A significant barrier to studying perturbations to human gut microbiota is the difficulty of direct sampling from the distal colon over time. Because such sampling is not practicable, the David Lab uses an ex vivo model of the distal colon that consists of a set of continuous flow bioreactors. Using this artificial gut system, we can culture complex ecosystems of human stool-derived microbes and perform long-term perturbation experiments. This enables us to see how community structure (i.e. which microbes are present) and activity (e.g. what metabolites they produce) change over time and in response to changes in nutrient availability.
We have used this system to test the effects of specific prebiotics, such as inulin, on a gut community over time. The community changes that occur within the artificial gut system have also been modeled by members of the David Lab using dynamic linear models.