Multiomic Signatures of Microbial Metabolites Following Prebiotic Fiber Supplementation

March 22, 2025 updated by: Michael Snyder, Stanford University
The investigators propose a comprehensive, multiomic study that will integrate longitudinal data associating changes in specific gut bacteria and host in response to prebiotic fiber supplementation. These data will guide the development of an integrative biological signature relating bacterial-derived metabolites with biological outcome in the host. The open sharing of data generated by the proposed research represents a significant public resource that will support and accelerate future novel studies.

Study Overview

Status

Active, not recruiting

Conditions

Intervention / Treatment

Detailed Description

Phenolics-rich prebiotic fiber has been correlated with a number of positive health outcomes, however their bioavailability is typically low. A large portion the gut microbiota metabolize these fibers releasing a range of phenolic acids, which are believed to be principle bioactive components driving reduction in disease risk. Despite this, little evidence exists linking specific gut bacteria with the metabolites they produce and the downstream biological effects that these compounds exert. With this study, the investigators propose to assemble a cohort of healthy individuals that will receive prebiotic supplementation, during comprehensive, longitudinal characterization of the microbiota and host changes with clinical markers and multiple omics assays. These multiomic data will then be integrated, generating unique biological signatures that define the role that microbial metabolites from specific bacteria play in host biological activity. To validate the biological function of these microbial metabolites, gnobiotic mice will be inoculated with the microbial strains identified. The newly identified metabolites will also be synthesized in vitro to demonstrate their structure, biological properties and applications. Through this study the investigators expect to gain a detailed and clear understanding of the physiological changes, at the mechanistic level, that occur in the microbiome and host in response to dietary supplementation with prebiotic fiber.

Study Type

Interventional

Enrollment (Estimated)

100

Phase

  • Not Applicable

Contacts and Locations

This section provides the contact details for those conducting the study, and information on where this study is being conducted.

Study Locations

  • United States
    • California
      • Stanford, California, United States, 94304
        • Stanford University

Participation Criteria

Researchers look for people who fit a certain description, called eligibility criteria. Some examples of these criteria are a person's general health condition or prior treatments.

Eligibility Criteria

Ages Eligible for Study

35 years to 65 years (Adult, Older Adult)

Accepts Healthy Volunteers

Yes

Description

Inclusion Criteria:

- good general health

Exclusion Criteria:

  • Chronic inflammatory conditions
  • Major organ disease
  • Heavy alcohol use
  • Pregnancy/lactation
  • Use of medication known to affect carbohydrate or lipid metabolism
  • Active eating disorder

Study Plan

This section provides details of the study plan, including how the study is designed and what the study is measuring.

How is the study designed?

Design Details

  • Primary Purpose: Basic Science
  • Allocation: Randomized
  • Interventional Model: Parallel Assignment
  • Masking: Single

Arms and Interventions

Participant Group / Arm
Intervention / Treatment
Experimental: ARM 1: Arabinoxylan, Beta-Glucan, Resistant Starch, Inulin
Participants will complete 4 cycles. For each cycle they will take 20g per day fiber supplement for 3 weeks, followed by a washout period of at least 6-8 weeks. In this arm, participants will take the fiber supplements in the following order: Arabinoxylan, Beta-Glucan, Resistant Starch, Inulin.
Dietary supplement: Fiber cycles ARM 1

Participants will complete 4 cycles. For each cycle they will take 20g per day fiber supplement for 3 weeks, followed by a washout period of at least 6-8 weeks.

On cycle 1, they will take 20g per day of Arabinoxylan. On cycle 2, they will take 20g per day of Beta-Glucan. On cycle 3, they will take 20g per day of Resistant Starch. On cycle 4, they will take 20g per day of Inulin.
Experimental: ARM 2: Arabinoxylan, Beta-Glucan, Inulin, Resistant Starch
Participants will complete 4 cycles. For each cycle they will take 20g per day fiber supplement for 3 weeks, followed by a washout period of at least 6-8 weeks. In this arm, participants will take the fiber supplements in the following order: Arabinoxylan, Beta-Glucan, Inulin, Resistant Starch.
Dietary supplement: Fiber cycles ARM 2

Participants will complete 4 cycles. For each cycle they will take 20g per day fiber supplement for 3 weeks, followed by a washout period of at least 6-8 weeks.

