建设微生物组大数据中心 发挥长期科学影响

Development of Comprehensive Microbiome Big Data Warehouse/Center for Long-term Scientific Impact

        张国庆(中国科学院上海生命科学研究院生物医学大数据中心 上海 200031)
        宁康(华中科技大学生命科学与技术学院 武汉 430074)
        职晓阳(云南大学生命科学学院微生物研究所 昆明 650091)
        刘婉(上海生物信息技术研究中心 上海 201203)
        徐萍(中国科学院上海生命科学研究院生命科学信息中心 上海 200031)
        周豪魁(中国科学院深圳先进技术研究院合成生物学工程研究中心 深圳 518055)
        胡黔楠(中国科学院上海生命科学研究院生物医学大数据中心 上海 200031)
        赵国屏(中国科学院上海生命科学研究院生物医学大数据中心 上海 200031)

         微生物组;微生物系统组;分类;生态;合成生物学

        microbiome;microbiophylome;classification;ecology;synthetic biology

        宏基因组研究的思想与技术推动了微生物组的兴起，积累了丰富的微生物基因组以及健康、动植物和环境相关的微生物宏基因组数据，形成了具备一定规模和影响力的数据库、标准化方法与分析工具。大多数平台聚焦于为项目或特定类型的微生物菌群提供数据支撑，难以满足更深入全面的微生物生物学研究需求。文章建议采用综合聚焦微生物分类单元总和的微生物系统组与聚焦特定生态位微生物种群总和的微生物组的思路，建设综合性的微生物组数据仓库，整合微生物分类、进化、生态以及相关“组学”数据与信息。在此基础上，进一步综合生命科学基础研究和系统合成生物学研究的数据，支撑经高水平质控的综合性参考数据库、标准化的拼接与注释以及一流的数据汇交、搜索分享、深度学习和分析挖掘方法的研究开发。由此，亦将进一步集成大型微生物组项目的元数据及数据，形成数据综合完整、管理安全高效，服务功能完备的微生物组大数据中心。

        It was the scientific concept and related technology of metagenomics that initiated the microbiome research. These microbiome research projects conducted globally have led to the acquisition huge amount of data and data sets of microbial genomes related to human health, animals, plants and environments. Consequently, various kinds of microbiome databases and analytical platforms are booming. However, besides the designed specific project-oriented status for some of the databases, most of the current microbiome data platforms merely focus on the development of reference data catalog and metagenome data sets, and mainly support the studies of "molecular ecology" aspect of microbiomes and/or the metagenome of a specific biotype. Thus, commonly expected applications in data integration-dependent megaanalysis, genomic information-based microbial taxonomy or comprehensive functional bioparts mining are largely hindered by lacking of proper data resources or sophisticated bioinformaticians capable of handling the complicated tasks.In this review, we introduce the concept of Microbiophylome, which is the sum of all microbes and member organisms of all kinds of microbiota with their genetic and multiple lifeomics information as well as their related biological structural/functional information. Comparing to the conventional Microbiome, which is the sum of all member microbes of various microbiota in a special ecological biotype with their genetic, mainly metagenome information and related biological function, Microbiophylome emphasizes the total information of every individual taxon of the whole microbial world. In other words, with respect to microbiology as an academic discipline, Microbiophylome is concerned more about the α-phase (taxonomy) and β-phase (phylogeny) of microbial biology while Microbiome is concerned more about the γ-phase (ecology), employing the knowledge of α- and β-phases. With the integration of the concepts of Microbiome and Microbiophylome, we suggest to establish a comprehensive microbiome data warehouse as a hub to integrate the data of microbial taxonomy, evolution and ecology as well as their related omics research. Via further integration of the data of basic research in life science and systems and synthetic biology, this data warehouse will support the development of comprehensive and QA/QC controlled reference databases, high quality standards-guided assembly and annotation and state of the art tools for data integration, searching, shared analysis and deep mining to facilitate future academic research and biotechnology R&D activities in microbiology and related fields. In addition, providing high-quality data standard and data SOPs for safe data integration and sharing, this data warehouse will be attractive for further systematic collection of meta-data of large-scale international projects. We have started this effort aiming at the eventual establishment of a microbiome big data center with complete and integrative data storage, safe and efficiency-guaranteed data management as well as comprehensive and user-friendly data service functions.