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An infant nasal microbial gene atlas uncovers intervention-driven microbiome shifts and salt-resistant pathogen expansion

Functional studies of how early-life interventions shape the airway microbiome remain scarce. Here, we performed metagenomic sequencing of 704 longitudinal nasal swabs from infants with and without cystic fibrosis (CF) to construct and characterize a non-redundant gene atlas of the infant nasal microbiome. We aimed to determine how the nasal microbiome is perturbed by early therapies, as CF is commonly treated with inhaled hypertonic saline to improve mucociliary clearance.

Citation:
Steinberg R, Pust MM, Arias-Rojas A, Pishchany G, Ramsey KA, Kieninger E, Moeller A, Casaulta C, Hilty M, Latzin P, Korten I, Xavier RJ. An infant nasal microbial gene atlas uncovers intervention-driven microbiome shifts and salt-resistant pathogen expansion. Cell Host and Microbe. 2026.  

Keywords:
Cystic fibrosis; gene atlas; haemophilus influenzae; hypertonic saline; infancy; inhalation; metagenomics; microbiome; upper airways

Abstract:
Functional studies of how early-life interventions shape the airway microbiome remain scarce. Here, we performed metagenomic sequencing of 704 longitudinal nasal swabs from infants with and without cystic fibrosis (CF) to construct and characterize a non-redundant gene atlas of the infant nasal microbiome. We aimed to determine how the nasal microbiome is perturbed by early therapies, as CF is commonly treated with inhaled hypertonic saline to improve mucociliary clearance.