Onion- and Cucumber-Derived Fructooligosaccharides Selectively Promote Bacteroides fragilis Growth in the Gut

To advance the development of precision dietary interventions, we sought to elucidate the regulatory relationships between diet and special microbes. Here, through a comprehensive meta-analysis, we identified significant associations between 1,452 dietary factors and gut microbial species. Using in vitro fecal fermentation and randomized feeding experiments, we demonstrated that onion and cucumber robustly and selectively promote the enrichment of Bacteroides fragilis. Futhermore, we revealed that a conserved fructooligosaccharides (FOS)-degrading gene (BF2326) in B. fragilis specifically targets the FOS present in onion and cucumber, thereby facilitating the selective enrichment of B. fragilis in the gut. Collectively, our findings uncover a directional carbohydrate utilization mechanism in B. fragilis, offering insights that may inform dietary recommendations and guide the development of therapeutic and nutritional strategies.