The tree-based dietary analysis method, which incorporates food identity and macronutrient quantity, improves the detection of associations between diet and gut microbiota compared to traditional nutrient-only or food-group approaches.

When people eat specific foods like fruits and cooked grains, certain types of fiber and starch pass through the stomach and small intestine without being broken down. These undigested compounds reach the colon, where different bacteria use them as food. Fruits provide pectin, which feeds bacteria that break it down into energy and acids, causing those bacteria to multiply. Cooked grains provide resistant starch, which feeds other bacteria that specialize in breaking it down, causing those bacteria to grow. The exact type of food eaten determines which bacterial species get the right food to thrive, making it possible to see clear links between what people eat and which bacteria are present.