{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T20:59:23Z","timestamp":1788296363964,"version":"build-2803163510"},"reference-count":19,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2025,6,9]],"date-time":"2025-06-09T00:00:00Z","timestamp":1749427200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Immunol."],"abstract":"<jats:sec><jats:title>Introduction<\/jats:title><jats:p>Skin microecology significantly affects health, with the microbiome being a complex community of microorganisms. Different niche preferences of microorganisms raise concerns about the adequacy of common sampling methods like swabbing and cyanoacrylate biopsy. In this study, we aim to contribute to a more suitable sampling strategy in acne microbiome studies.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>This study involved ten mild to moderate acne patients. Three sampling methods were used: swab sampling (S1), modified standardized skin surface biopsy (S2), and individual comedo extraction (S3). DNA was extracted and sequenced to analyze the microbiome data.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>There were significant differences in the bacterial and fungal microbiome data obtained by the three different sampling methods. <jats:italic>Staphylococcus<\/jats:italic> spp. (significantly higher in S3, <jats:italic>P<\/jats:italic>&amp;lt;0.05) and <jats:italic>Malassezia<\/jats:italic> spp. (higher in S3, <jats:italic>P<\/jats:italic>&amp;lt;0.05) were most affected by sampling methods. Bacterial phyla Proteobacteria (abundant in S1) and Bacteroidota (dominant in S2) also showed method-dependent variations.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>The choice of sampling method significantly impacts microbiome data, highlighting the need for accurate sampling to understand the relationship between the skin microbiome and acne. Standardizing sampling methods in future studies is essential for advancing skin microecology research.<\/jats:p><\/jats:sec><jats:sec><jats:title>Clinical trial registration<\/jats:title><jats:p><jats:uri>http:\/\/www.chictr.org.cn<\/jats:uri>, identifier ChiCTR-CPC-17012398.<\/jats:p><\/jats:sec>","DOI":"10.3389\/fimmu.2025.1566786","type":"journal-article","created":{"date-parts":[[2025,6,9]],"date-time":"2025-06-09T05:23:47Z","timestamp":1749446627000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":1,"title":["A noteworthy issue: microbiome data variation depending on sampling methods in skin microecology studies in acne vulgaris patients"],"prefix":"10.3389","volume":"16","author":[{"given":"De-Tian","family":"Xu","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qi","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jia-Yi","family":"Yang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guo-Rong","family":"Yan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ling-Lin","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiao-Jing","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pei-Ru","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jia","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiu-Li","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2025,6,9]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","DOI":"10.1016\/j.anaerobe.2012.07.001","article-title":"Sampling and detection of skin Propionibacterium acnes: current status","volume":"18","author":"Alexeyev","year":"2012","journal-title":"Anaerobe"},{"key":"B2","doi-asserted-by":"publisher","DOI":"10.1007\/s00248-016-0789-6","article-title":"Microbial ecology of the human skin","volume":"76","author":"Cundell","year":"2018","journal-title":"Microb Ecol"},{"key":"B3","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.00799-08","article-title":"Acne is not associated with yet-uncultured bacteria","volume":"46","author":"Bek-Thomsen","year":"2008","journal-title":"J Clin Microbiol"},{"key":"B4","doi-asserted-by":"publisher","DOI":"10.1111\/bjd.v181.4","article-title":"Homeostasis of the sebaceous gland and mechanisms of acne pathogenesis","volume":"181","author":"Clayton","year":"2019","journal-title":"Br J Dermatol"},{"key":"B5","doi-asserted-by":"publisher","first-page":"945","DOI":"10.1016\/j.jaad.2015.12.037","article-title":"Guidelines of care for the management of acne vulgaris","volume":"74","author":"Zaenglein","year":"2016","journal-title":"J Am Acad Dermatol"},{"key":"B6","doi-asserted-by":"publisher","first-page":"498","DOI":"10.1038\/jid.1965.164","article-title":"A new method for the quantitative investigation of cutaneous bacteria","volume":"45","author":"Williamson","year":"1965","journal-title":"J Invest Dermatol"},{"key":"B7","doi-asserted-by":"publisher","DOI":"10.1128\/jcm.28.5.941-943.1990","article-title":"Swab-wash method for quantitation of cutaneous microflora","volume":"28","author":"Keyworth","year":"1990","journal-title":"J Clin Microbiol"},{"key":"B8","doi-asserted-by":"publisher","first-page":"59","DOI":"10.1038\/jid.2010.281","article-title":"Propionibacterium acnes activates the IGF-1\/IGF-1R system in the epidermis and induces keratinocyte proliferation","volume":"131","author":"Isard","year":"2011","journal-title":"J Invest Dermatol"},{"key":"B9","doi-asserted-by":"publisher","first-page":"43","DOI":"10.1159\/000489396","article-title":"Is human sebum the source of skin follicular ultraviolet-induced red fluorescence? 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