Define and quantify the central microbiome: challenges and perspectives
The term “core microbiome” has become widely used in microbial ecology over the past decade. Generally speaking, the core microbiome refers to any set of microbial taxa, or the genomic and functional attributes associated with these taxa, which are characteristic of a host or environment of interest. Most often, core microbiomes are measured as microbial taxa shared between two or more samples from a particular host or environment. Despite the popularity of this term and its increasing use, there is little consensus on how a core microbiome should be quantified in practice. Here, we present a brief history of the basic microbiome concept and use a representative sample of the literature to review the different metrics commonly used to quantify the nucleus. Empirical analyzes used a wide range of measurements to quantify the core microbiome, including arbitrary cut-off values for occurrence and abundance, with the focal taxonomic level of the nucleus ranging from phyla to variant amplicon sequences. However, many of these measures are sensitive to sampling and other biases. The development of a standardized set of metrics to quantify the nucleus that explains such biases is needed to test specific hypotheses about the functional and ecological roles of major microbiomes.