相关实验视频

Updated: Jan 9, 2026

Investigation of Microbial Cooperation via Imaging Mass Spectrometry Analysis of Bacterial Colonies Grown on Agar and in Tissue During Infection

Investigation of Microbial Cooperation via Imaging Mass Spectrometry Analysis of Bacterial Colonies Grown on Agar and in Tissue During Infection

Published on: November 18, 2022

数据组合性对检测微生物群反应的影响

Brandon Hickman¹, Katri Korpela^1,2

¹Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland.

|December 2, 2025

概括

下一代测序 (NGS) 数据是构成性的,存在分析挑战. 目前对微生物群数据的规范化方法往往无法识别真正的生物信号,导致常见的错误阳性和负性.

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:

下一代测序 (NGS) 被广泛用于微生物社区分析.
国家统计系统数据的组成性质带来了重大的分析挑战.
准确识别微生物信号对于生物学解释至关重要.

研究的目的:

对微生物群组成数据的常用规范化方法的有效性进行评估.
为了比较相对丰度的表现,CLR,TMM和DESeq2.
评估正常化对识别真正的生物信号与人工制造物的影响.

主要方法:

模拟的组成微生物群数据被生成.
应用了四种规范化方法 (相对丰度,CLR,TMM,DESeq2).
通过将规范化数据与绝对丰度数据进行比较,使用差异解释和错误发现率来评估性能.

主要成果:

所有测试的规范化方法显示,与绝对丰度数据相比,解释差异减少.
正常化方法增加了假阳性和假阴性.
CLR,TMM和DESeq2的表现并没有超过相对丰度,有时会恶化结果.

结论:

当前的规范化方法不能一致地解决NGS数据组合性问题.
在组合NGS数据集中,假阳性和假阴性很普遍.
建议获得绝对丰度,以区分生物信号与组合元件.

关键词:

组合数据是指组成的数据.错误发现率错误发现率下一代测序的下一代测序.

更多相关视频

Quantitative Polymerase Chain Reaction-based Analyses of Murine Intestinal Microbiota After Oral Antibiotic Treatment

Quantitative Polymerase Chain Reaction-based Analyses of Murine Intestinal Microbiota After Oral Antibiotic Treatment

Published on: November 17, 2018

Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing

Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing

Published on: October 15, 2019

相关概念视频

Applications of Molecular Taxonomy

Applications of Molecular Taxonomy

Molecular taxonomy has revolutionized the understanding and classification of bacteria, providing precise insights into their diversity, evolutionary relationships, and ecological roles. By utilizing molecular techniques such as DNA sequencing and fingerprinting, researchers have made significant strides in various fields related to bacterial studies.Resolving Taxonomic AmbiguitiesMolecular taxonomy has been instrumental in distinguishing closely related bacterial species initially thought to...

Modern Molecular Taxonomy

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...