Profiling the small intestinal microbiota in vitro using 4 donors

Although there is clear evidence demonstrating the importance of the small intestinal microbiota (SIM) for nutrient utilization within the upper gastrointestinal tract, research is limited by difficulties accessing this community in vivo. Additionally, the high level of interindividual variability in taxonomic structure, which is well documented for the SIM, raises the question of how such divergent communities fill the same physiological roles. Here, we designed and evaluated an in vitro model of the terminal ileum representative of four unique donors and utilized it to interrogate interindividual variability. Shotgun sequencing was used to evaluate the in vitro community structure and untargeted metabolomics used to examine community function.