Optimisation of cutaneous microbiota sampling methodology

Balacco, DL, Bardhan, A, Ibrahim, H, Kuehne, SA ORCID: https://orcid.org/0000-0001-6790-8433, Grant, MM, Hirschfeld, J, Heagerty, AHM and Chapple, IL, 2025. Optimisation of cutaneous microbiota sampling methodology. Frontiers in Microbiomes. ISSN 2813-4338 (Forthcoming)

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Abstract

The cutaneous microbiome plays an essential role in guarding against invasive pathogens and maintaining healthy skin homeostasis. Several studies have demonstrated the importance of a healthy skin microbiome through its alteration in several diseases. Differing skin characteristics across the body (temperature, pH, humidity) create distinct ecological niches inhabited by diverse microbial communities. The study of cutaneous microbiota is further complicated by numerous variables at all stages of investigation, including study design, skin sampling method, sample storage, sample processing, sequencing, and data analysis. Utilisation of standardised approaches is critical for reproducibility and comparison between skin microbiome studies. However, there is a notable lack of standardisation of sampling methodologies in the literature. Studies have employed differing sampling strategies and conditions which may affect microbiota characterisation.

Here we performed a comparative analysis to determine whether the type of swab (cotton/eSwab), moistening solution (saline solution/phosphate buffered saline), duration of swabbing (30 sec/1 min), and sample storage temperature (room temperature/-80°C) affect sampling and identification of skin microbial communities using 16S sequencing. We report that the conditions analysed did not influence microbiome profiling allowing consistent sampling of the microbiota.

Item Type:	Journal article
Publication Title:	Frontiers in Microbiomes
Creators:	Balacco, D.L., Bardhan, A., Ibrahim, H., Kuehne, S.A., Grant, M.M., Hirschfeld, J., Heagerty, A.H.M. and Chapple, I.L.
Publisher:	Frontiers Media
Date:	17 March 2025
ISSN:	2813-4338
Identifiers:	Number Type 10.3389/frmbi.2025.1559981 DOI 2409688 Other
Divisions:	Schools > School of Science and Technology
Record created by:	Laura Borcherds
Date Added:	18 Mar 2025 16:28
Last Modified:	18 Mar 2025 16:28
URI:	https://irep.ntu.ac.uk/id/eprint/53268

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