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

Authors

Rina Das, Andrew Baldi, Sant-Rayn Pasricha, Lisa M Thompson, Anaité Díaz-Artiga, Laura Maria Grajeda, John P McCracken, Kelsey Jesser, Lance Waller, Matthew C Freeman, Thomas Clasen, Sheela S Sinharoy

Published in

International journal of hygiene and environmental health. Volume 276. Pages 114843. Jun 01, 2026. Epub Jun 01, 2026.

Abstract

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 OP communities showed anaerobic enrichment and rising alpha diversity, yielding stable, differentiated airway communities. Neither alpha nor beta diversity was consistently associated with WHO IMCI (Integrated Management of Childhood Illness) pneumonia (both severe and non-severe), cough, or hypoxemia, except for higher NP alpha diversity at birth, which predicted increased odds of fast breathing episodes (Shannon: adjusted OR = 4.81, 95% CI: 1.80, 7.46 & inverse Simpson: aOR = 1.20, 95% CI: 1.04, 1.43). Higher NP Bacteroidota relative abundance at birth was associated with lower odds of subsequent WHO IMCI pneumonia (aOR: 0.003, 95% CI 0.001-0.02; FDR = 0.10). Higher personal PM₂.₅ exposure at 3 months was associated with differential NP microbiome composition at 6 months, including lower Firmicutes abundance (β = -0.53; 95% CI: -0.82, -0.25; FDR = 0.17) and higher Prevotella abundance (β = 3.21; 95% CI: 1.90, 4.51; FDR = 0.08), consistent with PM₂.₅ acting as an ecological stressor that may predispose to airway dysbiosis. These findings reveal coordinated but site-specific patterns of microbial maturation in early infancy and suggest that predictable age-related shifts in community composition, together with both environmental exposures, shape upper airway microbial communities with implications for respiratory health.

PMID:
42224959
Bibliographic data and abstract were imported from PubMed on 02 Jun 2026.

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