Pharyngeal Microbiota in Pre-COPD and COPD: Associations with Clinical Pattern and Respiratory Infection

<b>Background/Objectives:</b> The pharyngeal microbiota plays a critical role in respiratory health by supporting immune modulation, colonization resistance, and metabolic functions. Disruptions in this microbial ecosystem are associated with respiratory diseases; however, standard diagnostics often target individual pathogens, overlooking overall microbial dynamics. This study investigates the composition and diversity of the pharyngeal microbiota in three populations: individuals with pre-COPD (with and without concurrent acute respiratory infection [ARI]) and those with stable COPD. <b>Methods:</b> Pharyngeal swabs were analyzed using 16S rDNA sequencing on the Illumina MiSeq platform. Taxonomic and functional profiles were generated with MicrobAT^®, while microbial diversity was evaluated using the Shannon index and PERMANOVA. Group differences in microbiota composition were assessed via Kruskal-Wallis tests and robust PCA. The sample size was estimated at 8 subjects per group to detect significant differences (α = 0.05, 80% power, SD ≈ 20). <b>Results:</b> Twenty-nine swabs were collected: 11 from pre-COPD subjects (PC), 9 from ARI patients receiving antibiotics, and 9 from individuals with stable severe COPD. Microbial diversity was preserved in the PC group (100%) but markedly reduced in ARI (25%) and COPD (15%). Microbiota composition differed significantly across groups (R² = 0.371, <i>p</i> = 0.001), particularly at the phylum level. Functional analysis revealed minimal deficits in PC (<10%) but major impairments in ARI (81%) and COPD (56%), indicating reduced microbial functional capacity. <b>Conclusions:</b> Broad-spectrum microbial analysis highlights the importance of assessing pharyngeal microbiota beyond traditional pathogen detection, offering potential for innovative diagnostic and therapeutic approaches.