The prebiotic potential of dietary onion extracts: shaping gut microbial structures and promoting beneficial metabolites

Onions are well-known vegetables that offer various health benefits. This study explores the impact of onion extracts on gut microbiome using an <i>in vitro</i> fecal incubation model and metabolome analysis. Fecal samples were collected from 19 healthy donors and incubated in the presence or absence of onion extracts for 24 h. To reduce inter-individual variability in the gut microbiome, we employed enterotyping based on baseline fecal microbiota: 14 subjects with a <i>Bacteroides</i>-dominant type (enterotype B) and 5 subjects with <i>Prevotella</i>-dominant type (enterotype P). Alpha diversity was significantly reduced in the onion-treated group compared to the non-treated control group in both <i>Bacteroides</i>- and <i>Prevotella</i>-dominant types. However, significant structural differences in bacterial communities were observed based on weighted UniFrac distance. Notably, short-chain fatty acid (SCFA)-producing bacteria, such as <i>Bifidobacterium</i>_388775, <i>Feacalibacterium</i>, and <i>Fusicatenibacter</i>, were overrepresented in response to onion extracts in enterotype B. Furthermore, genes related to butyrate production were significantly overrepresented in the onion-treated group within enterotype B. Consistent with the enriched taxa and the predicted metabolic pathways, SCFAs and their related metabolites were significantly enriched in the onion-treated group. Additionally, tryptophan metabolism-derived metabolites, including indolelactate (ILA) and indolepropionate (IPA), were elevated by 4- and 32-fold, respectively, in the onion-treated group compared to the control group. <i>In vitro</i> growth assays showed an increase in lactobacilli strains in the presence of onion extracts. These results provide evidence that onion extracts could serve as promising prebiotics by altering gut microbial structure and promoting the production of beneficiary metabolites, including SCFAs and indole derivatives, and enhancing the growth of probiotics.IMPORTANCEThis study is significant as it provides compelling evidence that onion extracts have the potential to serve as effective prebiotics. Utilizing an <i>in vitro</i> fecal incubation model and enterotyping to reduce inter-individual variability, the research demonstrates how onion extracts can alter gut microbial structure and promote the production of beneficial metabolites, including SCFAs and indole derivatives like ILA and IPA. Additionally, onion extract treatment enhances the growth of beneficial probiotics. The findings underscore the potential of onion extracts to improve gut health by enriching specific beneficial bacteria and metabolic pathways, thereby supporting the development of functional foods aimed at improving gut microbiota composition and metabolic health.