An efficient method for high molecular weight bacterial DNA extraction suitable for shotgun metagenomics from skin swabs
An efficient method for high molecular weight bacterial DNA extraction suitable for shotgun metagenomics from skin swabs
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DOI：
10.1101/2023.02.23.529690
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发表时间：
2023-02
影响因子：
3.9
通讯作者：
Iliana R. Serghiou;Dave J. Baker;Rhiannon Evans;M. Dalby;R. Kiu;Eleftheria Trampari;Sarah Phillips-Sarah-Philli
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文献类型：
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作者：
Iliana R. Serghiou;Dave J. Baker;Rhiannon Evans;M. Dalby;R. Kiu;Eleftheria Trampari;Sarah Phillips-Sarah-Philli
人体皮肤微生物群代表了多种复杂的微生物生态系统，在宿主健康中起着关键作用。研究这些群落的分子方法已经发展起来，但很大程度上局限于低通量定量和短扩增子测序，提供了有限的功能信息。霰弹枪宏基因组测序已成为微生物组研究的首选方法，因为它提供了关于生态位中存在的物种/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，这使得获得足够的DNA进行鸟枪宏基因组测序具有挑战性。在这里，我们描述了一个优化的高通量方法提取高分子量的DNA适合散弹枪宏基因组测序。我们在成人和婴儿的皮肤拭子上验证了提取方法和分析管道的性能。该管道有效地表征了细菌皮肤微生物群，成本和吞吐量适合较大的纵向样品集。该方法的应用将允许更深入地了解皮肤微生物组的群落组成和功能能力。确定不同人类微生物组内微生物群落的功能能力对于了解它们对健康的影响非常重要。提取足够的DNA具有挑战性，特别是从低生物量样本中提取DNA，如适合猎枪宏基因组学的皮肤拭子，这是分类分辨率和功能信息所必需的。在这里，我们描述了一种优化的DNA提取方法，可以从皮肤拭子中产生足够的DNA，适用于霰弹枪宏基因组学，并证明它可以用来有效地表征皮肤微生物群。这种方法将使未来的研究能够确定皮肤微生物群的分类和功能变化，这是开发干预措施以改善和维持皮肤健康所需要的。所有序列数据和代码可通过以下网址访问：NCBI Bio Project ID: PRJNA937622 DOI: https://github.com/quadram-institute-bioscience/coronahit_guppy DOI: https://github.com/ilianaserghiou/Serghiou-et-al.-2023-Codes
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 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. Impact Statement Determining the functional capabilities of microbial communities within different human microbiomes is important to understand their impacts on health. Extraction of sufficient DNA is challenging, especially from low biomass samples, such as skin swabs suitable for shotgun metagenomics, which is needed for taxonomic resolution and functional information. Here we describe an optimised DNA extraction method that produces enough DNA from skin swabs, suitable for shotgun metagenomics, and demonstrate it can be used to effectively characterise the skin microbiota. This method will allow future studies to identify taxonomic and functional changes in the skin microbiota which is needed to develop interventions to improve and maintain skin health. Data Summary All sequence data and codes can be accessed at: NCBI Bio Project ID: PRJNA937622 DOI: https://github.com/quadram-institute-bioscience/coronahit_guppy DOI: https://github.com/ilianaserghiou/Serghiou-et-al.-2023-Codes