Assessment of protocols for characterization of the human skin microbiome using shotgun metagenomics and comparative analysis with 16S metabarcoding

作者：Florian Plaza Oñate, Benoît Quinquis, Florence Thirion, Marine Gilles, Christian Morabito, Karine Valeille, Richard J. Martin, Bérengère Guidet, Catherine Kern, Sophie Pécastaings · 发表于：Microbiology Spectrum · 年份：2025 · DOI：10.1128/spectrum.01732-25 · 被引用次数：5 · 研究领域：Dermatology and Skin Diseases、Gut microbiota and health、Nonmelanoma Skin Cancer Studies

ABSTRACT The skin microbiome includes bacteria, fungi, and viruses, with composition varying significantly across body sites. Although 16S rRNA gene sequencing is common, it excludes non-prokaryotic taxa and offers limited functional data. Shotgun metagenomics provides broader taxonomic and functional insights but is challenging for low-biomass skin samples due to limited microbial DNA and high host contamination. In this study, we characterized the microbiome of the forehead and armpits in healthy individuals using shotgun metagenomics and assessed the strategies to improve sequencing success. We compared collection kits, DNA extraction protocols, and tested multiple displacement amplification (MDA). We found that sampling with D-Squame discs followed by an in-house DNA extraction protocol was the most effective combination to maximize DNA yields. MDA introduced significant compositional biases and is not recommended. Shotgun sequencing, without MDA, produced microbial compositions and diversity indices broadly consistent with 16S rRNA metabarcoding, although it showed discrepancies in the relative abundance of some genera. Consistent with prior studies, the armpit microbiome was dominated by Staphylococcus spp ., whereas the forehead microbiome was dominated by Cutibacterium spp . Critically, shotgun sequencing provided additional insights into viral and eukaryotic microorganisms and revealed the functional potential of microbial communities, demonstrating its clear advanta...