The daily dynamics of cystic fibrosis airway microbiota during clinical stability and at exacerbation

Abstract

Background: Recent work indicates that the airways of persons with cystic fibrosis (CF) typically harbor complex bacterial communities. However, the day-to-day stability of these communities is unknown. Further, airway community dynamics during the days corresponding to the onset of symptoms of respiratory exacerbation have not been studied.

Results: Using 16S rRNA amplicon sequencing of 95 daily sputum specimens collected from four adults with CF, we observed varying degrees of day-to-day stability in airway bacterial community structures during periods of clinical stability. Differences were observed between study subjects with respect to the degree of community changes at the onset of exacerbation. Decreases in the relative abundance of dominant taxa were observed in three subjects at exacerbation. We observed no relationship between total bacterial load and clinical status and detected no viruses by multiplex PCR.

Conclusion: CF airway microbial communities are relatively stable during periods of clinical stability. Changes in microbial community structure are associated with some, but not all, pulmonary exacerbations, supporting previous observations suggesting that distinct types of exacerbations occur in CF. Decreased abundance of species that are dominant at baseline suggests a role for less abundant taxa in some exacerbations. Daily sampling revealed patterns of change in microbial community structures that may prove useful in the prediction and management of CF pulmonary exacerbations.

Keywords: Airway microbiome; Cystic fibrosis; Lung microbiome; Respiratory exacerbation.

Figure 1

Baseline community structure. Bray-Curtis-based nonmetric multidimensional scaling plot showing daily sputum samples from four study subjects (subject A is red; subject B is green; subject C is black; subject D is blue), collected during clinically stable periods. Pairs of other symbols in gray are same sample replicate controls from subject A as described in Methods.

Figure 2

Daily change in community structure from baseline into exacerbation. Day-to-day changes in airway bacterial community structure in four persons with CF. Bray-Curtis dissimilarity between consecutive daily samples is shown during periods of clinical stability (blue) that ended with the onset of symptoms of exacerbation (pink). Dashed lines indicate more than one day between samples. Red horizontal line indicates the maximum Bray-Curtis dissimilarity between replicate control samples. Each plot ends on the day preceding the prescription of antibiotics for treatment of exacerbation.

Figure 3

Relative abundance of top OTUs in daily samples. Relative abundance of the top OTUs in consecutive daily sputum samples collected from four subjects during periods of clinical stability (white horizontal bars) and onset of exacerbation (black horizontal bars). Symbols below plots indicate days when maintenance antibiotics were taken. Each plot ends on the day preceding the prescription of antibiotics for treatment of exacerbation.

Figure 4

Community stability around exacerbation. Points represent the Bray-Curtis similarity (1 − Bray-Curtis dissimilarity) between the relative abundances of all OTUs at any given time point and the next time point, and range from 0 (no stability) to 1 (perfect stability). (See Methods for details.) The gray-shaded regions represent the ‘stability zone,’ which is the expected range of similarity for each subject. Periods of clinical stability (white horizontal bars) and onset of exacerbation symptoms (black horizontal bars) are indicated. Dashed vertical lines indicate transition between baseline and exacerbation. Each plot ends on the day preceding the prescription of antibiotics for treatment of exacerbation.

Figure 5

Community movement before and during exacerbation. Bray-Curtis-based nonmetric multidimensional scaling plots showing daily sputum samples from four subjects (subject A is red; subject B is green; subject C is black; subject D is blue) collected during periods of clinical stability (open circles) and at onset of symptoms of exacerbation (closed circles). A Arrows indicate relative influence of the specified OTUs on the position of samples in the ordination space. B Each subject's plot is shown separately with lines connecting samples from first (open triangle) to last (star) collected (stress = 0.151). Each subject's plot is magnified to fill the ordination space and highlight movement between that subject's samples. Baseline samples are enclosed by a dashed ellipse; exacerbation samples are enclosed by a solid ellipse.