Legend to Figures:
Figure 1. Airway of severe asthma subjects exhibits distinct
species-level microbiome profiles. (A) Barplot showing the average
species-level airway microbiome profiles across study cohorts. (B)
Boxplot illustrating species-level α-diversity of airway microbiome
across study cohorts. (C) Barplots showing log2 fold-change of
significantly differentially abundant airway microbial species across
study cohorts. (D) Barplots showing log2 fold-change of significantly
differentially abundant airway microbial species between the 4 groups of
San, SAs/ex, MMA and HC. Significance: ns (not significant,P >0.05), *P ≤0.05, **P ≤0.01 and
***P ≤0.001. Study cohorts: SAn (non-smokers with severe asthma);
SAs/ex (smokers or ex-smokers with severe asthma), MMA (non-smokers with
mild or moderate asthma) and HC (healthy controls).
Figure 2. Sputum inflammation type shows distinct species-level
microbiome profiles. (A) Barplot showing the average species-level
airway microbiome profiles according to granulocytic sputum inflammation
type. (B) Boxplot illustrating species-level ⍺-diversity of airway
microbiome according to granulocytic sputum inflammation type.
(C) Principle coordinate analysis (PCoA) based on Bray-Curtis
dissimilarity illustrating species-level β-diversity of airway
microbiomes in the 4 granulocytic sputum inflammation types and HC. (D)
Barplots showing log2 fold-change of significantly differentially
abundant airway microbial species according to granulocytic sputum
inflammation type. (E) Barplots showing log2 fold-change of
significantly differentially abundant airway microbial species between
each of the sputum granulocytic types and healthy control. Significance:
ns (not significant, P >0.05), *P≤ 0.05,
**P≤ 0.01 and ***P≤ 0.001. Granulocytic sputum inflammation
type: EOS: eosinophilic high (sputum eosinophil % ≥ 1.49%); NEU:
neutrophilic high (sputum neutrophil count % ≥ 73.6%); MIX: both
neutrophilic and eosinophilic high; PAU: paucigranulocytic (sputum
eosinophil % < 1.49% and sputum neutrophil count %
< 73.6%) and HC (healthy controls).
Figure 3. Molecular phenotypes of asthma exhibit distinct
microbiome profiles. (A) Barplot showing the average species-level
airway microbiome profiles across the 3 transcriptome-associated
molecular phenotypes (TACs) and in healthy controls (HC). (B) Boxplot
illustrating species-level α-diversity of airway microbiome across the
TACs and HC. (C) Principle coordinate analysis (PCoA) based on
Bray-Curtis dissimilarity illustrating species-level β-diversity of
airway microbiomes in the 3 TACs and HC (D) Barplots showing log2
fold-change of significantly differentially abundant airway microbial
species between the 3 TACs (E) Barplots showing log2 fold-change of
significantly differentially abundant airway microbial species between
each TAC and HCs. Significance: ns (not significant,P >0.05), *P ≤0.05, **P ≤0.01 and
***P ≤0.001.
Figure 4. Heatmap of Spearman’s correlation coefficientsbetween FEV1 (% predicted), FEV1/FVC ratio, exacerbations in previous
year, sputum neutrophil and eosinophil cell counts (%), blood
neutrophil and eosinophil counts, and fractional exhaled nitric oxide
(FeNO) levels against the abundance of top bacterial species for the 3
asthma cohorts. Significance of Spearman coefficient correlation: ns -
not significant (adjusted p > 0.05), with clear box;
*adjusted p ≤ 0.05; **adjusted p ≤ 0.01; ***adjusted p ≤ 0.001.
SAn: non-smokers with severe
asthma; SAs/ex: smokers or ex-smokers with severe asthma; MMA:
mild-moderate non-smoking asthma; HC: healthy non-smoking and
non-asthmatic.
Figure 5. Airway of severe asthma subjects exhibits temporal
stability in species-level microbiome profiles. (A) Barplots showing
the baseline and longitudinal follow-up of species-level airway
microbiome profiles in subjects with severe asthma, using the same order
of subject identifiers. (B) Paired boxplot illustrating species-level
α-diversity of airway microbiomes across in severe asthma cases. (C)
Principle coordinate analysis (PCoA) based on Bray-Curtis dissimilarity
illustrating species-level β-diversity of airway microbiomes at baseline
or longitudinal follow-up. Paired samples that are from the same subject
are connected by a line. (D) Boxplot showing the species-level microbial
compositional similarity across possible sample pairing: Within BL
(pairing between any two baseline samples), Within LT (pairing between
any two longitudinal follow-up samples), Unpaired (pairing between
baseline and longitudinal follow-up samples from different subjects),
and paired (pairing between baseline and longitudinal samples from the
same subject). Timepoint: BL (baseline) and LT (longitudinal follow-up).
Significance: ns (not significant, P >0.05),
*P ≤0.05, **P ≤0.01 and ***P ≤0.001.