human skin metagenomes

The skin microbiome is stable in healthy individuals despite constant exposure to the external environment. To assess the relationship between skin microbiota stability and patients with atopic dermatitis (AD), we sampled 49 subjects (33 AD patients and 16 healthy controls) at left and right antecubital fossae over two time-points that are 4 to 6 weeks apart. AD patients were recruited in a non-flare, stable disease state after minimum 7 days washout period and continued on standard of care therapy between visit 1 and 2. Principle coordinates analysis showed that skin microbiome profiles were mostly stable across visits for all subjects. Hierarchical clustering revealed two distinct groups that varied in species and functional composition. We refer to these distinct skin microbiome signatures as “microbial dermotypes” A and B. Differences between the microbial dermotypes were driven primarily by Propionibacterium, Corynebacterium and Streptococcus that had a lower abundance in dermotype B. While Staphylococcus aureus was significantly more abundant in AD patients, it was not a major driver of dermotype clustering. Interestingly, these microbial community compositions were maintained despite standard of care treatment. To identify mechanistic biomarkers correlated with host properties, we found that dermotype B is significantly correlated with higher IgE levels and objective SCORAD, but not increased transepidermal water loss or skin pH, and not linked to filaggrin mutations. This study suggests the skin microbiome can identify specific groups of AD patients and therefore could aid in patient stratification and provide avenues to identify novel therapeutic targets OR providing new information regarding AD pathogenesis.