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.

在过去十年中，“核心微生物组”一词已广泛用于微生物生态学。从广义上讲，核心微生物组是指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环境的特征。最常见的是，核心微生物组被测量为来自特定宿主或环境的两个或多个样本之间共享的微生物分类群。尽管这个术语很受欢迎并且使用越来越多，但对于如何在实践中量化核心微生物组几乎没有共识。在这里，我们简要介绍了核心微生物组概念的历史，并使用具有代表性的文献样本来回顾通常用于量化核心的不同指标。实证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，核心的焦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。开发一套标准化的指标来量化解释这种偏差的核心对于测试关于核心微生物组的功能和生态作用的特定假设是必要的。