考虑到16SrRNA复制数预测的不确定性及其对细菌多样性分析的影响
1Department of Biology, University of Virginia, 485 McCormick Road, Charlottesville, VA, 22904, USA.
ISME communications
|June 10, 2023
概括
16S rRNA基因拷贝数 (16S GCN) 变异可能会导致微生物多样性研究的偏差. 我们的新方法RasperGade16S准确地预测了16S GCN,具有强大的信心,改进了社区分析.
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.
- 计算生物学 计算生物学
背景情况:
- 16S rRNA基因拷贝数 (16S GCN) 在不同细菌物种之间有所不同.
- 这种变异可以在依赖16S rRNA读数的微生物多样性分析中引入偏差.
- 预测16S GCN的现有方法可能具有很高的不确定性,质疑复制号码校正的实用性.
研究的目的:
- 开发一种新的方法和软件,RasperGade16S,用于改进16S GCN预测中的建模和捕捉不确定性.
- 为16S GCN预测提供可靠的信心估计.
- 评估16S GCN校正对微生物群体分析的影响.
主要方法:
- 实现了一个最大概率框架,使用脉冲进化模型.
- 显式解释了物种内GCN变化和异质GCN演变速率.
- 利用交叉验证进行性能评估,并对各种细菌群体进行了测试.
主要成果:
- RasperGade16S提供了可靠的信心估计,在精度和回忆方面超过现有方法.
- 发现99%的测试社区的预测不确定性很小,支持使用16S GCN校正.
- 16S GCN变异对β多样性分析的影响有限 (例如,PCoA,NMDS,PERMANOVA).
结论:
- RasperGade16S提供了一种可靠的方法来预测16S GCN,并解决微生物多样性研究中的偏见.
- 对于大多数社区来说,16S GCN 校正是合理的,并且可以改善组合和功能配置.
- 虽然对α-多样性和组成很重要,但GCN变异对常见β-多样性指标的影响很小.
更多相关视频
12:37Efficient Nucleic Acid Extraction and 16S rRNA Gene Sequencing for Bacterial Community Characterization
Published on: April 14, 2016
38.8K
11:37Simultaneous DNA-RNA Extraction from Coastal Sediments and Quantification of 16S rRNA Genes and Transcripts by Real-time PCR
Published on: June 11, 2016
17.8K
相关概念视频
02:26Comparing Copy Number Variations and SNPs
17.8K
Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
17.8K
02:46Genome Copying Errors
4.3K
DNA replication is a well-evolved process that copies millions of base pairs with high fidelity during each cell division. Occasionally a wrong base or a long stretch of wrong bases may get added to the daughter strands. If the errors are left unchecked, cells might accumulate several mutations that might endanger their survival. Therefore, the copying errors are checked and repaired at three levels.
4.3K
02:57Real Time RT-PCR
57.5K
Real-time reverse transcription-polymerase chain reaction, or Real-time RT-PCR, is an analytical tool used to determine the expression level of target genes. The method involves converting mRNA to complementary DNA with the help of an enzyme known as reverse transcriptase, followed by the PCR amplification of the cDNA. These two processes can be performed simultaneously in a single tube or separately as a two-step reaction.
The real-time quantification of the number of amplified products is...
The real-time quantification of the number of amplified products is...
57.5K
02:24Ribosome Profiling
3.6K
Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
3.6K