Metatranscriptomics: A Tool for Clinical Metagenomics.

IF 4.6 Q2 MATERIALS SCIENCE, BIOMATERIALS
ACS Applied Bio Materials Pub Date : 2024-08-01 Epub Date: 2024-07-19 DOI:10.1089/omi.2024.0130
Shivani Tyagi, Pramod Katara
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引用次数: 0

Abstract

In the field of bioinformatics, amplicon sequencing of 16S rRNA genes has long been used to investigate community membership and taxonomic abundance in microbiome studies. As we can observe, shotgun metagenomics has become the dominant method in this field. This is largely owing to advancements in sequencing technology, which now allow for random sequencing of the entire genetic content of a microbiome. Furthermore, this method allows profiling both genes and the microbiome's membership. Although these methods have provided extensive insights into various microbiomes, they solely assess the existence of organisms or genes, without determining their active role within the microbiome. Microbiome scholarship now includes metatranscriptomics to decipher how a community of microorganisms responds to changing environmental conditions over a period of time. Metagenomic studies identify the microbes that make up a community but metatranscriptomics explores the diversity of active genes within that community, understanding their expression profile and observing how these genes respond to changes in environmental conditions. This expert review article offers a critical examination of the computational metatranscriptomics tools for studying the transcriptomes of microbial communities. First, we unpack the reasons behind the need for community transcriptomics. Second, we explore the prospects and challenges of metatranscriptomic workflows, starting with isolation and sequencing of the RNA community, then moving on to bioinformatics approaches for quantifying RNA features, and statistical techniques for detecting differential expression in a community. Finally, we discuss strengths and shortcomings in relation to other microbiome analysis approaches, pipelines, use cases and limitations, and contextualize metatranscriptomics as a tool for clinical metagenomics.

元转录组学:临床元基因组学工具。
在生物信息学领域,16S rRNA 基因的扩增子测序长期以来一直被用于微生物组研究中群落成员和分类丰度的调查。我们可以看到,枪式元基因组学已成为该领域的主流方法。这主要归功于测序技术的进步,现在可以对微生物组的全部基因内容进行随机测序。此外,这种方法还可以分析基因和微生物组的成员。虽然这些方法提供了对各种微生物组的广泛了解,但它们只是评估生物或基因的存在,而没有确定它们在微生物组中的积极作用。微生物组研究现在包括元转录组学,以解读微生物群落如何在一段时间内对不断变化的环境条件做出反应。元基因组研究确定了组成群落的微生物,但元转录组学探索的是群落中活性基因的多样性,了解它们的表达谱,观察这些基因如何对环境条件的变化做出反应。这篇专家综述文章对用于研究微生物群落转录组的计算元转录组学工具进行了严格审查。首先,我们阐述了需要进行群落转录组学研究的原因。其次,我们探讨了元转录组学工作流程的前景和挑战,首先是 RNA 群落的分离和测序,然后是量化 RNA 特征的生物信息学方法,以及检测群落中差异表达的统计技术。最后,我们讨论了与其他微生物组分析方法、管道、用例和局限性相关的优势和不足,并将元转录组学作为临床元基因组学的一种工具。
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
ACS Applied Bio Materials
ACS Applied Bio Materials Chemistry-Chemistry (all)
CiteScore
9.40
自引率
2.10%
发文量
464
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