Multi-Omic Analyses Reveal Bifidogenic Effect and Metabolomic Shifts in Healthy Human Cohort Supplemented With a Prebiotic Dietary Fiber Blend

Jea Woo Kang, Xinyu Tang, Charles J Walton, Mark J Brown, Rachel A Brewer, Rolando L Maddela, Jack Jingyuan Zheng, Joanne K Agus, Angela M Zivkovic, Jea Woo Kang, Xinyu Tang, Charles J Walton, Mark J Brown, Rachel A Brewer, Rolando L Maddela, Jack Jingyuan Zheng, Joanne K Agus, Angela M Zivkovic

Abstract

Dietary fiber, a nutrient derived mainly from whole grains, vegetables, fruits, and legumes, is known to confer a number of health benefits, yet most Americans consume less than half of the daily recommended amount. Convenience and affordability are key factors determining the ability of individuals to incorporate fiber-rich foods into their diet, and many Americans struggle to access, afford, and prepare foods rich in fiber. The objective of this clinical study was to test the changes in microbial community composition, human metabolomics, and general health markers of a convenient, easy to use prebiotic supplement in generally healthy young participants consuming a diet low in fiber. Twenty healthy adults participated in this randomized, placebo-controlled, double-blind, crossover study which was registered at clinicaltrials.gov as NCT03785860. During the study participants consumed 12 g of a prebiotic fiber supplement and 12 g of placebo daily as a powder mixed with water as part of their habitual diet in randomized order for 4 weeks, with a 4-week washout between treatment arms. Fecal microbial DNA was extracted and sequenced by shallow shotgun sequencing on an Illumina NovaSeq. Plasma metabolites were detected using liquid chromatography-mass spectrometry with untargeted analysis. The phylum Actinobacteria, genus Bifidobacterium, and several Bifidobacterium species (B. bifidum, B. adolescentis, B. breve, B. catenulatum, and B. longum) significantly increased after prebiotic supplementation when compared to the placebo. The abundance of genes associated with the utilization of the prebiotic fiber ingredients (sacA, xfp, xpk) and the production of acetate (poxB, ackA) significantly changed with prebiotic supplementation. Additionally, the abundance of genes associated with the prebiotic utilization (xfp, xpk), acetate production (ackA), and choline to betaine oxidation (gbsB) were significantly correlated with changes in the abundance of the genus Bifidobacterium in the prebiotic group. Plasma concentrations of the bacterially produced metabolite indolepropionate significantly increased. The results of this study demonstrate that an easy to consume, low dose (12 g) of a prebiotic powder taken daily increases the abundance of beneficial bifidobacteria and the production of health-promoting bacteria-derived metabolites in healthy individuals with a habitual low-fiber diet.

Clinical trial registration: www.clinicaltrials.gov/, identifier: NCT03785860.

Keywords: bifidobacteria; cholines; gut microbiome; indolepropionate; prebiotic.

Conflict of interest statement

JK and AZ have received research support from USANA Health Sciences, Inc. CW, MB, RB, and RM are employees of USANA Health Sciences, Inc. These interests have been reviewed and managed by the University of California, Davis in accordance with its Conflict-of-Interest policies. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The authors declare that this study received funding from USANA Health Sciences, Inc. The funder had the following involvement in the study: study conceptualization and manuscript review.

Copyright © 2022 Kang, Tang, Walton, Brown, Brewer, Maddela, Zheng, Agus and Zivkovic.

Figures

Figure 1
Figure 1
Study CONSORT diagram. Participants were recruited with screening, consent, and enrollment process. The treatment order was randomized into two groups, one group (red) supplemented with the placebo and the other group (green) supplemented with the prebiotic followed by a washout period and crossover to the other treatment for each group.
Figure 2
Figure 2
(A) Relative abundance of the gut microbiome at the phylum level and (B) the family level within the phylum Actinobacteria pre- and post-treatment with placebo or prebiotic. (C) Box plots of the genus Bifidobacterium counts pre- and post-treatment with placebo or prebiotic. (D–H) Box plots of Bifidobacterium species counts pre- and post-treatment with placebo or prebiotic (*P <0.05, **P < 0.01).
Figure 3
Figure 3
(A) Volcano plot of all detected genes. Genes with a logFC (post–pre treatment) > 0 and a –log(P-value) > 0.05 are colored blue and genes with a logFC <0 and a –log(P-value) > 0.05 are colored red. All the other genes are colored gray. (B–E) Box plot of gene counts pre- and post-treatment with placebo or prebiotic (P ≤ 0.05, unadjusted). (F–H) Correlation plot of changes (post–pre) in Bifidobacterium abundance against changes (post–pre) in gene counts for both placebo and prebiotic in 20 subjects (prebiotic: P ≤ 0.05, adjusted, Kendall T).
Figure 4
Figure 4
(A) Volcano plot of all metabolites in human plasma samples. Metabolites with a logFC > 0 and a –log(P-value) > 0.05 are colored blue and metabolites with a logFC <0 and a –log(P-value) > 0.05 are colored red. All the other metabolites are colored gray. (B–J) Box plots of IPA, TMAO, choline, and acylcholines concentrations pre- and post-treatment with placebo or prebiotic (unadjusted P-value).

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