Publication date: Jul 31, 2025

Microbial colonization in the nasopharynx and nasal cavity plays a defensive role in children. The coronavirus disease 2019 (COVID-19) pandemic may have an influence on the nasopharynx and nasal cavity microbiota. This study aimed to identify and compare the microbiota in the nasopharynx and nasal cavity before and during the COVID-19 pandemic in a healthy pediatric population. Separate mucosal swabs were collected from the nasopharynx and nasal cavity of healthy children before and during the COVID-19 pandemic. A 16S ribosomal RNA-based metagenomic approach was employed to characterize and analyze alterations in the nasopharyngeal and nasal microbiota to determine whether isolation measures, such as mask wearing, influence microbial ecology. The richness and diversity of the nasopharyngeal and nasal microbiota decreased during the COVID-19 pandemic compared with before the pandemic. Firmicutes and Proteobacteria were the most abundant phyla in the nasopharyngeal and nasal microbiota, respectively, both before and during the pandemic. Corynebacterium and Moraxella were the dominant genera in the nasopharyngeal and nasal microbiota during the COVID-19 pandemic, whereas Pseudomonas and Corynebacterium were dominant before the pandemic. Compared with pre-pandemic conditions, microbial colonization differed significantly for Cyanobacteria/Chloroplast and Bacteroidetes in the nasopharynx and for Planctomycetes in the nasal cavity during the COVID-19 pandemic. This study revealed a lower microbiota diversity during COVID-19, possibly accompanied by microbiota dysbiosis, increased risk of respiratory infections and inflammatory responses in healthy children. This study underscores the importance of reestablishing microbiota balance and highlights the need for personalized treatment and prophylactic strategies in routine public health practice. Supplementary file3 (MP4 150533 KB).

Semantics

Original Article