Human gut microbiome composition and tryptophan metabolites were changed differently by fast food and Mediterranean diet in four days: A pilot study

Diets rich in animal source foods vs. plant-based diets have different macronutrient composition, and they have been shown to have differential effects on the gut microbiome. In this study we hypothesized that diets with very different nutrient composition are able to change gut microbiome composition and metabolites in a very short period. We compared a fast food (FF) diet (i.e. burgers and fries) with a Mediterranean (Med) diet, which is rich in vegetables, whole grains, olive oil, nuts, and fish. Ten healthy subjects participated in a controlled cross-over study in which they consumed a Med diet and FF diet in randomized order for 4 days each, with a 4-day washout between treatments. Fecal DNA was extracted and the 16S V4 region amplified using PCR, followed by sequencing on an Illumina MiSeq. Plasma metabolites and bile acids were analyzed using LCMS. Certain bile-tolerant microbial genera and species including Collinsella, Parabacteroides, and Bilophila wadsworthia, were significantly increased after the FF diet. Some fiber-fermenting bacteria, including Lachnospiraceae and Butyricicoccus, increased significantly after the Med diet and decreased after the FF diet. Bacterially produced metabolites indole-3-lactic acid and indole-3-propionic acid, which have been shown to confer beneficial effects on neuronal cells, increased after the Med diet and decreased after the FF diet. Inter-individual variability in response to the treatments may be related to differences in background diet, for example as shown by differences in Bilophila response in relationship to the saturated fat content of the baseline diet. In conclusion, an animal fat rich, low fiber FF diet vs. a high fiber Med diet altered human gut microbiome composition and its metabolites after just 4 days.