The human skin microbiome

Abstract

Functioning as the exterior interface of the human body with the environment, skin acts as a physical barrier to prevent the invasion of foreign pathogens while providing a home to the commensal microbiota. The harsh physical landscape of skin, particularly the desiccated, nutrient-poor, acidic environment, also contributes to the adversity that pathogens face when colonizing human skin. Despite this, the skin is colonized by a diverse microbiota. In this Review, we describe amplicon and shotgun metagenomic DNA sequencing studies that have been used to assess the taxonomic diversity of microorganisms that are associated with skin from the kingdom to the strain level. We discuss recent insights into skin microbial communities, including their composition in health and disease, the dynamics between species and interactions with the immune system, with a focus on Propionibacterium acnes, Staphylococcus epidermidis and Staphylococcus aureus.

<b><i>Staphylococcus epidermidis</i></b>: A Potential New Player in the Physiopathology of Acne?

“…Thus, both such recognised commensals C. acnes and S. epidermidis seem to interact with the host, helping to protect the healthy skin from colonisation by pathogens [9, 16]. Figure 1 provides visual support.…”

“…This concomitant presence has raised questions about their respective role in the pathogenesis of acne [56, 57]. While there is no evidence that S. epidermidis plays an active role in the onset of acne, C. acnes is currently associated with acne [9]. …”

“…Metagenomic analysis and sequencing of the 16S ribosomal RNA gene are the predominant bacteriological sampling methods employed for analysing the bacterial composition of microbial communities, and choosing the most effective study design is crucial for obtaining meaningful analysis results [7]. Thus, physiological characteristics of different skin sites sampled have been associated with different levels of bacterial diversity including Actinobacteria such as Propionibacteria, very recently renamed Cutibacteria (comprising Cutibacterium acnes and also Cutibacterium granulosum and Cutibacterium avidum ), Proteobacteria, Bacteroides and Firmicutes; Staphylococcus epidermidis belongs to the latter group [5, 6, 8, 9]. Of these, C. acnes and S. epidermidis are two of the main commensal skin bacteria [3, 10-12].…”

16S rRNA sequence embeddings: Meaningful numeric feature representations of nucleotide sequences that are convenient for downstream analyses

“…and Streptococcus occurring in response to atopic dermatitis [46]. As 4263 Bacteroidetes 292 reads were introduced to the sample embedding, the classifier began to favor a "feces" 293 classification.…”

“…Various architectures exist, but their objective 44 is generally the same: capture semantic and lexical information of each word based on 45 that word's context -i.e., its neighboring set of words. Each word is represented in a 46 vector space of predefined length, where semantically similar words are placed near one 47 another. Thus, k -mer representations of sequences could be embedded in such a way 48 that their context is preserved (the position of k -mers relative to their neighbors), and 49 they become suitable for down-stream machine learning approaches.…”