P20 Optimizing skin swab collection methods for the assessment of host–microbiome interactions

Introduction and aims Currently, swabbing is the most common method of collecting skin samples. Unfortunately, owing to the low biomass environment of the skin, retrieving microbial DNA through this method, is often difficult and can misrepresent true taxa and host–microbiome interactions. Still, it is the most suitable and least invasive method. This study aims to establish optimized swab sample collection methods, including sample storage and conditions, to maximize DNA yield. This will aid in a better understanding of the complex interplay between the skin microbiome and skin health. Methods To test bacterial recovery, cotton, rayon and flocked swabs were immersed in 108 colony-forming units (CFU) per mL of Staphylococcus epidermidis and transferred into brain heart infusion (BHI) media. Swab aliquots were plated, and colonies were counted after 24 h. To evaluate transport media, flocked swabs were immersed in 108 CFU per mL suspensions then transferred into BHI, phosphate-buffered saline and in-house and commercial liquid amies solution. Colony counts and DNA extraction yields were assessed after immediate collection, 3 h at room temperature, and 24 h at 4 °C and −20 °C. This was repeated for Cutibacterium acnes and a skin bacteria model. Results Flocked swabs are more efficient than rayon and cotton swabs, at capturing S. epidermidis and C. acnes. All swabs were better at capturing C. acnes than S. epidermidis, with rayon swabs exhibiting the highest percentage increase of 460.4%. Between the four media types, BHI shows a consistently higher DNA recovery rate among all conditions, while commercial amies solution performs the worst in most conditions. All media types perform comparably in viable bacterial retention, suggesting performance differences in DNA preservation. Conclusions Our findings highlight the importance of suitable collection methods for the assessment of low biomass samples in both culturomics and further downstream processes. An accurate representation of microbial communities will allow for comprehensive interpretations of host–microbiome functions and their role in skin disease.