Field and laboratory guidelines for reliable bioinformatic and statistical analysis of bacterial shotgun metagenomic data.

IF 8.1 2区 工程技术 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY
Critical Reviews in Biotechnology Pub Date : 2024-09-01 Epub Date: 2023-09-20 DOI:10.1080/07388551.2023.2254933
Ostaizka Aizpurua, Robert R Dunn, Lars H Hansen, M T P Gilbert, Antton Alberdi
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引用次数: 0

Abstract

Shotgun metagenomics is an increasingly cost-effective approach for profiling environmental and host-associated microbial communities. However, due to the complexity of both microbiomes and the molecular techniques required to analyze them, the reliability and representativeness of the results are contingent upon the field, laboratory, and bioinformatic procedures employed. Here, we consider 15 field and laboratory issues that critically impact downstream bioinformatic and statistical data processing, as well as result interpretation, in bacterial shotgun metagenomic studies. The issues we consider encompass intrinsic properties of samples, study design, and laboratory-processing strategies. We identify the links of field and laboratory steps with downstream analytical procedures, explain the means for detecting potential pitfalls, and propose mitigation measures to overcome or minimize their impact in metagenomic studies. We anticipate that our guidelines will assist data scientists in appropriately processing and interpreting their data, while aiding field and laboratory researchers to implement strategies for improving the quality of the generated results.

细菌霰弹枪宏基因组数据的可靠生物信息学和统计分析的现场和实验室指南。
Shotgun宏基因组学是一种越来越具有成本效益的方法,用于分析环境和宿主相关的微生物群落。然而,由于微生物组和分析它们所需的分子技术的复杂性,结果的可靠性和代表性取决于所采用的现场、实验室和生物信息学程序。在这里,我们考虑了细菌鸟枪宏基因组研究中严重影响下游生物信息学和统计数据处理以及结果解释的15个现场和实验室问题。我们考虑的问题包括样品的内在特性、研究设计和实验室处理策略。我们确定了现场和实验室步骤与下游分析程序的联系,解释了检测潜在陷阱的方法,并提出了缓解措施,以克服或最大限度地减少其在宏基因组研究中的影响。我们预计,我们的指南将帮助数据科学家适当处理和解释他们的数据,同时帮助现场和实验室研究人员实施提高生成结果质量的策略。
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
Critical Reviews in Biotechnology
Critical Reviews in Biotechnology 工程技术-生物工程与应用微生物
CiteScore
20.80
自引率
1.10%
发文量
71
审稿时长
4.8 months
期刊介绍: Biotechnological techniques, from fermentation to genetic manipulation, have become increasingly relevant to the food and beverage, fuel production, chemical and pharmaceutical, and waste management industries. Consequently, academic as well as industrial institutions need to keep abreast of the concepts, data, and methodologies evolved by continuing research. This journal provides a forum of critical evaluation of recent and current publications and, periodically, for state-of-the-art reports from various geographic areas around the world. Contributing authors are recognized experts in their fields, and each article is reviewed by an objective expert to ensure accuracy and objectivity of the presentation.
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