Type 2-high asthma is associated with a specific indoor mycobiome and microbiome

Abstract

Background: The links between microbial environmental exposures and asthma are well documented, but no study has combined deep sequencing results from pulmonary and indoor microbiomes of patients with asthma with spirometry, clinical, and endotype parameters.

Objective: The goal of this study was to investigate the links between indoor microbial exposures and pulmonary microbial communities and to document the role of microbial exposures on inflammatory and clinical outcomes of patients with severe asthma (SA).

Methods: A total of 55 patients with SA from the national Cohort of Bronchial Obstruction and Asthma cohort were enrolled for analyzing their indoor microbial flora through the use of electrostatic dust collectors (EDCs). Among these patients, 22 were able to produce sputum during "stable" or pulmonary "exacerbation" periods and had complete pairs of EDC and sputum samples, both collected and analyzed. We used amplicon targeted metagenomics to compare microbial communities from EDC and sputum samples of patients according to type 2 (T2)-asthma endotypes.

Results: Compared with patients with T2-low SA, patients with T2-high SA exhibited an increase in bacterial α-diversity and a decrease in fungal α-diversity of their indoor microbial florae, the latter being significantly correlated with fraction of exhaled nitric oxide levels. The β-diversity of the EDC mycobiome clustered significantly according to T2 endotypes. Moreover, the proportion of fungal taxa in common between the sputum and EDC samples was significantly higher when patients exhibited acute exacerbation.

Conclusion: These results illustrated, for the first time, a potential association between the indoor mycobiome and clinical features of patients with SA, which should renew interest in deciphering the interactions between indoor environment, fungi, and host in asthma.

Keywords: Feno; Indoor environment; microbiome; mycobiome; severe asthma; type 2 asthma.

Graphical abstract

Fig 1

The α- and β-diversities of the EDCs from patients with SA according to T2 endotypes (n = 22). The α-diversity of bacterial (A) or fungal (B) communities from EDCs is shown using Chao1, Shannon, and Simpson indexes. C, Correlation between Feno levels and Chao1 fungal diversities. D, The β-diversity of fungal communities. Patients were split according to whether than had T2-high SA (dark gray, circles) or T2-low SA (light gray, triangles).

Fig 2

Taxonomic differences between Feno groups with T2 endotypes used as covariables across the 22 EDCs show significant enrichment of specifics taxa at the OTU level. Linear discriminant analysis (LDA) and effect size analysis identified bacterial (A) and fungal (B) taxa differentially enriched according to an LDA score cutoff at 2. The colors (dark and gray) represent each Feno group (level cutoff at 25 ppb), and the length represents the LDA score, which is the degree of significant difference (in log scale) for a given taxon. As the order of the numerator and denominator when calculating the effect size is determined by alphabetical order, it is possible to obtain an interpretation of the scale of the difference between 2 groups by using the absolute values of the effect size even though the LDA score is negative for a given taxon. Thus, any taxa colored according to the Feno variable may be interpreted as taxa being significantly increased in abundance compared with the other Feno group.

Fig 3

Comparison of diversity and composition of both sputum and EDC samples. The bacterial (left) and fungal diversities (right) based on Shannon indexes are presented for sputum and EDC samples (A). The proportion of Basidiomycota (a phylum primarily composed of environmental fungi) was higher in EDCs than in sputa (B). Principal coordinates analysis based on Bray-Curtis dissimilarity between sputum (dark gray, squares) and EDC (light gray, diamonds) samples for bacterial (C) and fungal (D) communities showed the highly individual signature of sputa compared with that of EDCs. Proportion of common bacterial (E) or fungal (F) taxa between EDCs and sputa collected at a stable state (STB) or during an exacerbation (EXA). For each OTU, the proportion was expressed as a percentage of the number of reads (ie, relative abundance). PERMANOVA, Permutational multivariate ANOVA.

Fig 4

Microbial core shared between the 22 pairs of indoor and respiratory samples. Venn diagrams show the proportion of common bacterial (A) and fungal (B) taxa (at the OTU level) between EDCs (green section) and sputa (SPU) collected either during an exacerbation (EXA) (the SPU were collected during an EXA [red section]) or during a stable state (STB) period (the SPU were collected during an STB [blue section]). Only OTUs present at least in 20% of each group of SPU (clustered according the presence or absence of an EXA when the SPU were collected) and in at least 90% of EDCs were taken into account and represented in the Venn diagrams. The bacterial core (A) showed only 1 OTU corresponding to Sphingomonas spp shared between EDCs and SPU collected during an EXA and 4 OTUs belonging to Streptococcus, Paracoccus, and Haemophilus species were shared independently from the clinical state of the patients. The fungal core (B) was larger than the bacterial core and was composed of 9 OTUs associated with SPU collected during an EXA, 1 OTU (ie, Alternaria brassicae) associated with SPU collected at STB, and 17 OTUs (including several medically relevant fungi, such as Malassezia, Aspergillus, and Cladosporium species) belonging to the fungal core independent from the clinical state.

Fig E1

Flowchart of the COBRA-ENV (indoor environment analysis of COhort of BRonchial obstruction and Asthma) study and samples distribution across time.

Fig E2

Histograms representing the relative abundance at the genus level of the EDC microbiome.

Fig E3

Histograms representing the relative abundance at the genus or species level of the EDC mycobiome.

Fig E4

Histograms representing the relative abundance at the genus level of the sputum microbiome.

Fig E5

Histograms representing the relative abundance at the genus or species level of the sputum mycobiome.