Features of the bronchial bacterial microbiome associated with atopy, asthma, and responsiveness to inhaled corticosteroid treatment

J Allergy Clin Immunol. 2017 Jul;140(1):63-75. doi: 10.1016/j.jaci.2016.08.055. Epub 2016 Nov 10.


Background: Compositional differences in the bronchial bacterial microbiota have been associated with asthma, but it remains unclear whether the findings are attributable to asthma, to aeroallergen sensitization, or to inhaled corticosteroid treatment.

Objectives: We sought to compare the bronchial bacterial microbiota in adults with steroid-naive atopic asthma, subjects with atopy but no asthma, and nonatopic healthy control subjects and to determine relationships of the bronchial microbiota to phenotypic features of asthma.

Methods: Bacterial communities in protected bronchial brushings from 42 atopic asthmatic subjects, 21 subjects with atopy but no asthma, and 21 healthy control subjects were profiled by using 16S rRNA gene sequencing. Bacterial composition and community-level functions inferred from sequence profiles were analyzed for between-group differences. Associations with clinical and inflammatory variables were examined, including markers of type 2-related inflammation and change in airway hyperresponsiveness after 6 weeks of fluticasone treatment.

Results: The bronchial microbiome differed significantly among the 3 groups. Asthmatic subjects were uniquely enriched in members of the Haemophilus, Neisseria, Fusobacterium, and Porphyromonas species and the Sphingomonodaceae family and depleted in members of the Mogibacteriaceae family and Lactobacillales order. Asthma-associated differences in predicted bacterial functions included involvement of amino acid and short-chain fatty acid metabolism pathways. Subjects with type 2-high asthma harbored significantly lower bronchial bacterial burden. Distinct changes in specific microbiota members were seen after fluticasone treatment. Steroid responsiveness was linked to differences in baseline compositional and functional features of the bacterial microbiome.

Conclusion: Even in subjects with mild steroid-naive asthma, differences in the bronchial microbiome are associated with immunologic and clinical features of the disease. The specific differences identified suggest possible microbiome targets for future approaches to asthma treatment or prevention.

Keywords: 16S ribosomal RNA; Asthma; T(H)2 inflammation; atopy; bacteria; corticosteroids; metabolic pathways; microbiome; short-chain fatty acids; three-gene mean.

Publication types

  • Multicenter Study
  • Randomized Controlled Trial

MeSH terms

  • Administration, Inhalation
  • Adrenal Cortex Hormones / therapeutic use
  • Adult
  • Asthma / drug therapy
  • Asthma / microbiology*
  • Bacteria / classification
  • Bacteria / genetics
  • Bacteria / isolation & purification
  • Bronchi / drug effects
  • Bronchi / microbiology*
  • Female
  • Fluticasone / therapeutic use
  • Humans
  • Hypersensitivity, Immediate / drug therapy
  • Hypersensitivity, Immediate / microbiology*
  • Male
  • Microbiota*
  • Middle Aged
  • RNA, Bacterial / genetics
  • RNA, Ribosomal, 16S / genetics
  • Young Adult


  • Adrenal Cortex Hormones
  • RNA, Bacterial
  • RNA, Ribosomal, 16S
  • Fluticasone