Abundant microorganisms that inhabit the human intestine are implicated in health and disease. The gut microbiome has been studied with metagenomic tools, and over 3 million genes have been discovered, constituting a 'parts list' of this ecosystem; further understanding requires studies of the interacting parts. Mouse models have provided a glimpse into the microbiota and host interactions at metabolic and immunologic levels; however, to provide more insight, there is a need to generate mathematical models that can reveal genotype-phenotype relationships and provide scaffolds for integrated analyses. To this end, we propose the use of genome-scale metabolic models that have successfully been used in studying interactions between human hosts and microbes, as well as microbes in isolation and in communities.
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