Figures
- FIGURE 1
Unsupervised hierarchical clustering of most abundant taxa for bronchoalveolar lavage samples. The dendrogram demonstrates two well-separated clusters: one dominated by supraglottic taxa and a second one with a lower abundance of them. Clusters were not determined by pre- or post-treatment with interferon-γ.
- FIGURE 2
Microbiomic changes during inhaled interferon (IFN)-γ. a) Comparison of α diversity (based on the Shannon Index where sequences were rarified at 1000 reads per sample) before and after treatment. b) Changes in β diversity (based on UniFrac distances) before and after IFN-γ (p-value based on PERMANOVA (permutational multivariate ANOVA)). PC: principal coordinate; ns: nonsignificant. c) β diversity distance (based on UniFrac distances) between pairs of samples comparing within subject (before–after IFN-γ) versus between subjects (p-value based on Mann–Whitney test). d) Linear discriminant analysis (LDA) effect size was calculated comparing 16S rRNA data at baseline and after IFN-γ.
- FIGURE 3
Co-occurrence network between taxa and biomarkers. Th: T-helper; IPF: idiopathic pulmonary fibrosis. compPLS was utilised to evaluate associations between the lung microbiome and local/systemic biomarkers, which were categorised as Th1, Th2, Th17 and/or IPF immunological phenotype. a) Associations between taxa and bronchoalveolar lavage (BAL) fluid cytokines. b) Associations between taxa and BAL cell supernatant cytokines. c) Associations between taxa and plasma cytokines. Negative associations are in red and positive associations are in grey; edge weight is scaled to represent the degree of confidence for the associations.
Tables
- TABLE 1
Demographics, pulmonary function and bronchoalveolar lavage (BAL) cell count differential
Subjects 10 Age years 69.0 (63.7–76.0) Male 8 (80) Smoking status Current 0 Ex 5 (50) Never 5 (50) Pack-years (smokers) 20 (10–30) Clinical Biopsy done 4 (40) PASP elevated 6 (60) PAP mmHg 36.8 (33.2–40.7) N-acetyl cysteine treatment 4 (40) Pulmonary function FVC % pred 73.5 (68.2–84.2) TLC % pred 71.0 (60.0–77.0) DLCO % pred 47.5 (39.5–56.5) 6MWT m 420 (287–490) BAL BAL cells obtained ×106 19.2 (13.8–31.9) Macrophages % 78.0 (69.0–91.2) Lymphocytes % 5.0 (3.0–9.3) Neutrophils % 9.0 (3.5–24.3) Eosinophils % 0.75 (0–2.25) Data are presented as n, median (interquartile range) or n (%). PASP: pulmonary artery systolic pressure; PAP: pulmonary arterial pressure; FVC: forced vital capacity; TLC: total lung capacity; DLCO: diffusing capacity of the lung for carbon monoxide; 6MWT: 6-min walk test.
Supplementary Material
Please note: supplementary material is not edited by the Editorial Office, and is uploaded as it has been supplied by the author.
Supplementary material 00008-2017_Supplementary_data
Supplementary Material
M.H. Badri 00008-2017_Badri
R. Bonneau 00008-2017_Bonneau
R. Condos 00008-2017_Condos
B. Kapoor 00008-2017_Kapoor
Z.D. Kurtz 00008-2017_Kurtz
M. Lesko 00008-2017_Lesko
Y. Li 00008-2017_Li
L.N. Segal 00008-2017_Segal
G. Smaldone 00008-2017_Smaldone
J. Wang 00008-2017_Wang
B.G. Wu 00008-2017_Wu
