Deciphering the role of skin surface microbiome on skin health: an integrative multi-omics approach reveals three distinct microbial / metabolic clusters

The advent of 16s RNA profiling and shotgun metagenomics have enabled a holistic approach to the study of the skin microbiome composition. Despite the interesting findings in this rapidly developing scientific area, the big question remains: What role does the microbiome play in skin physiology? To begin to answer this question we employed an integrative methodology on microbiome and metabolome data from skin surface samples collected from the volar forearm of healthy 3-6 month infants. While the infant skin metabolome is dominated by amino acids, lipids and xenobiotics, the primary phyla of the microbiome are Firmicutes, Actinobacteria and Proteobacteria. Zooming in to the species level revealed a large contribution of commensals belonging to Cutibacterium and Staphylococcus genera, including Cutibacterium acnes, Staphylococcus epidermidis and Staphylococcus aureus. This heterogeneity is further reflected when combining the microbiome with metabolome data. Integrative analyses enabled us to delineate the co-existence of three distinct metabolic / microbial clusters: one dominated by Cutibacterium linked to hydrophobic elements of the skin barrier, one associating Staphylococcus genus with amino acids relevant to the water holding capacity and pH regulation of the skin surface and one characterized by Streptococcus and independent of any particular metabolomic profile.