The microbial community of the cystic fibrosis airway is disrupted in early life

Abstract

Background: Molecular techniques have uncovered vast numbers of organisms in the cystic fibrosis (CF) airways, the clinical significance of which is yet to be determined. The aim of this study was to describe and compare the microbial communities of the lower airway of clinically stable children with CF and children without CF.

Methods: Bronchoalveolar lavage (BAL) fluid and paired oropharyngeal swabs from clinically stable children with CF (n = 13) and BAL from children without CF (n = 9) were collected. DNA was isolated, the 16S rRNA regions amplified, fragmented, biotinylated and hybridised to a 16S rRNA microarray. Patient medical and demographic information was recorded and standard microbiological culture was performed.

Results: A diverse bacterial community was detected in the lower airways of children with CF and children without CF. The airway microbiome of clinically stable children with CF and children without CF were significantly different as measured by Shannon's Diversity Indices (p = 0.001; t test) and Principle coordinate analysis (p = 0.01; Adonis test). Overall the CF airway microbial community was more variable and had a less even distribution than the microbial community in the airways of children without CF. We highlighted several bacteria of interest, particularly Prevotella veroralis, CW040 and a Corynebacterium, which were of significantly differential abundance between the CF and non-CF lower airways. Both Pseudomonas aeruginosa and Streptococcus pneumoniae culture abundance were found to be associated with CF airway microbial community structure. The CF upper and lower airways were found to have a broadly similar microbial milieu.

Conclusion: The microbial communities in the lower airways of stable children with CF and children without CF show significant differences in overall diversity. These discrepancies indicate a disruption of the airway microflora occurring early in life in children with CF.

Conflict of interest statement

Competing Interests: Mr. Todd DeSantis and Dr. Bettina John are paid employees of Second Genome, Inc. (www.secondgenome.com). Their association with Second Genome does not alter the authors' adherence to all journal policies. Second Genome is a gastrointestinal therapeutics company with a pipeline of intestinal microbiome modulators that impact metabolic diseases and IBD. The publication of the lists of organisms with observed differences in their abundance between the respiratory samples from healthy and diseased individuals does not influence the value of any of Second Genome's therapeutic assets. The Children's Medical and Research Foundation (http://www.cmrf.org/) is the principal fundraising body for Our Lady's Children's Hospital, Crumlin as well as the National Children's Research Centre and this foundation funds the corresponding authors salary. This does not alter the authors' adherence to PLOS ONE policies on sharing data and materials. For all other authors no competing interests exist.

Figures

Figure 1. Richness of the microbial communities present in the control lower airways and the CF upper and lower airways.

Box and Whiskers plot of Shannon's diversity indices for microbial communities present in the control lower airway, CF lower airway and the CF upper airway. * represents statistical significance (p = 0.001; two-tailed t test).

Figure 2. Bacterial community structures in the control lower airways and the CF upper and lower airways.

Principle coordinate analysis (PCoA) plots of A) UniFrac distances and B) weighted UniFrac distances of all airway microbial communities were created in R. Each community from each sample is represented as a filled circle and coloured by sample type and/or patient cohort; CF lower (CF BAL; red), CF upper (CF SWB; blue) and control lower (CN BAL; yellow) airway samples. The x-axis and y-axis represent 2-dimensions of percentage variation explained by the PCoA. Ellipses were included for visualisation purposes.

Figure 3. Taxa of differential abundance between the control and CF lower airway.

Circular Phylogenetic Tree was rendered in iToL and illustrates abundance changes between eOTUs present in the control lower (inner ring) and CF lower (outer ring) airways. The colour saturation indicates the degree of difference from the mean control lower value for the eOTU; where dark blue indicates a HybScore difference of −52326, white  = 0 (no change from mean control lower), dark red  = +61480. Two eOTUs remained of significantly differential abundance following Benjamini-Hochberg correction; Prevotella veroralis (*) and a CW040 (**). Following a permutation test, 62 taxa were found to be of significantly differential abundance, Corynebacterium (***) is highlighted. A detailed list of the 59 taxa of significantly differential abundance between categories is provided in the supplementary data (S2 File).