Our study suggests that oropharyngeal swabs can replace sputum to present the dynamic of lung microbiota associated with exacerbation events of COPD.

Growing evidence suggests that the airway microbiota might be involved in acute exacerbation of chronic obstructive pulmonary disease (AECOPD). Understanding this relationship requires examination of a large-scale population for a long duration to accurately monitor changes in the microbiome. This type of longitudinal study requires an appropriate sampling strategy, one option is to collect sputum or oropharyngeal swabs. Meanwhile, a comparative analysis of the changes that occur in these two specimen types has not been previously performed. This observational study was performed to explore whether oropharyngeal microbial community dynamics with time and what the relationship between oropharyngeal and sputum would be. 56 sputum samples and 56 oropharyngeal swab samples were collected from 4 patients suffering severe AECOPD, bacterial and fungal communities were evaluated using 16S rRNA and ITS sequencing. The interindividual differences of bacterial community structure were found, meanwhile, the core microbiomes were shared by both sputum and oropharyngeal samples including: Psychrobacter, Stenotrophomonas, Haemophilus, and Neisseria from Proteobacteria; Actinomyces, Rothia from Actinobacteria; Streptococcus, Granulicatella and Lactobacillus from Firmicutes; Leptotrichia from Fusobacteria; Prevotella from Bacteroidetes; Streptophyta from Cyanobacteria; Aspergillus and Acremonium from Ascomycota. Although the oropharyngeal samples showed higher bacterial alpha diversity, the relative abundance of the core microbiomes dynamics confirmed to a same pattern in both sample sites.