Objectives

The MICROBIOME study aimed to compare the bronchial bacterial microbiota in adults with steroid-naive atopic asthma, with atopy but no asthma, and non-atopic healthy subjects; and to determine whether inhaled corticosteroid treatment alters bronchial microbial community composition in adults with asthma.

Background

Recent studies have shown that the composition of lower respiratory tract bacteria (microbiota) differs between healthy adults and adults with asthma. Additionally, phenotypic features of asthma, such as measures of airway hyper-responsiveness, asthma control, and transcriptional response to steroids, correlate with patterns of bronchial microbiota composition. In most of the previous studies, subjects with asthma were treated with inhaled corticosteroids (ICS), casting some uncertainty on whether the findings reflect the effects of ICS treatment or of asthma itself. Similarly, many patients with asthma are atopic, raising the question as to whether asthma-associated differences in respiratory microbiota are related to underlying atopy. The MICROBIOME study sought to elucidate differences in bronchial microbiota associated with asthma versus atopy, and with important phenotypic features of this disease, such as responsiveness to ICS treatment.

Participants

The MIROBIOME study was conducted in adults at nine AsthmaNet sites. 84 subjects were enrolled: 42 atopic asthmatics (AA), 21 atopic non-asthmatics (ANA) and 21 non-atopic healthy control subjects (HC). Atopy was defined by serologic evidence (>0.35 kU/l) of sensitivity to more than 1 of 12 aeroallergens. Asthma was confirmed by airway hyperresponsiveness (methacholine PC20 ≤8 mg/mL or FEV1 improvement >12% post albuterol). At enrollment, subjects with asthma had been clinically stable for three months, and had an Asthma Control Questionnaire score of less than 1.5 without the use of a controller medication. Exclusion criteria included a history of smoking, respiratory infection within six weeks or antibiotic use within three months of enrollment.

Design

The MICROBIOME study was a multicenter clinical trial. Samples processed for microbiota analysis included oral wash, a saline flush (10 mL) of the bronchoscope suction channel (“scope-flush”) and protected bronchial brushings (BB). Potential oral contamination of BB was evaluated by comparing a random subset of 30 BB-paired scope-flushes. Nucleic acids were extracted using a modified bead-beating protocol. Bacterial communities from the subjects were profiled by 16S rRNA gene sequencing. 16S rRNA gene copy number was assessed by quantitative PCR using universal primers. A 97% sequence homology cut-off was used to define bacterial taxa (also referred to as operational taxonomic units; OTUs). Sequence-based bacterial community analysis could be performed in the same proportion (67%) of samples collected from AA, ANA, and HC subjects.

AA were randomized in a 2:1 ratio to treatment with inhaled fluticasone propionate (250 mcg) or placebo twice daily for six weeks and re-assessed post-treatment.

Expression levels of three bronchial epithelial genes (CLCA1, SERPINB2 and POSTN) previously shown to be induced by IL-13, were measured using RNA extracted in parallel with DNA to calculate the “three-gene mean” (TGM) score for each participant. Type 2-high asthma was defined by TGM scores greater than 1.117 (two standard deviations above the average TGM-score in HC), confirmed by unsupervised cluster and principal component analysis.

The primary outcome was a comparison of the microbial community richness, diversity, and evenness between AA, ANA, and HC subjects.

Conclusions

The bronchial bacterial microbiota of both atopic asthmatics and atopic non-asthmatics differ from that of healthy controls and also differ from each other. There were no significant changes in bacterial burden or diversity between measurements at baseline and after six weeks of treatment with ICS in adults with asthma.

Durack J, Lynch SV, Nariya S, et al. Features of the bronchial bacterial microbiome associated with atopy, asthma, and responsiveness to inhaled corticosteroid treatment. J Allergy Clin Immunol. 2017;140(1):63–75. doi:10.1016/j.jaci.2016.08.055

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