基准测量MicrobIEM - - 一个用户友好的工具,用于微生物组测序数据的消毒
Claudia Hülpüsch1,2,3, Luise Rauer1,2,4, Thomas Nussbaumer4
1Environmental Medicine, Faculty of Medicine, University of Augsburg, Stenglinstr. 2, 86156, Augsburg, Germany.
BMC biology
|November 23, 2023
概括
微生物组分析需要进行质量控制,以从16S rRNA基因测序数据中去除污染物. MicrobIEM是一种新的工具,可以有效地去除污染物,特别是在像人类皮肤这样的低生物质样本中.
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.
- 遗传学 遗传学 是一个
背景情况:
- 使用16S rRNA基因测序的微生物组分析在研究中很常见.
- 测序数据中的污染物可能会扭曲结果,特别是在像人类皮肤这样的低生物质环境中.
- 生物信息去除污染物对于准确的微生物组分析至关重要.
研究的目的:
- 介绍MicrobIEM,一种新的工具,用于使用负控对16SrRNA基因测序数据的生物信息学去除污染物.
- 评估MicrobIEM的性能与现有的净化方法相比.
- 为微生物质量控制提供一个用户友好的工具.
主要方法:
- 与五种已建立的污染清除方法进行微型IEM的基准测试.
- 使用四个16S rRNA amplicon测序数据集:三个具有不同污染水平和组成的模拟社区,以及一个皮肤微生物组数据集.
- 采用诸如Youden指数之类的评估措施来进行公正的评估.
主要成果:
- 除污染性能因算法参数和数据集类型而异.
- 基于控制的算法,包括MicrobIEM的比率过器,在分级模拟社区和低生物质样本中有效.
- MicrobIEM和Decontam的流行率过器成功地减少了皮肤微生物组数据集中的污染物,同时保留了相关的一般性.
结论:
- MicrobIEM 的比率过器是一种高效的净化方法,可与已知的工具相比较.
- MicrobIEM提供了一个用户友好的图形界面,具有交互式图表,用于参数选择.
- MicrobIEM是第一个为微生物组研究人员而设计的质量控制工具,不需要编码专业知识.
相关概念视频
Rapid Identification of Pathogens
MALDI-TOF MS has transformed clinical microbiology by offering a rapid and reliable method for pathogen identification. The traditional approach to microbial identification typically involves time-consuming culture techniques and biochemical tests, which can delay the initiation of appropriate antimicrobial therapy. MALDI-TOF MS avoids these delays by using characteristic ribosomal protein mass patterns of microbial cells, enabling accurate species-level identification within minutes.Principle...
Methods to Assess Microbial Communities
Microbial communities, comprising bacteria, archaea, and eukaryotic microorganisms, inhabit diverse ecosystems and play crucial roles in environmental and biological processes. Their diversity is defined by three main parameters: species richness (the number of distinct species), species abundance (the relative quantity of each species), and species evenness (how uniformly individual species are distributed in various locations). These factors together shape the structure and ecological balance...
Methods to Assess Microbial Populations
Assessing microbial populations is crucial for understanding microbial roles in health, ecology, and industry. Various complementary techniques—both culture-based and molecular—enable detailed analysis of microbial abundance, diversity, and function.Viable Plate CountThe viable plate count is a traditional culture-based method used to estimate the number of living microbes in a sample. After serial dilution, the sample is spread onto nutrient agar plates. Each viable cell forms a visible...
Automated Microbial Diagnostics
Automated diagnostic analyzers have transformed clinical microbiology by providing rapid and reliable methods for pathogen identification and antibiotic susceptibility testing. Among these systems, the Vitek 2 is widely used because it automates the traditionally labor-intensive processes of microbial identification (ID) and antibiotic susceptibility testing (AST), delivering standardized and timely results that are essential for effective patient care.Microbial Identification with ID CardsThe...
Modern Molecular Taxonomy
Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...


