谱系特异性的微生物蛋白质预测使人类肠道内的蛋白质生态的大规模探索成为可能
Matthias A Schmitz1, Nicholas J Dimonaco2,3, Thomas Clavel1
1Functional Microbiome Research Group, RWTH University Hospital, Aachen, Germany.
Nature communications
|April 3, 2025
概括
在元基因组学中,精确的微生物基因预测通过一种新的谱系特定方法得到了改进. 这种方法增强了蛋白质的识别,揭示了隐藏的微生物功能,并使得更好的微生物组分析.
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:
- 微生物遗传密码和基因结构各异,但在元基因组分析中经常被忽视.
- 这导致蛋白质预测不准确,阻碍了功能基因分配和生态系统理解.
研究的目的:
- 开发一种特定于基因谱系的基因预测方法,从元基因组数据准确识别微生物蛋白质.
- 提高对微生物生态系统,特别是人类肠道微生物组的功能理解.
主要方法:
- 采用基于分类学赋值的正确遗传代码实施了特定于血统的基因预测方法.
- 删除不完整的蛋白质预测,并优化了小蛋白质的预测.
- 将该方法应用于9634个人类肠道元基因组和3594个基因组,创建了MiProGut蛋白质目录和InvestiGUT分析工具.
主要成果:
- 增加了捕获的表达微生物蛋白的78.9%,揭示了以前隐藏的功能组.
- 确定了3,772,658个小蛋白质集群,形成了一个改进的人类肠道微生物蛋白质目录 (MiProGut).
- 开发了InvestiGUT,将蛋白序列与样本元数据集成为生态和宿主协会研究.
结论:
- 准确的蛋白质预测对于功能性微生物组分析至关重要.
- 开发的谱系特异性方法显著提高了微生物蛋白质的捕获和功能分配.
- 这项工作为对微生物群落及其宿主相互作用进行更深入的生态研究提供了必要的工具.
相关概念视频
02:47Protein Families
15.2K
Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism. Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members. If these new proteins contain similar amino acids in key...
15.2K
02:05Gene Evolution - Fast or Slow?
7.0K
The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
In contrast, regions which code...
7.0K
02:54Evolutionary Relationships through Genome Comparisons
5.6K
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
5.6K