Respiratory microbiota composition in bronchiolitis and its association with recurrent wheezing in infants

Background Bronchiolitis is associated with an increased risk of recurrent wheezing. Although host-microbiome interactions may contribute to this respiratory morbidity, the specific microbial features and underlying mechanisms remain poorly understood. We investigated respiratory and intestinal microbiota alterations during acute bronchiolitis and their association with recurrent wheezing during follow-up. Methods We performed 16S rRNA gene sequencing of nasopharyngeal and fecal samples from 80 infants hospitalized with bronchiolitis and 10 healthy controls, who were followed for 12 months. Microbial diversity, community composition, differential abundance, and co-abundance network structure were analyzed. Microbial features associated with recurrent wheezing were evaluated using multivariable logistic regression and integrated into cross-niche predictive models adjusted for clinical and environmental covariates. Results Nasopharyngeal microbiota showed reduced richness and significant compositional differences in infants with bronchiolitis, whereas intestinal diversity remained comparatively preserved. Dolosigranulum and Corynebacterium were consistently depleted across bronchiolitis phenotypes. Among infants with bronchiolitis, Haemophilus was enriched in those who subsequently developed recurrent wheezing, whereas Burkholderia-Caballeronia-Paraburkholderia was independently associated with lower odds of wheezing. In the gut, the Ruminococcus gnavus group was independently associated with increased wheezing risk. A cross-niche model integrating Burkholderia-Caballeronia-Paraburkholderia and Ruminococcus gnavus achieved an AUC of 0.786 (95% CI, 0.681–0.891), with a higher AUC than niche-specific models. Network analysis revealed coordinated reductions across multiple nasopharyngeal modules during bronchiolitis, while a module associated with lower odds of recurrent wheezing contained Burkholderia-Caballeronia-Paraburkholderia and Haemophilus with an inverse co-abundance relationship. Conclusions Our findings support a community-level and multi-compartment view of post-bronchiolitis wheezing, in which respiratory community structure and intestinal microbial features provide complementary information on subsequent respiratory vulnerability. This approach may help refine microbiome-based characterization of heterogeneous clinical trajectories following bronchiolitis.