Distinct upper and lower airway microbiota profiles in pediatric Mycoplasma pneumoniae-associated lobar pneumonia

Lobar pneumonia remains a major public health concern in the pediatric population. This study aimed to elucidate the distinct microbial profiles of the upper and lower respiratory tracts in children with Mycoplasma pneumoniae (MP)-associated lobar pneumonia. We performed 16S rRNA gene sequencing on paired nasopharyngeal swab (NPS) and bronchoalveolar lavage fluid (BALF) samples. Based on MP infection status, the cohort was stratified into Group A (MP-positive, n = 28) and Group B (MP-negative, n = 12). A total of 40 children were enrolled, of whom 38 paired samples were ultimately included in the sequencing analysis. Distinct microbiota profiles at the phylum and genus levels characterized children with MP-associated lobar pneumonia. Alpha diversity analysis revealed reduced lower airway diversity in MP-positive compared to MP-negative children. Principal coordinate analysis (PCoA) demonstrated distinct separation of bacterial communities between the upper and lower airways in MP-positive patients ( q < 0.001), whereas no such segregation was observed in MP-negative individuals ( q = 0.102). Furthermore, significant differences in overall community composition were detected between MP-positive and MP-negative groups in both the upper ( q < 0.001) and lower airways ( q < 0.001). Notably, after excluding Mycoplasma sequences, the structural differences in the lower airway microbiota persisted ( q < 0.001), whereas the differences in alpha diversity were no longer significant. Our findings reveal distinct, site-specific microbial signatures in pediatric MP-associated lobar pneumonia and MP infection primarily reshapes the lower airway microbial composition rather than globally reducing diversity. Consequently, BALF remains crucial for characterizing this site-specific pathology.