Combining metagenomics, metatranscriptomics and viromics to explore novel microbial interactions: towards a systems-level understanding of human microbiome.
Combining metagenomics, metatranscriptomics and viromics to explore novel microbial interactions: towards a systems-level understanding of human microbiome.
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DOI：
10.1016/j.csbj.2015.06.001
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发表时间：
2015
影响因子：
6
通讯作者：
Ochoa-Leyva A
中科院分区：
文献类型：
--
作者：
Bikel S;Valdez-Lara A;Cornejo-Granados F;Rico K;Canizales-Quinteros S;Soberón X;Del Pozo-Yauner L;Ochoa-Leyva A
实验方法的进步和高性能生物信息学工具的发展极大地提高了我们对与人类生态位相关的微生物群落的理解。许多研究证明，微生物丰度和组成的变化与人类的健康和疾病状态有关。大多数关于人类微生物组的研究通常集中在一个水平的生物信息的分析上，即元基因组学或亚转录组学。在这篇综述中，我们描述了一些不同的实验和生物信息学策略，用于分析人类微生物组的16S rRNA基因图谱和鸟枪式测序数据。我们还讨论了元基因组学、后转录组学和病毒学相结合的一些最新见解如何能够更详细地描述口腔和肠道微生物群中微生物和病毒之间的相互作用。最近对病毒物的研究已经开始变得重要，因为病毒可能参与微生物的生物失调。此外，元转录组学和元基因组分析相结合表明，相当一部分微生物转录本可以相对于它们的微生物基因组丰度进行差异调控。因此，结合元基因组学、后转录组学和病毒学来理解微生物组中的分子相互作用是在系统水平上理解人类微生物组的主要挑战之一。
The advances in experimental methods and the development of high performance bioinformatic tools have substantially improved our understanding of microbial communities associated with human niches. Many studies have documented that changes in microbial abundance and composition of the human microbiome is associated with human health and diseased state. The majority of research on human microbiome is typically focused in the analysis of one level of biological information, i.e., metagenomics or metatranscriptomics. In this review, we describe some of the different experimental and bioinformatic strategies applied to analyze the 16S rRNA gene profiling and shotgun sequencing data of the human microbiome. We also discuss how some of the recent insights in the combination of metagenomics, metatranscriptomics and viromics can provide more detailed description on the interactions between microorganisms and viruses in oral and gut microbiomes. Recent studies on viromics have begun to gain importance due to the potential involvement of viruses in microbial dysbiosis. In addition, metatranscriptomic combined with metagenomic analysis have shown that a substantial fraction of microbial transcripts can be differentially regulated relative to their microbial genomic abundances. Thus, understanding the molecular interactions in the microbiome using the combination of metagenomics, metatranscriptomics and viromics is one of the main challenges towards a system level understanding of human microbiome.