Review synthesizes pilot data on nasal microbiota and respiratory outcomes in infants

Background and objective. Early-life susceptibility to viral respiratory infections is associated with long-term respiratory morbidity in children. Currently, no reliable tools exist to predict susceptibility to these infections. Because the endogenous microbiota can influence pathogen virulence and airway inflammation, it represents a potential target for prevention. In this pilot study, we hypothesised that distinct nasal microbial communities are associated with susceptibility to viral respiratory infections and wheezing outcomes during the first year of life. Methods. We analyzed 90 nasal swabs from 55 infants enrolled in the AERIAL study, representing asymptomatic samples collected at scheduled visits (~4 months) and symptomatic samples. Bacterial profiling was done blind to clinical data using full-length 16S rRNA sequencing, and bacterial load was quantified using a pan-bacterial TaqMan assay. Results. Bacterial diversity was similar between asymptomatic and symptomatic swabs, with community composition differences largely driven by inter-individual variation. In paired samples, symptomatic swabs showed reduced diversity but no change in bacterial load. Virus-bacteria interactions were observed in rhinovirus-positive swabs, but not SARS-CoV-2-positive swabs. Two nasal endotypes were identified, dominated by Moraxella or Streptococcus and differing in alpha diversity. Endotypes were associated with age at wheeze onset, and their relationship with wheezing episode rates showed a suggestive sex-dependent pattern that warrants further investigation. Conclusion. Our pilot data suggest that the nasal microbiota might shape early wheezing outcomes in a sex dependent manner, and highlight the value of longitudinal studies for clarifying how host-bacteria-virus interactions in early life.