一种用于评估基于16S rRNA基因的微生物群概况研究中的模拟社区样本的工具
Sudarshan A Shetty1,2, Jolanda Kool1, Susana Fuentes1
1Center for Infectious Disease Control, National Institute for Public Health and the Environment, Antonie van Leeuwenhoeklaan 9, Bilthoven 3721 MA, Netherlands.
Microbiome research reports
|December 4, 2023
概括
研究人员现在可以使用基于R的工具chkMocks来评估微生物组测序质量. 它将实验模拟社区与其理论组成进行比较,识别技术偏见和工作流程中的错误.
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.
背景情况:
- 微生物组测序研究对于理解微生物群落至关重要.
- 技术偏见和错误可能会严重影响微生物组数据的准确性.
- 评估样本处理工作流程的可靠性至关重要.
研究的目的:
- 引入 chkMocks,这是一个基于 R 的新型工具,用于评估微生物组测序数据质量.
- 使研究人员能够将模拟社区的实际组成与已知的理论组成进行比较.
- 为识别和理解微生物组研究中的技术偏差提供一种方法.
主要方法:
- 开发chkMocks,一个基于R的通用软件工具.
- 使用模拟社区作为与生物样本一起处理的技术控制.
- 将实验模拟社区的分类学或功能组成与它们的理论对应物进行比较.
- 产生实验和理论数据之间的视觉比较和相关性分析.
主要成果:
- chkMocks提供了对模拟社区处理的定量和视觉评估.
- 该工具有助于识别预期和观察到的社区组成之间的差异.
- 结果使研究人员能够评估他们特定的测序和处理管道的性能.
- 相关性分析突出了实验工作流程的准确度.
结论:
- chkMocks是微生物组测序质量控制的一个有价值的工具.
- 该软件有助于检测和减轻技术偏差和错误.
- 实施chkMocks可以提高微生物组研究的可靠性和可重复性.
- 研究人员可以使用chkMocks来优化他们的样本处理工作流程,以提高数据完整性.
相关概念视频
01:30Methods 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...
01:19Methods 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...
01:22Introduction to the Human Microbiota
Microorganisms colonize various regions of the human body, including the mouth, nasal passages, throat, stomach, intestines, urogenital tract, and skin. The total number of microbial cells is estimated to range from 10¹³ to 10¹⁴—comparable to, or exceeding, the number of human somatic cells. This host–microbiome relationship has led to the conceptualization of humans as supraorganisms, wherein microbial communities perform vital roles in development, immunity, and disease...
01:25Rapid 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...
01:24Automated 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...