Defining and quantifying the core microbiome: Challenges and prospects
Defining and quantifying the core microbiome: Challenges and prospects
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DOI：
10.1073/pnas.2104429118
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发表时间：
2021-12-21
影响因子：
11.1
通讯作者：
Roy, Kaustuv
中科院分区：
文献类型：
--
作者：
Neu, Alexander T.;Allen, Eric E.;Roy, Kaustuv
在过去的十年里，“核心微生物组”这一术语在微生物生态学中得到了广泛的应用。广义地说，核心微生物群指的是任何一组微生物分类群，或与这些分类群相关的基因组和功能属性，它们是宿主或感兴趣的环境的特征。最常见的是，核心微生物群是指来自特定宿主或环境的两个或两个以上样本共享的微生物分类群。尽管这个术语很受欢迎，它的使用也越来越多，但对于核心微生物组在实践中应该如何量化，几乎没有达成共识。在这里，我们介绍了核心微生物组概念的简要历史，并使用具有代表性的文献样本来回顾常用的不同度量标准来量化核心。经验分析使用了广泛的指标来量化核心微生物组，包括任意出现和丰度截止值，核心的重点分类水平从门到扩增子序列变体。然而，这些指标中的许多都容易受到抽样和其他偏差的影响。为了测试关于核心微生物群的功能和生态作用的具体假设，有必要制定一套标准化的度量标准来量化造成这种偏见的核心。
The term "core microbiome" has become widely used in microbial ecology over the last decade. Broadly, the core microbiome refers to any set of microbial taxa, or the genomic and functional attributes associated with those taxa, that are characteristic of a host or environment of interest. Most commonly, core microbiomes are measured as the microbial taxa shared among two or more samples from a particular host or environment. Despite the popularity of this term and its growing use, there is little consensus about how a core microbiome should be quantified in practice. Here, we present a brief history of the core microbiome concept and use a representative sample of the literature to review the different metrics commonly used for quantifying the core. Empirical analyses have used a wide range of metrics for quantifying the core microbiome, including arbitrary occurrence and abundance cutoff values, with the focal taxonomic level of the core ranging from phyla to amplicon sequence variants. However, many of these metrics are susceptible to sampling and other biases. Developing a standardized set of metrics for quantifying the core that accounts for such biases is necessary for testing specific hypotheses about the functional and ecological roles of core microbiomes.