Investigating the lasting effects of SARS-CoV-2 infection and the lung microbiome: no persistent microbial alterations in recovered COVID-19 patients with persistent radiological or respiratory abnormalities

Severe acute respiratory syndrome coronavirus 2 (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 microbiome of 38 adult coronavirus disease 2019 (COVID-19) patients with persistent respiratory symptoms and/or radiological abnormalities was analysed. The aim was to investigate whether the lasting radiological abnormalities reported in this cohort were associated with an altered airway. Thirty-six bronchoalveolar lavage fluid samples from patients underwent 16S rRNA gene amplicon sequencing and were compared to 28 non-fibrotic control samples from a previously published study. COVID-19 patients had statistically significantly greater number of genera but at uneven abundances, though not statistically significant compared to non-fibrotic controls. Permutational ANOVA (PERMANOVA) suggested that COVID-19 can influence the lung microbiome composition after accounting for multivariate dispersion. Further analysis showed differences in the relative abundances of Actinomyces , Neisseria , Haemophilus , Rothia and Gemella . Indicator species analysis showed that a COVID-19 lung microbiome profile could be driven in part by differences in Fusobacterium , Actinomyces , Catonella , Oribacterium and Mycobacterium . Associations with clinical parameters were lacking apart from CT lung opacification, which revealed a significant negative association with the number of genera. Differential abundance analysis with MaAsLin2 pointed towards Porphyromonas as a potential explaining genus, though this was not significant after post hoc corrections. DESeq2 revealed enriched oral taxa in the BAL samples, suggesting potential oral-translocation reflective of a disease state. Our findings suggest that individuals with persistent radiological abnormalities following SARS-CoV-2 infection have experienced subtle shifts in their microbiome profile, but these are not strongly associated with clinical phenotypes and, therefore, unlikely of significance.