Did you know our skin is covered with a plethora of microbes that are invisible to the naked eye? The human body is a habitat for hundreds of trillions microorganisms, including bacteria, viruses, fungi, and even arthropods, and outnumber the human cells in our bodies. For the most part, these microbes don’t harm us or cause disease or infection. In fact, they have important roles in our health. These functions range from developing and maintaining the immune system to providing protection against more pathogenic microbes.
How do we identify and characterize these vast populations of microbes residing on our skin? This is an area of intense focus in my laboratory at the University of Pennsylvania. Our lab uses DNA sequencing techniques to identify and characterize the skin microbiome. We engage in a range of investigations, including studies that aim to more deeply understand the healthy human skin microbiome, to studies that characterize and identify microbes and their functions in skin disease, such as atopic dermatitis, psoriasis, and impaired wound healing.
A challenge for researchers embarking on a skin microbiome study is determining what type of method will provide the desired information. We just completed a new study comparing these different methods and how they perform in identifying microbes that live on the skin. We learned that - methods matter!
One method that is commonly used is sequencing genes that are specific to bacteria, the 16S ribosomal RNA (16S rRNA) gene. The unique thing about 16S rRNA genes is that they contain DNA sequences that allow us to identify what bacteria they came from. We found that the region of the 16S rRNA gene that is sequenced and analyzed is crucial for identifying microbes that are typically exclusively present on the skin.
Another method that is gaining more traction is whole metagenomic shotgun (WMS) sequencing. This method isn’t specific to a gene, but instead all DNA that is extracted from microbial cells is sequenced and analyzed. The advantage is that WMS provides information beyond the identity of the bacteria, such as different genes that are present in the microbial genomes, providing functional insight into their activities. For now, 16S rRNA gene sequencing is the more practical choice for many studies because it is less expensive and resource-intensive than WMS sequencing, but again the goal of the experiment is important to consider when designing any experimental strategy.
These types of studies are extremely important for scientists in our field to perform experiments that produce high quality and reproducible data. While no standard methodology exists, we hope to at least help others make informed decisions when embarking on skin microbiome experiments. We can expect new and improved methods to study the skin microbiome to emerge in the years to come, owing in part to rapidly advancing DNA sequencing technologies and data analysis tools and pipelines.
GOJO, a large manufacturer of hand hygiene products, is working with me and other scientists to understand the functional role of the skin microbiome, as it relates to the hand microbiome. Our hands play a critical role in transmitting microorganisms between people, and the dynamics of hand microbial communities and factors impacting them are important to understand. The work that my lab does will help GOJO scientists and other scientists to conduct larger, controlled studies with optimal scientific methods to increase the understanding of the microbial populations of our hands and the relationship with health outcomes.
If you have questions about the skin or hand microbiome, feel free to share these with us and we will respond to your comments.