The Skin Microbiome: Current Techniques, Challenges, and Future Directions

Abstract

Skin acts as a barrier that promotes the colonization of bacteria, fungi, archaea, and viruses whose membership and function may differ depending on the various specialized niches or micro-environments of the skin. The group of microorganisms inhabiting the skin, also known as the skin microbiome, offers protection against pathogens while actively interacting with the host’s immune system. Some members of the skin microbiome can also act as opportunistic pathogens. The skin microbiome is influenced by factors such as skin site, birth mode, genetics, environment, skin products, and skin conditions. The association(s) of the skin microbiome with health and disease has (have) been identified and characterized via culture-dependent and culture-independent methods. Culture-independent methods (such as high-throughput sequencing), in particular, have expanded our understanding of the skin microbiome’s role in maintaining health or promoting disease. However, the intrinsic challenges associated with the low microbial biomass and high host content of skin microbiome samples have hindered advancements in the field. In addition, the limitations of current collection and extraction methods and biases derived from sample preparation and analysis have significantly influenced the results and conclusions of many skin microbiome studies. Therefore, the present review discusses the technical challenges associated with the collection and processing of skin microbiome samples, the advantages and disadvantages of current sequencing approaches, and potential future areas of focus for the field.

Comparison of the full-length sequence and sub-regions of 16S rRNA gene for skin microbiome profiling

“…However, the sub-region has more unique microbial biomarkers with lower LDA values, especially for PaS and CiraS samples with high environmental exposure, and microbial community diversity. We posit that the main reason for this phenomenon is that 16S hypervariable regions sequencing reads contain limited sequence variation, as well as inherent preferences in primer binding and microbial annotation, which introduce systematic errors during the analysis of different types of samples, resulting in varying outcomes for the same type of samples analyzed in different 16S hypervariable regions ( 14 , 16 ).…”

“…Furthermore, the inherent stability and individual specificity of the skin microbiome present novel forensic applications, where microbial traces on objects or at crime scenes may provide unique identifiers or insights into environmental interactions ( 8 – 12 ). However, the microbiome’s variability across different skin areas, influenced by unique microenvironmental factors such as pH, moisture levels, and sebaceous gland activity poses challenges ( 13 – 15 ). Therefore, a thorough taxonomic characterization of skin microbial communities, alongside the creation of uniform research protocols tailored to various skin types and DNA qualities (which are often compromised in forensic contexts), is critical for progressing in this domain.…”

The Next Generation Fecal Microbiota Transplantation: To Transplant Bacteria or Virome

“…To address this limitation, mature multiomics sequencing strategies, such as the introduction of metatranscriptome analysis, can be employed. [ 115 ] Besides, the human gut microbiome is a highly complex and heterogeneous ecosystem, with significant variations even within the same individual's microbiota. [ 116 ] Careful attention to experimental design, including refined sample collection processes with reduced variation, and enhanced data analysis techniques such as absolute microbiome measurements, can also contribute to overcoming the challenges associated with certifying the efficacy of defined bacterial consortia across a large and diverse population.…”

An Overview of the Relevance of Human Gut and Skin Microbiome in Disease: The Influence on Atopic Dermatitis

“…One of the main characteristics of the human skin microbiome is its high diversity and interpersonal variation, with a slightly higher concentration in hair follicles. This is extremely important for the health of the skin, as it plays an essential role in its protection against external and potentially harmful substances [15,48,49].…”