Long term effects of COVID-19 on the oral and lower airway microbiota

Long term effects of COVID-19 affect millions of patients worldwide and are more common with severe COVID-19 infections. The microbiota has diverse effects on health. We investigated the oral and lower airway microbiota during follow-up in patients hospitalised with COVID-19. PHOSP-COVID is a UK multicentre cohort study following up patients hospitalised with COVID-19. Participants provided oral rinse and spontaneous sputum samples at follow-up. Previous work clustered participants by ongoing health impairment. Microbiota characterisation at 6-months follow-up was performed by 16S rRNA sequencing. Alpha and beta diversity were measured by Shannon-Wiener diversity index and Weighted-Unifrac respectively. Differentially abundant taxa were identified using 3 discriminant methods. The oral microbiota was associated with ongoing health impairment (mild: n=253, very severe: n=135) (alpha diversity: p=0.002; beta diversity: p=0.011); with higher abundance of Streptococcus and Rothia; and lower abundance of Neisseria, Haemophilus and Prevotella in patients with very severe impairments. Recovery was not significantly associated with the oral microbiota (recovered: n=482, not recovered: n=233). The lower airway microbiota was associated with ongoing health impairment (mild: n= 88, very severe: n=54), non-recovery, and gastrointestinal symptoms (recovered: n=93, not recovered: n=182, gastrointestinal: n=40) (alpha diversity: p=0.016-0.022; beta diversity: p=0.033-0.043); with lower abundance of Neisseria. Ongoing health impairment post-COVID-19 is associated with the oral and lower airway microbiota. Gastrointestinal symptoms association with the lower airway microbiota possibly suggests gut-lung crosstalk post-COVID-19.