Early-life Nasal Microbiota Dynamics Relate to Longitudinal Respiratory Phenotypes in Urban Children

BACKGROUND

Five distinct respiratory phenotypes based on latent classes of longitudinal patterns of wheezing, allergic sensitization and pulmonary function measured from 0-7 years have been described in urban children.

OBJECTIVE

To determine whether distinct respiratory phenotypes associate with early-life upper respiratory microbiota development and environmental microbial exposures.

METHODS

Microbiota profiling was performed using 16S rRNA-based sequencing of nasal samples collected at 12 (n=120) or 36 (n=142) months of age and paired house dust samples collected at 3 months (12-month, N=73; 36-month, N=90) from all four centers in the Urban Environment and Childhood Asthma (URECA) cohort.

RESULTS

In these high-risk urban children, nasal microbiota increased in diversity between 12 and 36 months of age (ß= 2.04, P=0.006). Age-related changes in microbiota evenness differed significantly by respiratory phenotypes (Interaction P=0.0007) increasing most in the transient-wheeze group. At 12 months of age, respiratory illness (R2=0.055, p=0.0001) and dominant bacterial genus (R2=0.59, p=0.0001) explained variance in nasal microbiota composition and enrichment of Moraxella and Haemophilus members was associated with both transient- and high-wheeze phenotypes. By 36 months, nasal microbiota significantly associated with respiratory phenotypes (R2=0.019, P=0.0376) and Moraxella dominated microbiota associated specifically with atopy-associated respiratory phenotypes.

CONCLUSION

Nasal microbiota development over the course of early childhood and composition at three years of age associates with longitudinal respiratory phenotypes. These data provide evidence for an early-life window of airway microbiota development that is influenced by environmental microbial exposures in infancy and associated with wheeze- and atopy-associated respiratory phenotypes through 7 years of age.