Microbial diversity within the airway microbiome in chronic pediatric lung diseases

Abstract

The study of the airway microbiome in children is an area of emerging research, especially in relation to the role microbial diversity may play in acute and chronic inflammation. Three such pediatric airway diseases include cystic fibrosis, asthma, and chronic lung disease of prematurity. In cystic fibrosis, the presence of Pseudomonas spp. is associated with decreased microbial diversity. Decreasing microbial diversity is also associated with poor lung function. In asthma, early viral infections appear to drive changes in bacterial diversity which may be associated with asthma risk. Premature infants with Ureaplasma spp. are at higher risk for chronic lung disease due to inflammation. Microbiome changes due to prematurity also appear to affect the inflammatory response to viral infections post-natally. Importantly, microbial diversity can be measured using metataxonomic (e.g., 16S rRNA sequencing) and metagenomic (e.g., shotgun sequencing) approaches. A metagenomics approach may be preferable as it can provide further granularity of the sample composition, identifying the bacterial species or strain, information on additional microbial components, including fungal and viral components, information about functional genomics of the microbiome, and information about antimicrobial resistance mutations. Future studies of pediatric airway diseases incorporating these techniques may provide evidence for new treatment approaches for these vulnerable patient populations.

Keywords: Asthma; Cystic fibrosis; Microbiome; Pediatrics; Translational medicine.

Copyright © 2017 Elsevier B.V. All rights reserved.

Figures

Figure 1. Taxonomic profiles based on 16S targeted amplicon data of a cohort of eight children with cystic fibrosis

Only genera with a minimum total observation count of 0.1% per subject are shown. Pseudomonas, Staphylococcus, Haemophilus, Streptococcus, Prevotella, Gemella, Bacteroides, Fusobacterium, and Enterobacteraiaceae_unclassified were identified at relative abundances of at least 10% in one or more of the eight subjects.

Figure 2. Metagenomic profiles comparing cohorts of asthma (AS) and control (CN) subjects

Only species with a minimum total observation count of 0.1% are shown. Asthma patients have a dominance of Moraxella catarrhalis within their microbiomes. In addition to being able to report bacteria at the species level, fungi such as Aspergillus niger and Aspergillus fumigatus, and yeast such as Candida dublinensis are also reported as part of the microbial composition using this approach.

Figure 3. Functional profiles and functional properties mapped to 171 SEED metabolic pathways comparing cohorts of asthma and control subjects

Panel A. Each color in the functional profile represents different SEED functions that were identified in the cohort, demonstrating the similarities and differences between asthmatics and healthy controls. Panel B. This extended error bar plot shows functional properties differing significantly between asthmatics (AS) and healthy controls (CL) with an effect size of one percent. Several pathways are significant, including one involved in virulence functions (adhesion).