Phylogenetic Measures of the Core Microbiome

Abstract Background A useful 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, few have included phylogeny-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 describing the diversity of core microbiomes from a single type of habitat, the turnover between core microbiomes from two different types of habitats, and the shared diversity across core microbiomes from two or more different types of habitats. As compared to non-phylogenetic metrics, our phylogenetic metrics show greater consistency across taxonomic rank and/or phylogenetic level, as well as 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 allow seamless integration of microbiome properties across taxonomic rank and/or phylogenetic level. 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.