MetaGenoPolis, INRAE, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA.
Biomolecules. 2023 Oct 11;13(10):1505. doi: 10.3390/biom13101505.
Recent attention has highlighted the importance of oral microbiota in human health and disease, e.g., in Parkinson's disease, notably using shotgun metagenomics. One key aspect for efficient shotgun metagenomic analysis relies on optimal microbial sampling and DNA extraction, generally implementing commercial solutions developed to improve sample collection and preservation, and provide high DNA quality and quantity for downstream analysis. As metagenomic studies are today performed on a large number of samples, the next evolution to increase study throughput is with DNA extraction automation. In this study, we proposed a semi-automated DNA extraction protocol for human salivary samples collected with a commercial kit, and compared the outcomes with the DNA extraction recommended by the manufacturer. While similar DNA yields were observed between the protocols, our semi-automated DNA protocol generated significantly higher DNA fragment sizes. Moreover, we showed that the oral microbiome composition was equivalent between DNA extraction methods, even at the species level. This study demonstrates that our semi-automated protocol is suitable for shotgun metagenomic analysis, while allowing for improved sample treatment logistics with reduced technical variability and without compromising the structure of the oral microbiome.
最近的研究强调了口腔微生物群在人类健康和疾病中的重要性，例如在帕金森病中，特别是使用鸟枪法宏基因组学。鸟枪法宏基因组分析的一个关键方面依赖于优化的微生物采样和 DNA 提取，通常采用商业化的解决方案来改善样品的收集和保存，并为下游分析提供高质量和高数量的 DNA。由于今天对大量的样本进行了宏基因组研究，下一个提高研究通量的发展方向是 DNA 提取自动化。在这项研究中，我们提出了一种半自动化的 DNA 提取方案，用于从商业试剂盒中收集的人类唾液样本，并将结果与制造商推荐的 DNA 提取方法进行了比较。虽然两种方案的 DNA 产量相似，但我们的半自动化 DNA 方案产生的 DNA 片段大小明显更大。此外，我们还表明，两种 DNA 提取方法的口腔微生物组组成是等效的，甚至在物种水平上也是如此。这项研究表明，我们的半自动化方案适用于鸟枪法宏基因组分析，同时允许改进样本处理的物流，减少技术变异性，而不影响口腔微生物组的结构。
