Association of Disease Severity With Skin Microbiome and Filaggrin Gene Mutations in Adult Atopic Dermatitis

Abstract

Importance: Skin microbiome correlates with disease severity for lesional and nonlesional skin, indicating a global influence of atopic dermatitis (AD). A relation between skin microbiome and filaggrin gene (FLG) mutations proposes a possible association between skin microbiome and host genetics.

Objectives: To assess skin and nasal microbiome diversity and composition in patients with AD and compare with healthy controls, and to investigate the microbiome in relation to disease severity and FLG mutations in patients with AD.

Design, setting, and participants: An observational case-control study of 45 adult healthy controls and 56 adult patients with AD was carried out from January 2015 to June 2015 in a tertiary referral center, Department of Dermatology, Bispebjerg Hospital, Denmark.

Exposures: Bacterial swabs were taken from patients with AD (lesional skin, nonlesional skin, and anterior nares) and from healthy controls (nonlesional skin and anterior nares). Eczema severity was assessed and FLG mutations noted. Bacterial DNA was extracted from swabs, and V3-V4 16S rDNA regions amplified with PCR. Samples were analyzed at Statens Serum Institut September 2015 to September 2016. Bioinformatics analyses of the microbiome were analyzed using R statistical software (version 3.3.1, R Foundation Inc).

Main outcomes and measures: Skin microbiomes were investigated using next-generation sequencing targeting 16S ribosomal RNA.

Results: Microbiome alpha diversity was lower in patients with AD compared with healthy controls in nonlesional skin (effect size, 0.710; 95% CI, 0.27-1.15; P = .002), lesional skin (effect size, 0.728; 95% CI, 0.35-1.33; P = .001), and nose (effect size, 1.111; 95% CI, 0.48-0.94; P < .001). Alpha diversity was inversely correlated with disease severity for lesional (effect size, 0.530; 95% CI, 0.23-1.64; P = .02) and nonlesional skin (effect size, 0.451; 95% CI, 0.04-2.44; P = .04) in patients with AD. Microbiome composition in AD nonlesional skin was linked to FLG mutations.

Conclusions and relevance: An altered microbiome composition in patients with AD in nonlesional skin, lesional skin, as well as nose, suggests a global influence of AD. Microbiome composition in AD nonlesional skin is associated with FLG mutations, proposing a possible association between the skin microbiome and host genetics.

Figure 1.. Shannon Diversity Index for Skin Samples and Nose Samples of Patients With AD and Healthy Controls

Shannon diversity index, which considers both the richness (number of different species) and evenness (how evenly the species are distributed), is shown for skin samples of patients with AD (nonlesional skin and lesional skin) (A) and healthy controls, as well as nose samples (B). Differences in microbiome diversity were found between patients with AD and healthy controls for both skin and nose. Boxes indicate the 25th percentile, median, and 75th percentile. Dots represent each individual sample. Whiskers show the minimum and maximum ranges. AD indicates atopic dermatitis.

Figure 2.. Barplots of Bacterial Species in Skin Samples of Patients With Atopic Dermatitis (AD) and Healthy Controls

Barplots of bacterial species in skin samples of patients with AD and healthy controls, performed at genus level, except for Staphylococcus, which was kept at species level. Hierarchical clustering was performed according to similarity of the microbiome, and 5 different clusters were identified (I-V). Barplots were performed for AD lesional skin, AD nonlesional skin, and healthy control skin. Disease severity (SCORAD) and FLG mutation status are shown for patients with AD.

Figure 3.. Shannon Diversity Index in Relation to Disease Severity (SCORAD)

Shannon diversity index in relation to the Severity Scoring of Atopic Dermatitis (SCORAD) results for both AD lesional and nonlesional skin. SCORAD was divided into 3 groups: mild, moderate, severe. Microbiome diversity was associated with SCORAD in AD lesional skin but also in AD nonlesional skin. The group for severe AD had few patients; however, a clear trend for the association with SCORAD on microbiome diversity is visible for both lesional skin and nonlesional skin. Boxes indicate the 25th percentile, median, and 75th percentile. Dots represent each individual sample. Whiskers show the minimum and maximum ranges. AD indicates atopic dermatitis.

Figure 4.. Skin Microbiome in Relation to FLG Mutations

The relation between FLG mutations and skin microbiome in AD lesional skin and nonlesional skin was analyzed. The principal coordinate analysis (PCoA) plot shows a difference in skin microbiome between those with filaggrin mutations and those without in AD nonlesional skin (P = .02), but not in AD lesional skin (P = .64).