Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK.
School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7TJ, UK.
Microb Genom. 2023 Jul;9(7). doi: 10.1099/mgen.0.001058.
The human skin microbiome represents a variety of complex microbial ecosystems that play a key role in host health. Molecular methods to study these communities have been developed but have been largely limited to low-throughput quantification and short amplicon-based sequencing, providing limited functional information about the communities present. Shotgun metagenomic sequencing has emerged as a preferred method for microbiome studies as it provides more comprehensive information about the species/strains present in a niche and the genes they encode. However, the relatively low bacterial biomass of skin, in comparison to other areas such as the gut microbiome, makes obtaining sufficient DNA for shotgun metagenomic sequencing challenging. Here we describe an optimised high-throughput method for extraction of high molecular weight DNA suitable for shotgun metagenomic sequencing. We validated the performance of the extraction method, and analysis pipeline on skin swabs collected from both adults and babies. The pipeline effectively characterised the bacterial skin microbiota with a cost and throughput suitable for larger longitudinal sets of samples. Application of this method will allow greater insights into community compositions and functional capabilities of the skin microbiome.
人类皮肤微生物组代表了各种复杂的微生物生态系统，这些生态系统在宿主健康中起着关键作用。用于研究这些群落的分子方法已经开发出来，但在很大程度上仅限于低通量定量和基于短扩增子的测序，为群落提供了有限的功能信息。作为微生物组研究的首选方法， shotgun 宏基因组测序提供了关于特定环境中存在的物种/菌株及其编码基因的更全面的信息。然而，与肠道微生物组等其他区域相比，皮肤的细菌生物量相对较低，这使得获得用于 shotgun 宏基因组测序的足够 DNA 具有挑战性。在这里，我们描述了一种优化的高通量方法，用于提取适合 shotgun 宏基因组测序的高分子量 DNA。我们验证了该提取方法和分析流程在成人和婴儿皮肤拭子上的性能。该流程可以有效地描述皮肤细菌微生物组，其成本和通量适合更大规模的纵向样本集。该方法的应用将有助于更深入地了解皮肤微生物组的群落组成和功能能力。
