Upper respiratory microbiome composition and associations with air pollution and infant respiratory health: a longitudinal study in Guatemala

The early-life composition and maturation of the upper respiratory microbiome, and their associations with environmental exposures and respiratory health, remain poorly characterized. We collected nasopharyngeal (NP) and oropharyngeal (OP) samples (n = 257) from a cohort of 114 Guatemalan infants at birth and six months between February and August 2019. We analyzed their NP and OP microbiomes using 16S rRNA gene sequencing and examined associations with air pollution and respiratory outcomes during the first year of life. Results show that NP and OP microbiomes exhibited distinct developmental trajectories, with NP diversity declining and OP diversity increasing by six months, accompanied by age-related compositional restructuring. Taxonomic succession was anatomically site-specific; NP communities matured toward lower alpha diversity with facultative dominance, whereas…