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Updated: Sep 13, 2025

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

QIIME2增强了多安普利康测序数据分析:一个标准化和验证的开源管道,用于全面的16S rRNA基因分析

Armando G Licata¹, Marica Zoppi¹, Chiara Dossena¹

¹Integrated Biology of Rare Tumors, Department of Experimental Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy.

Microbiology spectrum

|July 25, 2025

概括

这项研究开发了一种经过验证的,开源的QIIME2和R管道,用于多安普利康16SrRNA基因测序. 该管道提供了标准化和可复制的微生物分析,对于临床和研究应用至关重要.

科学领域:

微生物学和生物信息学
基因组测序和分析

背景情况:

多子16SrRNA基因测序提供了全面的微生物多样性见解,但由于开源管道的文档和验证有限,面临着挑战.
生物信息学工作流程缺乏标准化,阻碍了临床和实验微生物组研究中的可重复性.

研究的目的:

开发和基准标准化,开源QIIME2和R管道用于使用半导体测序进行16SrRNA基因分析.
为了比较开源管道与商业,封闭源代码软件的准确性和分辨率.
为了验证该管道在儿科癌症队列中的有效性,调查父母对儿童微生物组的影响.

主要方法:

开发一个基于QIIME2和R的生物信息管道,用于多安普利康16SrRNA基因测序.
使用5个模拟微生物群落和12对儿童护理人员便样本对进行基准测试.
多区域 (V2-9) 测序方法与单区域分析和商业软件的比较.

主要成果:

多区域开源管道产生了与专有软件输出几乎相同的微生物配置文件,具有增强的测序深度和分类分辨率.
开源和商业方法都显示出类似的微生物丰富性,准确的模拟社区重建和高可重复性 (R = 0.99,P < 0.0001).
对儿科样本的应用确定了不同的微生物变体,儿童和照顾者之间更为相似,这表明父母的影响.

结论:

已经建立了一个经过验证的,开源的QIIME2和R管道用于多安普利康16SrRNA测序,提供了一个标准化和可重复的框架.
该管道有效地利用多安普利康数据进行详细的微生物变体分析,超越传统的基因级限制.
采用开源解决方案对于确保微生物组研究的科学可再生性和适应性至关重要.

关键词:

16S元基因组学的研究在 QIIME2 中,QIIME2 包含了 QIIME2 及 QIIME2.模拟社区模拟社区儿科瘤在儿童瘤.

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Efficient Nucleic Acid Extraction and 16S rRNA Gene Sequencing for Bacterial Community Characterization

Efficient Nucleic Acid Extraction and 16S rRNA Gene Sequencing for Bacterial Community Characterization

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Next-generation Sequencing of 16S Ribosomal RNA Gene Amplicons

Next-generation Sequencing of 16S Ribosomal RNA Gene Amplicons

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