Effect of inhaled corticosteroids on microbiome and microbial correlations in asthma over a 9-month period

The effect of inhaled corticosteroids (ICS) on the airway microbiome requires longitudinal research for corroboration. Asthma patients, not undergoing ICS treatment (baseline), were enrolled and prescribed ICS; all these patients were followed up with regular visits at 3 months (visit 1) and 9 months (visit 2). Induced sputum was collected, and fungal microbiota (mycobiome) and bacterial microbiota (bacteriome) were estimated using 16S rRNA and internal transcribed spacer (ITS) sequencing. Bacterial α diversity indices were not significantly different between baseline, visit 1, and visit 2. Visit 1 showed lower fungal evenness than the baseline, and visit 2 showed lower fungal diversity and evenness than the baseline. Fungal, but not bacterial, community compositions differed significantly between the baseline, visit 1, and visit 2. The most abundant bacterial phyla and genera did not differ significantly between the baseline, visit 1, and visit 2. Compared with the baseline, visit 1 showed significantly increased frequency of the fungal phylum Ascomycota and lower frequency of Basidiomycota. We found sharply decreased fungal genera Wallemia, Cladosporium, Penicillium, and Alternaria at visit 1 and visit 2 compared with the baseline, although the differences were not statistically significant. We also found the proportion of Basidiomycota was positively correlated with percentages of sputum eosinophils and neutrophils. The proportions of Saccharomyces, Wallemia, and Aplosporella were positively correlated with percentage of sputum eosinophils. Moreover, we identified distinct inter- and intra-kingdom interactions in baseline, visit 1, and visit 2. Therefore, ICS use altered the airway microbial diversity, evenness, community composition, and microbial connections.