Impact of dietary carbohydrates and protein on the ileum and caecum microbiome

The host gut physiology and the availability of dietary nutrients creates distinct habitats along the gastrointestinal tract. The aim of this study was to compare the microbiome of the ileum and caecum under different diet conditions varying in the intake of carbohydrate types (glucose, sucrose, resistant starch type II and III, guar gum and inulin) and protein. For a subset of the diets, we also investigated the changes in the caecal microbiome under a challenge with dextran sodium sulphate to induce colitis.