Challenges in modeling the human gut microbiome

developed to allocate metabolic resources to individual microbes and infer the ecological interaction, spatial dynamics and communitylevel assembly processes9, 10. The paper by Magnúsdóttir et al. 1 describes AGORA, a resource of GEMs for> 700 gut microbes that account for most of the dominant species in the human gut microbiota. Here we point out several drawbacks associated with these GEMs as functional models for simulating metabolic interactions between either gut symbionts or the gut microbiota and their host. A quality check of the 773 GEMs in AGORA suggests that most of the models are incapable of quantitative predictions without further manual curation and support from experimental data. We illustrate this by benchmarking all 773 AGORA GEMs against 70 metabolic models from BiGG11, another GEM repository.First, we evaluated the ability of the AGORA models to predict growth. The COBRA …