marked in COVID-19 patients admitted to ICU. The presence of increased RSI scores, together with high levels of Pepsin indicates that increased micro-aspiration may occur, representing a possible interaction between the microbiome in the GI and lung in COVID-19 patents that requires further study. Such work would benefit from insights from biological samples taken from samples reflecting the continuum of the aerodigestive tract.