Introduction
Skin consists of diverse bacteria, fungi, and viruses that make up the skin microbiome. Skin microbiome research has only recently come to light. Studying skin microbiome is challenging because it consists of highly diverse but low abundant microorganisms often termed as a ‘microbial desert”. Dysbiosis of skin microbiome can cause several skin diseases including atopic dermatitis and other inflammatory diseases. Current culture dependent and independent techniques not only lacks sensitivity but also leads to biased microbiome research as they cannot differentiate between real signal and noise. Hence, it is crucial to optimise the molecular methods to study microbiome to advance our knowledge of skin infections, wound healing, and sepsis prevention.
Method
We aimed to carry out a pilot study to optimise skin microbiome study protocols to describe the composition of skin microbiome in healthy children. Samples were collected from 6 healthy children from the cubital fossa, cheek and axilla using a (i) FLOQ swab, and (ii) skin scrapings with a glass slide. Samples were collected from the left and right sides of the body and repeated one week later. Full-length 16S rRNA sequencing was performed (PacBio Sequel II) to compare the results of different primers on the diversity and ecology of bacteria between different sites. Samples were compared to standard mock communities processed along with skin samples.
Results
From six children, 78 FLOQ and 78 skin scraping samples were collected. We have shown a diverse microbial profile of healthy children over two time points at species level resolution with high diversity between body sites. Overall, our results support the FLOQ swab as the preferred sampling method for future studies. Results have highlighted that the skin microbiome is a highly diverse, low biomass environment that previous culture techniques have been unable to identify. Our study provides the methodology to explore further the skin microbiome in health and disease.
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