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Updated: May 22, 2025
Noninvasive Sampling of Mucosal Lining Fluid for the Quantification of In Vivo Upper Airway Immune-mediator Levels
Published on: August 7, 2017
Upper and lower airway microbiota across infancy and childhood
Ariel J Hernandez-Leyva1,2, Anne L Rosen1,2, Christopher P Tomera1,2
1Division of Allergy and Immunology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA.
Insights
The upper and lower airway microbiomes in children rarely share common microbes. The nasopharyngeal microbiome composition changes with age, indicating a developmental trajectory in children.
Area of Science:
- Microbiology
- Pediatric Medicine
- Genomics
Background:
- The upper and lower respiratory tracts present distinct environments influencing microbial colonization.
- Investigating the relationship between these distinct airway microbiomes is technically challenging.
Purpose of the Study:
- To identify relationships between microbial taxa colonizing the nasopharynx and trachea across childhood.
- To understand the assembly and developmental trajectory of the airway microbiota in children.
Main Methods:
- V4 16S rRNA gene sequencing was used to profile nasopharyngeal swabs and tracheal aspirates.
- Samples were collected from 172 subjects aged 20 weeks to 18 years.
- Analysis included 80 subject-matched pairs of upper and lower airway samples.
Main Results:
- The nasopharynx is colonized by a few, highly abundant taxa, while tracheal aspirates show greater microbial diversity.
- Microbial communities in the upper and lower airways are unlikely to share common taxa.
- Nasopharyngeal microbiota composition strongly correlates with subject age, showing a developmental pattern.
Conclusions:
- The upper and lower airway microbiota in children are distinct and do not correlate in diversity.
- Nasopharyngeal microbiota exhibits a stereotypic developmental trajectory during childhood and adolescence.
- Findings enhance understanding of airway microbiota assembly and may aid in predicting airway diseases.
Background:
The upper and lower respiratory tracts feature distinct environments and responses affecting microbial colonization but investigating the relationship between them is technically challenging. We aimed to identify relationships between taxa colonizing the nasopharynx and trachea across childhood.
Methods:
We employed V4 16S rRNA gene sequencing to profile nasopharyngeal swabs and tracheal aspirates collected from 172 subjects between 20 weeks and 18 years of age. These samples were collected prior to elective procedures over the course of 20 weeks in 2020 from subjects enrolled in a cross-sectional study. After extraction, sequencing, and quality control, we studied the remaining 147 of 172 nasopharyngeal swabs and 95 of 172 tracheal aspirates, including 80 subject-matched pairs of samples.
Results:
Sequencing data revealed that the nasopharynx is colonized by few, often highly abundant taxa, while the tracheal aspirates feature greater diversity. The patterns of colonization identified in the nasopharynx correlate with subject age across childhood.
Conclusion:
Our data suggests that there are relatively few species that colonize both the nasopharyngeal tract and the trachea. Furthermore, we observe a pattern of change in the nasopharyngeal microbiota that is correlated with age, suggesting a possible developmental progression of the nasopharyngeal microbiota across childhood.
Impact:
The airway microbiota in childhood plays important roles in respiratory health and immune development. In this work, we report on paired nasopharyngeal swab and tracheal aspirate samples from a cross-sectional cohort of children from infancy to 18 years. We find that the upper and lower airway microbiota are unlikely to share taxa and do not correlate in terms of diversity. We show that the composition of the upper airway microbiota is strongly correlated with age, with a stereotypic developmental trajectory during childhood and adolescence. Our results inform our understanding of airway microbiota assembly and may be used to predict airway disease in young children.
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