The small intestine drives diet induced alterations of the human gut microbiome

The microbiota at different locations of the gastrointestinal tract is quite distinct. Studies of the modulation of the gut microbiota by diet in humans have predominantly focussed on the large intestine, i.e., faecal microbiota. However, diet is also expected to have a major impact on the microbial ecosystem of the small intestine. Growing evidence implicates the interplay between diet, microbiota, and the small intestine mucosa in the maintenance of metabolic and immune homeostasis, as well as in a number of different diseases1. However, despite its relevance for human health, the impact of dietary modulation on the small intestinal microbiota largely remains unexplored due to the invasiveness of the sampling procedures targeting this part of the human intestinal tract. Here, we employ a minimally invasive method to determine the small intestinal microbiota composition, and show that high-carbohydrate and high-protein diets elicit profound changes in this ecosystem. The results also show that the changes observed in the colon microbiota originate in the small intestine, underpinning that the small intestinal microbiota shapes the gut microbiota in response to diet.