Poster Presentation Australian Society for Microbiology Annual Scientific Meeting 2024

A comparison of sample collection approaches for human skin microbiota and mycobiota studies (#91)

Chiara Senti 1 , Anna Franzoni 1 , Simone Paghera 1 , Giulia Gorni 1 , Giulia Cinghia 1 , Cristiano Sabelli 1
  1. Copan Italia Spa, Brescia, BS, Italy

Introduction: 

While the collection of human skin bacteria and fungi commonly involves the use of either dry or pre-wetted swabs1,2, there is currently limited research comparing the effectiveness of these approaches. This study aims to explore the recovery of skin bacterial and fungal DNA using both dry and pre-wetted Copan Self Skin FLOQSwabs® to optimize sample collection for human skin microbiome and mycobiome studies.  

Materials & Methods: 

In vitro tests were conducted to standardize the collection process, where a suspension of Trichophyton mentagrophytes was deposited onto twenty-four collection areas (20 cm2) distributed across three VITRO-SKIN® models. Half of these collection areas were swabbed using dry FLOQSwabs® and half using FLOQSwabs® pre-wetted with 30μl of Dulbecco's Phosphate Buffered Saline. Fungal DNA was extracted using QIAamp DNA Mini (Qiagen) on QIAcube (Qiagen) and amplified using Trichophyton mentagrophytes Genesig kit (Primerdesign). Following the standardized in vitro assessments, further tests were conducted to gather data from real samples. Thus, 16S rRNA sequencing was performed on dry and pre-wetted self-collected FLOQSwabs® obtained from cheeks of four donors.  

Results: 

Regarding the in vitro test, when compared to the Ct value of the stock (28.60), dry and pre-wetted FLOQSwabs® exhibited a mean Ct value of 28.61 (σ=0.32) and 30.29 (σ=0.42), respectively.  
Moreover, all dry and pre-wetted FLOQSwabs® used for cheek sampling yield enough bacterial DNA for subsequent 16S rRNA sequencing. The performance of the two collection approaches was further assessed by evaluating the number of ASVs and reads per sample. Additionally, the percentage of Unclassified bacteria by classification level (from Phylum to Genus level) was considered to evaluate the quality of profiling. All parameters provide comparable results regardless of the collection method used. Due to variable bacteria distribution on skin, these parameters should be considered as indicators. 

Conclusions: 

The performance of dry and pre-wetted FLOQSwabs® was similarly consistent both in vitro and in self-collected samples. Additional in vitro tests will be conducted to assess the skin bacterial DNA recovery, and Internal Transcribed Spacer region sequencing will be performed on dry and pre-wetted cheek FLOQSwabs®. 

  1. Ogai K et al. Comparison of Techniques for Collecting Skin Microbiome Samples: Swabbing Versus Tape-Stripping. Front Microbiol (2018).
  2. Bieber K et al. DNA chip-based diagnosis of onychomycosis and tinea pedis. J Dtsch Dermatol Ges (2022).