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

Abstract

Onions are well-known vegetables that offer various health benefits. This study explores the impact of onion extracts on gut microbiome using an in vitro 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 Bacteroides-dominant type (enterotype B) and 5 subjects with Prevotella-dominant type (enterotype P). Alpha diversity was significantly reduced in the onion-treated group compared to the non-treated control group in both Bacteroides- and Prevotella-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 Bifidobacterium_388775, Feacalibacterium, and Fusicatenibacter, 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. In vitro 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 in vitro 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.

Keywords: enterotype; gut microbiome; metabolites; onion extracts; prebiotics; short-chain fatty acids; tryptophan metabolism.

Fig 1

Gut enterotyping of all participants. (A) Calinski-Harabasz (CH) index to determine the optimal number of clusters. (B) Principal coordinate analysis plot showing enterotype of subjects based on relative genus abundance using the Jensen-Shannon divergence distance and partitioning around medoids clustering algorithm. Samples were color-coded by enterotyping results. Covariance ellipses were projected for each cluster, and bound of cluster was marked two standard deviations (2σ) in each direction from the mean of cluster. Red represents Bacteroides-dominant enterotype and blue represents Prevotella-dominant enterotype, respectively. (C) Bacterial taxa plot based on relative abundance in each enterotype. The black asterisks indicate the most statistically abundant taxa in either B- or P-type. (D) Histogram showing differentially abundant taxa between enterotypes using LefSe (LDA scores > 3 and adjusted P value of <0.05). Negative (red bars) and positive (blue bars) LDA scores indicate overrepresented genus in either enterotype B or P, respectively.

Fig 2

The effect of onion extracts on changes in gut microbial structure according to enterotype. (A) Alpha diversity represented by Faith’s PD index, observed features, and Shannon’s metrics. Data are shown in median ± 25th percentile, Mann-Whitney test. NS, nonsignificant, *P < 0.05,, ***P < 0.001. (B) Beta diversity evaluated by weighted UniFrac distance. Permutational multivariate analysis of variance was used to test statistical differences between control and onion-treated groups, Mann-Whitney test. **P < 0.01, ***P < 0.001. (C) Intragroup distance using weighted UniFrac distance between groups. Data shown and error bars are mean ± SEM (non-parametric t-test). ***P < 0.001.

Fig 3

Differences in microbial structure between control and onion groups according to enterotype. (A) Microbial taxa plot at genus level between groups in each enterotype. Red and blue asterisks denote differentially enriched or decreased taxa, respectively, as determined by LEfSe (LDA score > 3.0). (B) Bar chart showing differentially abundant taxa between groups using LEfSe (LDA score > 3.0 and Benjamini-Hochberg corrected P value of Wilcoxon test < 0.05). Red asterisks indicate taxa enriched in the onion-treated group, whereas blue asterisks denote taxa decreased in the onion-treated group compared to the control group. (C) Relative abundance of Bifidobacterium adolescentis and Faecalibacterium prausnitzii in control and onion groups using feature analysis according to enterotype. Statistical analysis was performed using Mann-Whitney test with significance represented as *P < 0.05, **P < 0.01, ***P < 0.001 and non-significant (NS).

Fig 4

(A) Predicted KEGG functional pathway profiles that are distinctly present in each group. Bar chart represents differentially abundant KEGG pathways that were selected based on the following criteria: LDA score > 3 and adjusted P value of <0.05. The pathways that overlap with metabolites of interest in the following panels are indicated with red and black asterisks. (B) Volcano plots of differentially enriched metabolites between control and onion-treated groups. All metabolites and those with annotations based on publicly available database, such as KEGG and Human Metabolome Database, are indicated by light and dark gray circles, respectively. The metabolites that are overlapped with predictive functional KEGG pathways generated using 16S rRNA data are shown in red and blue circles. Statistical significance (adjusted P < 0.05) was determined based on unpaired t-test after two-stage step-up correction (indicated by horizontally dotted red line). (C) A schematic representation of the short-chain fatty acid (SCFA) biosynthesis pathways. Letters colored by red are metabolites that are highly enriched in the onion-treated group. (D) Comparison of amounts of SCFAs between the control and onion-treated groups. (E) A schematic representation of tryptophan metabolism and Stickland fermentation pathways (blue letters). (F) Comparison of amounts of tryptophan metabolites between the control and onion-treated groups. The red dotted line represents the mean of the onion-treated group, while the black dotted line represents the mean of the control group.

Fig 5

The growth enhancement of probiotics in the presence of onion extracts for 24 h. All strains were inoculated in a microplate and preactivated through incubation for 4 days. After growing for 4 days, the bacteria were serially diluted and incubated for 24 h in the presence or absence of onion extracts. The absorbance at 600 nm was measured at 0 or 24 h post-incubation. Data shown and error bars are mean with range; mean of two biological replicates.