Metabolomic insights into the prebiotic and metabolic regulatory properties of ellagic acid and urolithins on probiotic-like bacteria in vitro

Mounting evidence suggests that dietary polyphenols exert health benefits partly through their favorable interactions with gut bacteria. However, little is known about polyphenol’s metabolic regulatory effects towards individual bacteria at the molecular level. Ellagic acid (EA), a polyphenol abundantly present in plant-based foods, was found to exhibit prebiotic properties through differential interactions with probiotic-like bacteria, including the EA-to-urolithin converting species such as Gordonibacter urolithinfaciens (G. uro). This study aimed to investigate the crosstalk between EA and EA-responsive beneficial bacteria, including both conventional and next-generation probiotics originating from the human gut, and to understand the underlying mechanism by which EA exerts prebiotic activities in vitro. The influence of EA and urolithins on probiotic bacteria was investigated at the levels of fecal microbiota and individual strains via anaerobic culturomics and metabolomics approaches. Results indicate that dietary-level EA favorably regulated gut microbial composition through the enrichment of probiotic genera (e.g., Bifidobacterium and Akkermansia) in vitro. Regarding individual bacteria, EA supplementation promoted the growth of Lacticaseibacillus rhamnosus GG and Bifidobacterium infantis. Integrated targeted and untargeted metabolomic analyses of intracellular and extracellular metabolites revealed that EA/urolithins modulated metabolic pathways associated with amino acid metabolism, energy production and oxidative stress. Furthermore, G. uro exhibited strong EA uptake ability, facilitating the urolithin bioconversion and cellular accumulation in a dose-dependent manner. Overall, this study provides in-depth understanding on how dietary polyphenols with prebiotic properties regulate the growth and metabolic functions of probiotic-like bacteria.