Supplementary Material for: The Skin and Nose Microbiome and Its Association with Filaggrin Gene Mutations in Pediatric Atopic Dermatitis

<b><i>Background:</i></b> Interactions between the skin barrier, immune system, and microbiome underlie the development of atopic dermatitis (AD). <b><i>Objective:</i></b> To investigate the skin and nasal microbiome in relation to filaggrin gene (<i>FLG</i>) mutations. <b><i>Methods:</i></b> A cross-sectional study including 77 children with difficult-to-treat AD. The entire encoding region of <i>FLG</i> was screened for mutations using single molecule molecular inversion probes and next-generation sequencing. Bacterial swabs from the anterior nares, lesional and nonlesional skin were analyzed using 16S rRNA sequencing. For skin samples, additional qPCR was performed for <i>Staphylococcus aureus</i> and <i>Staphylococcus epidermidis</i>. <b><i>Results:</i></b> The prevalence of patients with a mutation in <i>FLG</i> was 40%, including 10 different mutations. Analyzing bacterial swabs from all three niches showed a significant effect for both niche and <i>FLG</i> mutation status on the overall microbiome composition. Using a subset analysis to test the effect of <i>FLG</i> mutation status per niche separately did not show a significant association to the microbiome. Shannon diversity and <i>S. aureus</i> abundance were significantly affected by the niche, but not by the presence of an <i>FLG</i> mutation. <b><i>Conclusions:</i></b> Our results suggest only a minor role for <i>FLG</i> mutation status on the overall microbiome, which is rather caused by differences in the present genera than by microbe richness and evenness.