Integrated Multi-Omics Analysis Reveals Differential Effects of Fructo-Oligosaccharides (FOS) Supplementation on the Human Gut Ecosystem

Abstract

Changes in the gut ecosystem, including the microbiome and the metabolome, and the host immune system after fructo-oligosaccharide (FOS) supplementation were evaluated. The supplementation of FOS showed large inter-individual variability in the absolute numbers of fecal bacteria and an increase in Bifidobacterium. The fecal metabolome analysis revealed individual variability in fructose utilization in response to FOS supplementation. In addition, immunoglobulin A(IgA) tended to increase upon FOS intake, and peripheral blood monocytes significantly decreased upon FOS intake and kept decreasing in the post-FOS phase. Further analysis using a metagenomic approach showed that the differences could be at least in part due to the differences in gene expressions of enzymes that are involved in the fructose metabolism pathway. While the study showed individual differences in the expected health benefits of FOS supplementation, the accumulation of "personalized" knowledge of the gut ecosystem with its genetic expression may enable effective instructions on prebiotic consumption to optimize health benefits for individuals in the future.

Keywords: fructo-oligosaccharides; gut ecosystem; metabolome; microbiome; omics analysis.

Figure 1

Changes in the total number of bacteria in the fecal microbiota upon FOS supplementation. (a) The absolute number of bacteria in each individual by real-time 16S rRNA gene qPCR. (b) The composition of microbiota at the genus level in fecal samples using 16S rRNA gene amplicon sequencing. These figures were constructed by the top 10 bacteria at the genus level, respectively. (c) PCoA analysis using Bray–Curtis distance of fecal microbiome colored by individuals (Upper) and sampling periods (Lower). (d) The total number of each bacterium in feces at the genus level. The upper figure is illustrated for each individual and the lower figure is summarized for the sample period. * = padj < 0.05.

Figure 2

Differences of fecal metabolites upon intake of FOS. (a) Score plots of PCA for metabolic profiles of feces colored by individuals (Left) and sampling periods (Right). (b) Loading plot of PCA for fecal metabolome. Blue bars indicate PC1 direction and red bars indicate PC2 direction in the PCA plot in a. PC2 negative direction was influenced by the sugar region (rectangle). (c) The correlation network of feces was constructed as described in the Materials and Methods. The line between each element was connected to the calculated correlation coefficient and elements with p < 0.05. The size of each element reflects the relative value within each measurement. The amount of fecal IgA was shown in magenta, bacteria in green, and metabolites in blue. (d) Relative intensity of fructose in individual fecal samples. (e) PCoA based on Euclidean distance of the changes in fructose concentration over time in feces from individuals shown in (b). ADONIS revealed that ID04, ID09 and ID11 were significantly different from the others (R2 = 0.52348, p = 0.009). (f) Relative intensity of fecal SCFAs measured by NMR.

Figure 3

KEGG pathways in carbohydrate metabolism with the metagenomic analysis. (a) Relative abundance of the KEGG orthologies (KOs) associated with carbohydrate metabolism in fecal samples was inferred based on the metagenome analysis. (b) A comparison of KOs of the fructose and mannose metabolism pathways in individuals obtained from the metagenome analysis of fecal samples using a heatmap calculated by multiplying individual metagenomic genes and a number of bacteria. The green rectangle indicates the gut microbial fructose and mannose metabolism KOs with high variability, and red and blue rectangles indicate groups of individuals having relatively higher and lower expressions of these highly variable KOs, respectively. (c) A list of 16 KOs with high individual variability in gene expression that was identified from (b). (d) Summary of a metabolic pathway that involves many KOs listed in (c).

Figure 4

FOS intake and the immune system. (a) Fecal IgA at different time points. (b) The absolute number of immune cells at each time point. Proportion of immune cells was analyzed using FACS with antibodies listed in Table S2. CD19+ B, B cells; CD3+ T, T cells; NK, natural killer cells; cDC, conventional dendritic cells; pDC, plasmacytoid dendritic cells; NKT, natural killer T cells. * = padj < 0.05, ** = padj < 0.01.