冰山3.0:细菌中整合和结合元素的功能分类和分析
Meng Wang1, Guitian Liu1, Meng Liu1
1State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China.
Nucleic acids research
|October 23, 2023
概括
ICEberg 3.0是一个升级的数据库,详细介绍了细菌整合和结合元件 (ICE),包括它们在人类微生物组中的功能和作用. 本资源增强了对ICE生物学和微生物社区动态的理解.
科学领域:
- 微生物学 微生物学
- 生物信息学是一种生物信息学.
- 基因组学就是基因组学.
背景情况:
- 细菌的整合性和结合性元素 (ICE) 是移动基因元素,对于水平基因转移至关重要.
- 了解ICE的功能和相互作用对于理解微生物进化和社区动态至关重要.
- 以前的ICEberg版本提供了有价值的数据,但需要进一步改进以进行全面分析.
研究的目的:
- 为了介绍ICEberg 3.0,一个升级的数据库,提供了对细菌ICE的扩展见解.
- 加强ICE货物基因功能及其作用的表征.
- 为了促进人类微生物群内的ICE的探索.
主要方法:
- 利用文本挖掘和手动策划来扩展ICEberg数据库.
- 开发了ICE货物基因功能的系统分类,分为六组.
- 集成了ICEfinder 2.0管道用于货物基因预测.
- 来自2405个人类微生物样本的精选数据用于识别假定的ICE.
主要成果:
- 冰山3.0现在包括2065个ICE,607个IME和275个CIME,其中430个经过实验支持.
- 系统地对货物基因功能进行分类,可以更深入地了解ICE的生物特征.
- 该数据库包含来自人类微生物样本的1386个假定ICE,揭示了细菌-ICE-货物网络动态.
结论:
- 冰山3.0显著增强了冰山生物学研究,特别是货物基因功能和微生物群相互作用.
- 更新的数据库有助于对ICE的动态环境进行更深入的调查.
- 本资源支持研究ICE对微生物群落和进化的影响.
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