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Background  Atopic dermatitis (AD) patients have an altered skin bacterial community, with an abundance of  Staphylococcus aureus  associated with flares, highlighting that microbial organisms may be important for disease exacerbation. Despite strong evidence of association between bacterial skin colonisation and AD, very limited knowledge regarding the eukaryotic microbial community, including fungi and ectoparasites, in AD exists. In this study, we compared the skin and nasal eukaryotic microbial community between adult AD patients ( n  = 55) and non-AD healthy controls ( n  = 45) using targeted  18S rRNA  amplicon sequencing. Analysis was based on the presence or absence of eukaryotic microorganisms.    Results  The cutaneous composition of the eukaryotic microbial community and the alpha-diversity differed significantly between AD patients and non-AD individuals, with increased species richness on AD skin. Alpha-diversity and beta-diversity were similar on lesional and non-lesional skin of patients. The ectoparasite  Demodex folliculorum  and the yeast  Geotrichum candidum  were significantly more prevalent on the skin of AD patients. The prevalence of  D. folliculorum  on lesional skin was greater among patients recently treated with topical corticosteroid.  Malassezia  was one of the most frequently detected genera at all sites, with  M. globosa  and  M. restricta  being the most prevalent.  M. restricta  was under represented in the anterior nares of AD patients as compared to the non-AD control population.    Conclusion  Significant differences in the eukaryotic microbial communities were found between AD patients and non-AD individuals, with the most striking finding being the significantly overrepresentation of  D. folliculorum  on AD skin. Whether  D. folliculorum  can contribute to skin inflammation in AD needs further investigation.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12866-021-02139-9.

Identification of cutaneous fungi and mites in adult atopic dermatitis: analysis by targeted 18S rRNA amplicon sequencing