The skin microbiota is characterized by high intra- and inter-variability among individuals, due to a multitude of intrinsic and extrinsic parameters such as genetics, lifestyles or pollution. This variability may be heightened due to sampling method as the skin is a multilayer organ and its outermost layer consists of dead cells. In order to investigate this biological variability in a reproducible way, we studied how sampling procedure and DNA extraction methods influence the qualitative and quantitative gathering of bacterial communities. Here, we tested a new sampling procedure that consists in exerting a slight abrasion (scrubbing) on the skin prior to swabbing and extracting DNA in order to remove squames and access deeper ecological niches. Scrubbed and non-scrubbed samples were collected from a panel of six volunteers, and four DNA extraction methods were performed on the samples. The abundance, diversity and structure of the bacterial communities were measured using qPCR technics and 16S rDNA gene-metabarcoding. Bacterial community abundance was significantly impacted by the DNA extraction method (in favor of a method designed for tissues) but not by sampling procedure, as scrubbing does not increase bacterial biomass gathered. Bacterial α- and β-diversities were both affected by DNA extraction methods and sampling procedure. Scrubbing reveals different microbial composition by gathering bacteria living in deeper skin layer, resulting in a lower intra-personal variability. The taxonomic analysis showed that more bacteria belonging to anaerobes groups were present in scrubbed samples. We conclude that DNA extraction methods designed for tissue are not necessarily associated with high qualitative efficiency and slight scrubbing prior DNA extraction reduces intrapersonal variability and give access to a new microbial diversity.

中文翻译：

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采样和DNA提取方法对皮肤微生物群评估的影响。

由于多种内在和外在参数，例如遗传学，生活方式或污染，皮肤微生物群的特征在于个体之间的高度内部和内部变异性。由于皮肤是多层器官，并且其最外层由死细胞组成，因此这种可变性可能由于采样方法而变大。为了以可再现的方式研究这种生物变异性，我们研究了采样程序和DNA提取方法如何影响细菌群落的定性和定量收集。在这里，我们测试了一种新的采样程序，该程序包括在擦拭和提取DNA之前先对皮肤进行轻微擦伤（擦洗），以去除鳞屑并进入更深的生态位。洗涤和非洗涤样品是从6名志愿者的小组中收集的，对样品进行了四种DNA提取方法。使用qPCR技术和16S rDNA基因元条形码测量了细菌群落的丰度，多样性和结构。DNA提取方法（有利于为组织设计的方法）对细菌群落的丰度有显着影响，但不受采样程序影响，因为洗涤不会增加收集到的细菌生物量。细菌的α和β多样性都受到DNA提取方法和采样程序的影响。擦洗通过收集生活在更深层皮肤中的细菌来揭示不同的微生物组成，从而降低了个人内部变异性。分类学分析显示，洗涤后的样品中存在更多属于厌氧菌的细菌。