Bulletin of Chinese Academy of Sciences (Chinese Version)


microbiome; microbiophylome; classification; ecology; synthetic biology

Document Type



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.

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Bulletin of Chinese Academy of Sciences


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