Functional potential of the airway microbiome for predicting wheezing phenotype in preschool children

Microbial colonization of the airway may play a role in the pathogenesis of asthma; however, no study has examined the effect of the airway microbiome on childhood asthma or its prognosis. Here, we analyzed the airway microbiota to identify biomarkers that predict the phenotypes associated with preschool wheezing. Nasopharyngeal swab samples were collected from children enrolled in the KOREA (I) study, and high-throughput sequencing was used to examine the structure and functional dynamics of the airway microbiome with respect to asthma phenotypes. The microbiome of children in the asthma and remission groups was more diverse than that of the control group. Proteobacteria were predominant in all groups; however, the proportion of this phylum was lower in the asthma and remission groups. By contrast, the proportion of Firmicutes was highest in the asthma group, whereas that of Fusobacteria was highest in the remission group. The relative abundance of Firmicutes was negatively associated with methacholine PC20 levels (P = 0.014), that of Streptococcus was significantly and negatively associated with FEV1 % predicted (P = 0.023), and that of Staphylococcus was negatively associated with methacholine PC20 (P = 0.013). Arachidonic acid metabolites, lysine residues, and glycosaminoglycans produced by the microbiome were associated with airway inflammation. Differences in profiles of functional genes among the three groups resulted from different microbiome compositions. Thus, alterations in the airway microbiome may affect the prognosis of preschool wheezing phenotypes. Therefore, the airway microbiome can be used to develop biomarkers, treatments, and prophylactics for asthma in preschool children.