Increasing plant protein sources in the diet modulates gut microbiota and tryptophan metabolism in men at cardiometabolic risk

This study investigated the effect of partially substituting dietary animal with plant protein (PP) sources on the fecal microbiota composition and metabolome in men with increased cardiometabolic risk. In a randomized, controlled, crossover feeding trial (NCT04236518), 19 men with high plasma triglycerides and waist circumference completed two 4-week isoenergetic diets: a flexitarian diet high in PP sources (FLEX, 64% PP) and a more animal-based control diet (CON, 36% PP). Fecal microbiota (shotgun metagenomics: taxa and metabolic pathways) and metabolome (targeted LC-MS) profiles were assessed before and after each diet and integrated with the host plasma metabolome. Delta values (Δ_d28-d1) were computed (<i>n</i> = 15 participants with all samples available), inter-individual variation was extracted to account for cross-over design, and OPLS-DA analyses comparing FLEX and CON Δ_d28-d1 were performed. Variables were selected based on their contribution to the diet discrimination effect (VIP > 1.5) and significant differences between groups (<i>p</i>-value < 0.05 from the paired Wilcoxon signed-rank test). The gut microbiota diversity remained unchanged, but FLEX reduced taxa associated with animal-based diets (e.g., <i>Alistipes putredinis</i>). Compared to CON, FLEX increased fecal xanthurenic acid and decreased the genetic potential for indole production. Combined with previously reported plasma changes (increased indole propionic acid and decreased indoxyl sulfate after FLEX), these findings suggest a shift away from indole production toward kynurenine and indole propionic acid-related tryptophan pathways, possibly driven by higher fiber intake, particularly from legumes. A one-month flexitarian diet thus modulated in men specific microbial taxa and metabolism, particularly tryptophan catabolism. These coordinated changes in microbial composition, functional potential, and metabolites indicate that diets higher in PP sources influence gut microbiota activities relevant to cardiometabolic health.