Random Graphical Model of Microbiome Interactions in Related Environments

The microbiome constitutes a complex microbial ecology of interacting components that regulates important pathways in the host. Most microbial communities at various body sites tend to share common substructures of interactions, while also showing diversity related to the needs of the local environment. The aim of this paper is to develop a method for inferring both the common core and the differences in such microbiota systems. The approach combines two elements: (i) a random graph model generating networks across environments, and capturing potential relatedness at the structural level, with (ii) a Gaussian copula graphical model for the inference of environment-specific networks from multivariate microbial data. We propose a Bayesian approach for the joint inference of microbiota systems from metagenomic data for a number of body sites. The analysis of human microbiome data shows how the proposed random graphical model is able to capture varying levels of structural similarity across the different body sites and how this is supported by their taxonomical classification. Beyond a stable core, the inferred microbiome systems show interesting differences between the body sites, as well as interpretable relationships between various classes of microbes.