Consumption of a Leuconostoc holzapfelii-enriched synbiotic beverage alters the composition of the microbiota and microbial extracellular vesicles

Abstract

Synbiotics, the combination of probiotics and prebiotics, are known to confer health benefits via intestinal microbiota modulation. However, significant intestinal microbiota alterations can be difficult to determine in intervention studies based on solely bacterial stool metagenomic analysis. Intestinal microbiota constituents secrete 20-200-nm-sized extracellular vesicles (EVs) containing microbial DNA, proteins, and lipids that are distributed throughout the body, providing an alternative target for microbiota metagenomic analysis. Here, we determined the impact of a synbiotic beverage enriched with the kimchi-derived bacterium Leuconostoc holzapfelii (L. holzapfelii) on the intestinal microbiota and local and circulatory microbiota-derived EV composition of healthy Korean adults. We isolated microbial DNA from stool bacteria, stool EVs, and urinary EVs and conducted next-generation sequencing of the 16S rDNA V3-V4 regions before and after synbiotic consumption. The species diversity of circulating urinary EVs was significantly increased after synbiotic consumption, while stool bacterial and EV diversity remained unchanged. Furthermore, we found that while a single genus was decreased among the stool bacteria constituents, stool EVs and urinary EVs showed significant alterations in four and eight genera, respectively. Blood chemistry assays revealed that synbiotic consumption significantly lowered aspartate aminotransferase (AST) serum levels, particularly in subjects with starting levels above the normal range (>40 UI/L). In conclusion, the L. holzapfelii-enriched synbiotic beverage greatly altered serum AST levels and microbial EV composition in urine and stool, while only minor changes were observed in the gut microbiota composition. Based on these findings, we suggest the potential use of microbiota-derived EVs as surrogate markers in future predictive diagnosis studies.

Fig. 1. Composition of stool bacteria before and after consumption of a synbiotic beverage.

a Alpha diversity measured by Chao1, b composition of the microbiome at the phylum level, c individual microbiome at the phylum level, d composition of the microbiome at the genus level, and e individual microbiome at the genus level

Fig. 2. Composition of microbiota-derived stool EVs before and after consumption of a synbiotic beverage.

a Alpha diversity measured by Chao1, b composition of the microbiome at the phylum level, c individual the microbiome at the phylum level, d composition of the microbiome at the genus level, and e individual microbiome at the genus level

Fig. 3. Composition of microbiota-derived urinary EVs before and after consumption of a synbiotic beverage.

a Alpha diversity measured by Chao1, b composition of the microbiome at the phylum level, c individual microbiome at the phylum level, d composition of the microbiome at the genus level, and e individual microbiome at the genus level