Microbiota diversity and differences in the respiratory tract of children with pneumonia

ABSTRACT Importance Although studies have examined the link between microbiota and airways, the understanding of microbial imbalances in the upper respiratory tract (URT) and lower respiratory tract (LRT) in pediatric pneumonia remains limited. Objective To elucidate the microbial communities within these areas, shedding light on the microbiota's contribution to pneumonia progression and the underlying metabolic shifts. Methods Pharyngeal swabs and bronchoalveolar lavage fluid samples were gathered from children with pneumonia and sequenced for 16S rDNA gene. Microbiota composition and differences between URT and LRT were analyzed. Results Proteobacteria (40.91%), Firmicutes (25.61%), and Actinobacteria (12.77%) were the three most abundant phyla in the airways of the children with pneumonia. Richness (P = 0.003), Chao1 (P = 0.003), and abundance‐based coverage estimator (P = 0.003) indices were significantly higher in the LRT than URT. Streptococus infantis was more abundant in the URT, whereas Cyanobacteria at the phylum level, Alphaproteobacteria and Chloroplast at the class level, Pseudomonadales, Burkholderiales, and Streptophyta at the order level, Moraxellaceae and Corynebacteriaceae at the family level, Moraxella and Corynebacterium at the genus level were more prevalent in the LRT. Multiple pathways such as d‐glutamine and d‐glutamate metabolism (P = 0.0032) were significantly activated in the URT, whereas inorganic ion transport metabolism (P = 0.0239) and tryptophan metabolism (P = 0.0284) were significantly activated in the LRT. Streptococcus genus negatively impacted blood indicators in those children. Interpretation Our study characterizes the LRT and URT microbiota in pediatric pneumonia children and links them to clinical features, enhancing our understanding of the disease's pathogenesis.