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Background  This study of the oropharyngeal microbiome complements the previously published AZIthromycin in Severe ASThma (AZISAST) clinical trial, where the use of azithromycin was assessed in subjects with exacerbation-prone severe asthma. Here, we determined the composition of the oropharyngeal microbial community by means of deep sequencing of the amplified 16S rRNA gene in oropharyngeal swabs from patients with exacerbation-prone severe asthma, at baseline and during and after 6 months treatment with azithromycin or placebo.    Results  A total of 1429 OTUs were observed, of which only 59 were represented by more than 0.02% of the reads. Firmicutes, Bacteroidetes, Fusobacteria, Proteobacteria and Actinobacteria were the most abundant phyla and  Streptococcus  and  Prevotella  were the most abundant genera in all the samples. Thirteen species only accounted for two thirds of the reads and two species only,  i.e. Prevotella melaninogenica  and  Streptococcus mitis/pneumoniae,  accounted for one fourth of the reads.  We found that the overall composition of the oropharyngeal microbiome in patients with severe asthma is comparable to that of the healthy population, confirming the results of previous studies. Long term treatment (6 months) with azithromycin increased the species  Streptococcus salivarius  approximately 5-fold and decreased the species  Leptotrichia wadei  approximately 5-fold. This was confirmed by Boruta feature selection, which also indicated a significant decrease of  L. buccalis / L. hofstadtii  and of  Fusobacterium nucleatum . Four of the 8 treated patients regained their initial microbial composition within one month after cessation of treatment.    Conclusions  Despite large diversity of the oropharyngeal microbiome, only a few species predominate. We confirm the absence of significant differences between the oropharyngeal microbiomes of people with and without severe asthma. Possibly, long term azithromycin treatment may have long term effects on the composition of the oropharygeal microbiome in half of the patients.    Electronic supplementary material  The online version of this article (doi:10.1186/s12866-017-1022-6) contains supplementary material, which is available to authorized users.

Influence of chronic azithromycin treatment on the composition of the oropharyngeal microbial community in patients with severe asthma