Diversity of the human skin microbiome early in life

Abstract

Within days after birth, rapid surface colonization of infant skin coincides with significant functional changes. Gradual maturation of skin function, structure, and composition continues throughout the first years of life. Recent reports have revealed topographical and temporal variations in the adult skin microbiome. Here we address the question of how the human skin microbiome develops early in life. We show that the composition of cutaneous microbial communities evolves over the first year of life, showing increasing diversity with age. Although early colonization is dominated by Staphylococci, their significant decline contributes to increased population evenness by the end of the first year. Similar to what has been shown in adults, the composition of infant skin microflora appears to be site specific. In contrast to adults, we find that Firmicutes predominate on infant skin. Timely and proper establishment of healthy skin microbiome during this early period might have a pivotal role in denying access to potentially infectious microbes and could affect microbiome composition and stability extending into adulthood. Bacterial communities contribute to the establishment of cutaneous homeostasis and modulate inflammatory responses. Early microbial colonization is therefore expected to critically affect the development of the skin immune function.

Figure 1

Hierarchical clustering of infant skin samples taken from arms, foreheads, and buttock (a) taken together and (b) analyzed by sampled site. The most predominant 17 classes were chosen to be used in hierarchical clustering to assess the relationships between samples. (c) UNIFRAC-based principal component analysis demonstrates clustering according to body site. Each point corresponds to samples from a single location for each study participant. The percent variability for each principal component shown is PC1: 42.97%, PC2: 13.09%, and PC3: 8.29%. Clr, cluster; Loca, location.

Figure 2

Relative abundance of the most predominant genera in the various age groups, averaged over all body sites. Superscripts indicate phylum: 1, Firmicutes; 2, Actinobacteria; 3, Bacteriodetes; 4, Proteobacteria.

Figure 3

Relative abundance of the most predominant genera on the arm (a), forehead (b), and buttock (c) in the various infant age groups. The predominant genera seen were Streptococcus, Staphylococcus, and Corynebacterium in the arm samples and Streptococcus, Staphylococcus, and Propionibacterium in the forehead samples. Along with Streptococcus and Staphylococcus, Clostridium, Runinococcus, and Finegoldia were also predominately seen in samples taken from the buttocks. Statistical analysis was performed across age groupings and significance indicated by the notation a, b, where a is significantly different than b. Superscripts indicate phylum: 1, Firmicutes; 2, Actinobacteria; 3, Bacteriodetes; 4, Proteobacteria; 5, Acidobacteria. (d) Biplot of the distance based redundancy analysis of microbial communities on the buttocks. Coordinates for the species arrows are correlations with each axis, and only the 10 most important (based on the magnitude of correlations) genera are shown. The 95% confidence ellipses for the age groups also are shown.