Host genetic diversity is an important selection environment for microbiota, which in turn may influence characteristics of host physiology and disease. To assess this relation across the whole genome and microbiome, we sampled intestinal mRNA and luminal microflora from Collaborative Cross emerging lines of mice. In addition, for these same mice, we acquired various metabolic phenotypes and basal behavioral measure that can be correlated to the genetic diversity of the population, the gene co-expression networks in the gut and the individual microbiomes. Using GeneWeaver, the networks of microbe and gene coexpression set were examined to identify molecular relations among various biological processes and various disease states.

See also Chesler5, a related intestinal microbiome study for 10 inbred strains including the 8 CC founders.