International Human Microbiome Standards. AWF

A detailed understanding of human-microbe symbiosis requires a precise characterization of human-associated microorganisms, the human microbiome. To progress towards this ambitious goal it is of utmost importance that the data generated in each of many large projects involved in human metagenome research be optimally comparable. The International Human Microbiome Standards (IHMS) project coordinated the development of standard operating procedures designed to optimize data quality and comparability in the human microbiome field. Overall, IHMS focused on all key aspects of from human sample identification, collection and processing to DNA sequence generation and analysis. We herein outline IHMS contribution concerning sample identification, collection and processing. Consideration was given to the requirement for high throughput treatment of large sample sets. A suite of sample collection procedures were compared allowing the management of different conditions and delivery-time for appropriately identified samples. The 8 partners of IHMS and 15 contributors across 12 different countries further participated in a study designed to identify the critical features and optimal protocols for DNA preparation. Contributors were offered to treat aliquots of two fecal samples using their own lab procedures. Stringent selection criteria were applied for DNA yield and quality. Full metagenomic sequencing and analysis allowed to assess the recovery of diversity and specific bacterial taxa. An initial subset of 3 satisfactory protocols was selected and analysed with respect to sequencing and data analysis standards. A final set of 14 SOPs, covering all stages of the process, have been produced. It must be kept in mind that the specific area of nucleic acids preparation does see constant evolutions and improvements, such that IHMS protocols may not be regarded as optimal in the long run. Yet they will highlight critically key feature, may serve as benchmark and help move towards automation. Supported by the European Commission under the 7th Framework Programme, IHMS Project organizes public access to downloadable SOPs and enables exchanges between users and providers of the standards For mode details, see : http://www.microbiome-standards.org/要深入理解人类与微生物的共生关系，需对人体共生微生物——人类微生物组（human microbiome）进行精准的特征描述。为推进这一宏伟目标，确保人类宏基因组研究众多大型项目所产生的数据具备最优可比性至关重要。国际人类微生物组标准（International Human Microbiome Standards, IHMS）项目统筹制定了标准操作流程（standard operating procedures，下文简称SOP），旨在优化人类微生物组研究领域的数据质量与可比性。总体而言，IHMS覆盖了从人体样本识别、采集与处理，到DNA序列生成与数据分析的全部核心环节。本文将阐述IHMS在样本识别、采集与处理方面的工作成果。研究充分考量了大样本集的高通量处理需求，对比了一系列样本采集流程，以适配不同实验条件与经准确识别的样本的递送时限要求。IHMS的8家合作机构与来自12个国家的15名贡献者进一步参与了一项研究，旨在明确DNA制备流程的关键特征与最优方案。贡献者可采用各自实验室的流程处理两份粪便样本的等分试样，研究针对DNA得率与质量设定了严格的筛选标准。通过全宏基因组测序与分析，可评估微生物多样性与特定细菌类群的恢复情况。研究初步筛选出3份符合要求的方案，并依据测序与数据分析标准对其开展分析。最终形成了覆盖该流程全环节的14项SOP。需注意的是，核酸制备领域始终处于不断发展与完善之中，因此从长远来看，IHMS的方案未必始终处于最优状态。但这些方案仍能明确指出关键特征，可作为基准参考，并助力研究向自动化方向迈进。本项目由欧盟委员会第七框架计划资助，IHMS项目提供可下载的SOP公开获取渠道，并支持标准使用者与提供者之间的交流。如需了解更多细节，请访问：http://www.microbiome-standards.org/