Asthma Phenotypes Associated With Bacterial and Fungal Biomarkers

Endobronchial brush samples from individuals with T2-low inflammation had significantly more fungal diversity compared with those with T2-high inflammation.

Bacterial and fungal microbiota may be associated with asthma phenotypes, according to a study recently published in The Journal of Asthma and Clinical Immunology. Microbial signatures may serve as effective biomarkers in distinguishing among asthma phenotypes. 

This cross-sectional study included bronchoalveolar lavage (BAL) and endobronchial brush (EB) samples from 39 individuals with asthma and 19 healthy controls. All samples were examined with internal transcribed spacer-based microbiota and 16S gene sequencing. All sequences observed in the microbiota were categorized into exact sequence variants, with a threshold of 300 cells/μL blood eosinophil count for the T2 phenotype. The primary objective of the study was to test for an association between fungal structure in airways and T2 inflammation, clinical variables, and atopy. Correlations between clinical parameters and certain exact sequence variants were tested using generalized linear models. 

EB samples from individuals with T2-low inflammation had significantly more fungal diversity compared with those with T2-high inflammation (P <.05), as did healthy controls (P <.01). BAL samples did not vary significantly between T2-high, T2-low, and control participants. With EB samples, Trichoderma were found to be enriched among those with T2-high inflammation, while Penicillium was found to be enriched among participants with atopy. With BAL, T2-high participants showed enriched Fusarium, Cladosporium, Aspergillus, and Alternaria, while T2-low participants had enriched Mycosphaerella. 

Significant associations were identified between certain fungal exact sequence variants and BAL fluid cell counts, fractional exhaled nitric oxide values, corticosteroid use, and forced expiratory volume in 1 second via generalized linear models. Individuals with asthma differed from healthy participants in bacterial-fungal co-occurrence patterns (P <.05). Through random forest models, EB samples were associated with 80% accuracy in predicting asthma status and BAL samples were associated with 75% accuracy. 

Limitations to this study included a small sample size and heterogeneity in medication usage in patients with asthma.

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The researchers concluded that the study demonstrated “a potential association between the fungal and bacterial microbiota and asthma associated phenotypes and endotypes, significant coregulation between bacterial and fungal genera in co-occurrence networks, and correlation between select predicted bacterial functional pathways and clinical parameters.” They added that the findings “provide potential new biomarkers that may be useful, particularly when combined with other clinical and biological markers, to distinguish asthma endotypes.”


Sharma A, Laxman B, Naureckas ET, et al. Associations between fungal and bacterial microbiota of airways and asthma endotypes [published online July 3, 2019]. J Allergy Clin Immunol. doi:10.1016/j.jaci.2019.06.025