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Stanford Team Reports In Vitro Development of Complex Gut Microbiome

Researchers from Stanford University this week report the in vitro construction and characterization of a complex gut microbiome, resulting in a model system that captures much of the biology of a native microbiome. While efforts to model the human gut microbiome in mice have led to important insights, the model communities studied to date have been defined or complex, but not both, limiting their utility. To overcome this issue, the scientists constructed and characterized in vitro a defined community of 104 bacterial species composed of the most common taxa from the human gut microbiota. As reported in Cell this week, the team systematically perturbed this community and its growth medium to uncover strain-nutrient and strain-strain interactions that underlie its composition. They further augment the community by filling open niches using an iterative, ecology-based process and show that the expanded community is more resilient to perturbation and resistant to pathogen colonization. The team also shows that mice colonized by this new community are phenotypically similar to mice harboring an undefined human fecal sample, "suggesting that our consortium and augmentation process lay the foundation for developing complete, defined models of the human gut microbiome."