Phylogenetic Measures of the Core Microbiome
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Background
A fundamental concept in microbial ecology is the ‘core microbiome.’ Typically, core microbiomes are defined as the microbial taxa, genes, or functions shared by a threshold number of microbiome samples from a particular type of habitat (e.g., a particular type of host or a particular type of environment/ecosystem). In defining the core microbiome, the goal is to capture the portion of the microbial community that is conserved across samples from the focal habitat. Recently, there has been growing interest in developing methods to better characterize core microbiomes. As a result, numerous occurrence- and abundance-based measures have been defined. However, none have included phylogenetically aware metrics for analyzing core microbiomes.
Results
In this paper, we develop the concept of the ‘core community phylogeny’ – a phylogeny where branches are selected based on their presence in multiple samples from a single type of habitat. We then use the core community phylogeny to define phylogenetic metrics for the diversity of core microbiomes from a single type of habitat, for turnover between core microbiomes from two different types of habitat, and for shared diversity across core microbiomes from two or more different types of habitat. As compared to non-phylogenetic metrics, our phylogenetic metrics show greater consistency across taxonomic rank and less sensitivity to strain variation across microbiome samples. Thus, our metrics address key challenges in the interpretation of core microbiomes.
Conclusions
We provide a phylogenetic framework for characterizing and comparing core microbiomes. Importantly, the methods that we propose allows integration of microbiome properties across taxonomic rank. Ultimately, this will provide both a more consistent picture of the core microbiome, as well as novel biological insight into the conserved components of microbial communities.
