A step-by-step procedure for analysing the 16S rRNA-based microbiome diversity using QIIME 2 and comprehensive PICRUSt2 illustration for functional prediction

IF 2.3 3区 生物学 Q3 MICROBIOLOGY
Ankita Srivastava, Yusuf Akhter, Digvijay Verma
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引用次数: 0

Abstract

Short-read sequencing technology has emerged as a preferred tool to analyse the bacterial composition of a niche by targeting hypervariable regions of the 16S rRNA gene. It targets the short hypervariable regions of the 16S rRNA gene and uncovers the taxonomic profile and their associated pathways. QIIME 2 is preferred and ready-to-use pipelines that perform stepwise analysis of massive short reads of 16S rRNA genes. This wrapper comprises several tools that include quality checking, denoising, taxonomic classification, alignment, and diversity analysis. However, it demands huge bioinformatic analysis practices which are quite challenging to many microbiologists working in the field of traditional microbiology. This paper, therefore, aims to make microbiologists familiar with the steps of computational analysis for processing 16S rRNA-based sequences. Here, we are presenting stepwise processing of NGS sequences using the QIIME 2 platform along with their analyses, which include installing QIIME 2, importing and processing data, quality checks, taxonomy assignments, and diversity analysis. Besides, the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2) has also been illustrated to understand the correlation between metabolic and physiological footprints of the different species observed during microbiome analysis. Therefore, this paper can be used as a handy toolkit for those researchers who are less familiar with its associated bioinformatic analysis.

利用 QIIME 2 和用于功能预测的 PICRUSt2 综合图解,逐步分析基于 16S rRNA 的微生物组多样性。
短程测序技术已成为一种首选工具,可通过瞄准 16S rRNA 基因的超变区分析生态位的细菌组成。它以 16S rRNA 基因的短超变区为目标,揭示分类概况及其相关途径。QIIME 2 是对 16S rRNA 基因的大量短读数进行逐步分析的首选和即用管道。该软件包由多个工具组成,包括质量检查、去噪、分类学分类、比对和多样性分析。然而,它需要大量的生物信息分析实践,这对许多在传统微生物学领域工作的微生物学家来说颇具挑战性。因此,本文旨在让微生物学家熟悉处理基于 16S rRNA 序列的计算分析步骤。在此,我们将介绍使用 QIIME 2 平台逐步处理 NGS 序列及其分析,包括安装 QIIME 2、导入和处理数据、质量检查、分类分配和多样性分析。此外,本文还说明了通过重建未观察状态对群落进行系统发育调查(PICRUSt2)的方法,以了解在微生物组分析过程中观察到的不同物种的代谢和生理足迹之间的相关性。因此,对于不太熟悉相关生物信息分析的研究人员来说,本文可作为一个方便的工具包。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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来源期刊
Archives of Microbiology
Archives of Microbiology 生物-微生物学
CiteScore
4.90
自引率
3.60%
发文量
601
审稿时长
3 months
期刊介绍: Research papers must make a significant and original contribution to microbiology and be of interest to a broad readership. The results of any experimental approach that meets these objectives are welcome, particularly biochemical, molecular genetic, physiological, and/or physical investigations into microbial cells and their interactions with their environments, including their eukaryotic hosts. Mini-reviews in areas of special topical interest and papers on medical microbiology, ecology and systematics, including description of novel taxa, are also published. Theoretical papers and those that report on the analysis or ''mining'' of data are acceptable in principle if new information, interpretations, or hypotheses emerge.
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