NEW research reveals that the composition of the lower respiratory tract microbiota is closely linked to COVID-19 severity and may serve as a predictor of disease outcomes.
While previous studies have examined gut and oropharyngeal microbiota in viral infections, including SARS-CoV-2, the role of microbial communities in the lower respiratory tract remains underexplored. In this study, researchers applied metatranscriptomic and metagenomic analyses to bronchoalveolar lavage fluid and sputum samples from 116 patients with COVID-19. Participants were stratified by clinical severity into mild, severe, and critical groups. Microbial richness (Chao index), diversity (Shannon index), and genus-level taxa were evaluated in relation to disease severity and clinical outcomes, including ICU admission, mechanical ventilation, and survival.
The study demonstrated distinct microbial signatures associated with each stage of COVID-19 severity. In mild cases, Firmicutes dominated the microbiota profile, while severe cases exhibited an increase in Bacteroidetes. Critical cases were marked by a higher abundance of Actinobacteria and Proteobacteria. The presence of Streptococcus and Rothia decreased as disease severity increased. Importantly, the Chao index, a marker of microbial richness, increased with disease severity and was significantly associated with ICU admission, mechanical ventilation, and overall survival. The Shannon index, a marker of microbial diversity, correlated with mortality risk. Additionally, the study found significant differences in viral genotypes across severity categories.
The findings demonstrate strong associations between respiratory microbiota and COVID-19 severity, suggesting that microbial profiles may offer insights into disease progression. Further research will be needed to assess whether interventions targeting the respiratory microbiota could support clinical management or risk stratification in COVID-19 and other respiratory illnesses.
Reference
Wang D et al. Altered microbiota of the lower respiratory tract and its association with COVID-19 severity analysed by metagenomics and metatranscriptomics. Commun Biol. 2025;8(1):804.
