Microbial resolution of whole genome shotgun and 16S amplicon metagenomic sequencing using publicly available NEON data
Microbial resolution of whole genome shotgun and 16S amplicon metagenomic sequencing using publicly available NEON data
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DOI：
10.1371/journal.pone.0228899
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发表时间：
2020-02-13
期刊：
影响因子：
3.7
通讯作者：
Leddy, Menu B.
中科院分区：
文献类型：
--
作者：
Brumfield, Kyle D.;Huq, Anwar;Leddy, Menu B.
微生物在生物圈中无处不在，在地球的地球化学和人类健康中发挥着至关重要的作用。然而，鉴定这些微生物并确定它们的功能是具有挑战性的。在比较宏基因组学中广泛使用的方法，16 S扩增子测序和全基因组鸟枪测序（WGS），提供了DNA测序分析的途径，以鉴定微生物并评估各种环境中的多样性和丰度。然而，在过去的十年中，并行高通量DNA测序的进步引入了主要的障碍，即方法的标准化，数据存储，结果的可重复的互操作性和数据共享。由美国国家科学基金会建立的国家生态观测网络（氖）使所有研究人员能够解决区域到大陆范围内各种环境挑战的问题，并提供来自美国各地实地的高质量，综合和标准化数据。在宏基因组学领域，允许评估和比较项目结果的标准化程序正变得越来越重要。我们证明了使用公开可用的氖土壤宏基因组测序数据集与使用子系统技术（MG-RAST）服务器的开放访问宏基因组快速注释相结合的可行性，以说明WGS与16 S扩增子测序相比的优势。选择来自氖研究人员制备的表层土壤样品的四个WGS和四个16 S扩增子序列数据集进行比较，使用2014年4月至7月在科罗拉多相同地点收集的标准化方案。样品中检测到的优势细菌门在测序方法之间一致。然而，WGS产生了更高的微生物分辨率，提高了准确性，并允许鉴定更多属的细菌，古细菌，病毒和真核生物，以及使用16 S扩增子测序未检测到的推定功能基因。氖开放数据将有助于未来研究表征和量化与不断变化的水生和陆地生态系统相关的复杂生态过程。
Microorganisms are ubiquitous in the biosphere, playing a crucial role in both biogeochemistry of the planet and human health. However, identifying these microorganisms and defining their function are challenging. Widely used approaches in comparative metagenomics, 16S amplicon sequencing and whole genome shotgun sequencing (WGS), have provided access to DNA sequencing analysis to identify microorganisms and evaluate diversity and abundance in various environments. However, advances in parallel high-throughput DNA sequencing in the past decade have introduced major hurdles, namely standardization of methods, data storage, reproducible interoperability of results, and data sharing. The National Ecological Observatory Network (NEON), established by the National Science Foundation, enables all researchers to address queries on a regional to continental scale around a variety of environmental challenges and provide high-quality, integrated, and standardized data from field sites across the U.S. As the amount of metagenomic data continues to grow, standardized procedures that allow results across projects to be assessed and compared is becoming increasingly important in the field of metagenomics. We demonstrate the feasibility of using publicly available NEON soil metagenomic sequencing datasets in combination with open access Metagenomics Rapid Annotation using the Subsystem Technology (MG-RAST) server to illustrate advantages of WGS compared to 16S amplicon sequencing. Four WGS and four 16S amplicon sequence datasets, from surface soil samples prepared by NEON investigators, were selected for comparison, using standardized protocols collected at the same locations in Colorado between April-July 2014. The dominant bacterial phyla detected across samples agreed between sequencing methodologies. However, WGS yielded greater microbial resolution, increased accuracy, and allowed identification of more genera of bacteria, archaea, viruses, and eukaryota, and putative functional genes that would have gone undetected using 16S amplicon sequencing. NEON open data will be useful for future studies characterizing and quantifying complex ecological processes associated with changing aquatic and terrestrial ecosystems.