微生物组数据中心:一个开放式访问平台,集成环境元数据,分类学和功能注释,用于全面的元基因组组装基因组数据集
Hiroshi Mori1, Takatomo Fujisawa2,3, Koichi Higashi2
1Department of Informatics, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka, 411-8540, Japan. hmori@nig.ac.jp.
Microbiome
|March 17, 2026
概括
微生物组数据中心 (Microbiome Datahub) 提供了一个集中的,高质量的原始元基因组组装基因组 (MAG) 资源,并提供标准化的注释. 这个平台提高了微生物基因组数据的可访问性和可重复使用性,用于研究.
科学领域:
- 微生物基因组学 微生物基因组学
- 生物信息学是一种生物信息学.
- 转基因组学是指转基因组学.
背景情况:
- 大基因组组装基因组 (MAGs) 对于理解未培养的微生物至关重要,但通常会受到公共存储库中不一致的数据质量和注释的影响.
- 现有的二级数据库重建了MAG,无法代表原始发布的数据集.
研究的目的:
- 开发微生物组数据中心,这是一个开放式访问平台,用于汇总和重新注释INSDC的原始MAG.
- 为微生物基因组学研究提供标准化,高质量和可重复使用的资源.
主要方法:
- 从INSDC系统地汇总和重新注释了214,427个MAG.
- 标准化的基因预测 (DFAST),质量评估 (CheckM),分类学分配 (GTDB-Tk) 和功能注释 (PZLAST,MBGD,KEGG).
- 使用元基因组和微生物环境本体学和表型推断 (Bac2Feature) 的环境元数据注释.
主要成果:
- 微生物组数据中心托管了214,427个高质量的MAG (平均每天的数据). 80.5%的完整性,1.8%的污染).
- 该平台提供了基因组学和环境多样化的MAG,包括新的集群和未分配的蛋白质,表明显著的新奇性.
- 推断出来的表型特征揭示了微生物类的生态差异化.
结论:
- 微生物组数据中心集成了多种MAG数据,包括基因组序列,注释和表型预测,可通过Web,API和下载访问.
- 这种全面的资源通过提高数据的可重复使用性,促进了微生物组和微生物基因组学研究的加速.
相关概念视频
Genome Annotation and Assembly
21.4K
The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
21.4K
Environmental Applications of Microorganisms
1.4K
Microorganisms play a pivotal role in maintaining ecosystem balance by recycling essential elements such as carbon, nitrogen, and phosphorus, as well as supporting processes like bioremediation, wastewater treatment, and biofuel production.Microbes in Elemental CyclesIn the carbon cycle, microorganisms decompose organic matter, releasing carbon dioxide via aerobic respiration. This carbon dioxide is subsequently used by photosynthetic organisms to synthesize organic compounds, closing the...
1.4K
Microbial Classification System
1.5K
Classification is the process of organizing organisms into hierarchically inclusive groups based on their phenotypic similarities or evolutionary relationships. A species comprises one or more strains, and closely related species are grouped into genera. Genera are further classified into families, families into orders, orders into classes, and so forth, up to the domain level, which is the broadest taxonomic rank derived from a combination of phenotypic and genotypic data.The nomenclature of...
1.5K
Genome-wide Association Studies-GWAS
16.5K
Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...
GWAS does not require the identification of the target gene involved in...
16.5K


