Investigating the lasting effects of SARS-CoV-2 infection and the lung microbiota: No persistent microbial alterations in recovered COVID-19 patients with persistent radiological or respiratory abnormalities.
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SARS-CoV-2 was a global pandemic where infected individuals experienced mild or severe disease. Unfortunately, some patients who experienced severe disease also had lasting abnormalities. The lung microbiota of thirty-eight adult COVID-19 patients with persistent respiratory symptoms and/or radiological abnormalities were analysed. The aim was to investigate if the lasting physical abnormalities reported in this cohort were associated with microbiota composition. Thirty-six bronchoalveolar lavage fluid samples of these patients underwent 16S rRNA gene amplicon sequencing and we included twenty-eight non-fibrotic control samples from a previously published study. No significant differences were observed in alpha or beta diversity between the two groups. Permanova suggested that COVID-19 had no effect on the lung microbiota, and further analysis showed differences in the relative abundances of Actinomyces, Neisseria, Haemophilus, Rothia and Gemella. Indicator species analysis showed that a recovered COVID-19 lung microbiota profile could be driven in part by differences in Fusobacterium, Actinomyces, Catonella, Oribacterium and Mycobacterium. Our findings suggest that individuals with persistent respiratory symptoms or radiological abnormalities following SARS-CoV-2 infection resemble the lung microbiota of non-fibrotic controls.