On cycle 1, they will take 20g per day of Arabinoxylan. On cycle 2, they will take 20g per day of Beta-Glucan. On cycle 3, they will take 20g per day of Inulin. On cycle 4, they will take 20g per day of Resistant Starch.
Experimental: ARM 3: Arabinoxylan, Resistant Starch, Beta-Glucan, Inulin
Participants will complete 4 cycles. For each cycle they will take 20g per day fiber supplement for 3 weeks, followed by a washout period of at least 6-8 weeks. In this arm, participants will take the fiber supplements in the following order: rabinoxylan, Resistant Starch, Beta-Glucan, Inulin.
Dietary supplement: Fiber cycles ARM 3

Participants will complete 4 cycles. For each cycle, they will take 20g per day fiber supplement for 3 weeks, followed by a washout period of at least 6-8 weeks.

On cycle 1, they will take 20g per day of Arabinoxylan. On cycle 2, they will take 20g per day of Resistant Starch. On cycle 3, they will take 20g per day of Beta-Glucan. On cycle 4, they will take 20g per day of Inulin.
Experimental: ARM 4: Arabinoxylan, Resistant Starch, Inulin, Beta-Glucan
Participants will complete 4 cycles. For each cycle they will take 20g per day fiber supplement for 3 weeks, followed by a washout period of at least 6-8 weeks. In this arm, participants will take the fiber supplements in the following order: Arabinoxylan, Resistant Starch, Inulin, Beta-Glucan.
Dietary supplement: Fiber cycles ARM 4

Participants will complete 4 cycles. For each cycle, they will take 20g per day fiber supplement for 3 weeks, followed by a washout period of at least 6-8 weeks.

On cycle 1, they will take 20g per day of Arabinoxylan. On cycle 2, they will take 20g per day of Resistant Starch. On cycle 3, they will take 20g per day of Inulin. On cycle 4, they will take 20g per day of Beta-Glucan.
Experimental: ARM 5: Arabinoxylan, Inulin, Beta-Glucan, Resistant Starch
Participants will complete 4 cycles. For each cycle they will take 20g per day fiber supplement for 3 weeks, followed by a washout period of at least 6-8 weeks. In this arm, participants will take the fiber supplements in the following order: Arabinoxylan, Inulin, Beta-Glucan, Resistant Starch.
Dietary supplement: Fiber cycles ARM 5

Participants will complete 4 cycles. For each cycle, they will take 20g per day fiber supplement for 3 weeks, followed by a washout period of at least 6-8 weeks.

On cycle 1, they will take 20g per day of Arabinoxylan. On cycle 2, they will take 20g per day of Inulin. On cycle 3, they will take 20g per day of Beta-Glucan. On cycle 4, they will take 20g per day of Resistant Starch.
Experimental: ARM 6: Arabinoxylan, Inulin, Resistant Starch, Beta-Glucan
Participants will complete 4 cycles. For each cycle they will take 20g per day fiber supplement for 3 weeks, followed by a washout period of at least 6-8 weeks. In this arm, participants will take the fiber supplements in the following order: Arabinoxylan, Inulin, Resistant Starch, Beta-Glucan.
Dietary supplement: Fiber cycles ARM 6

Participants will complete 4 cycles. For each cycle, they will take 20g per day fiber supplement for 3 weeks, followed by a washout period of at least 6-8 weeks.

On cycle 1, they will take 20g per day of Arabinoxylan. On cycle 2, they will take 20g per day of Inulin. On cycle 3, they will take 20g per day of Resistant Starch. On cycle 4, they will take 20g per day of Beta-Glucan.
Experimental: ARM 7: Beta-Glucan, Arabinoxylan, Resistant Starch, Inulin
Participants will complete 4 cycles. For each cycle they will take 20g per day fiber supplement for 3 weeks, followed by a washout period of at least 6-8 weeks. In this arm, participants will take the fiber supplements in the following order: Beta-Glucan, Arabinoxylan, Resistant Starch, Inulin.
Dietary supplement: Fiber cycles ARM 7

Participants will complete 4 cycles. For each cycle, they will take 20g per day fiber supplement for 3 weeks, followed by a washout period of at least 6-8 weeks.

On cycle 1, they will take 20g per day of Beta-Glucan. On cycle 2, they will take 20g per day of Arabinoxylan. On cycle 3, they will take 20g per day of Resistant Starch. On cycle 4, they will take 20g per day of Inulin.
Experimental: ARM 8: Beta-Glucan, Arabinoxylan, Inulin, Resistant Starch
Participants will complete 4 cycles. For each cycle they will take 20g per day fiber supplement for 3 weeks, followed by a washout period of at least 6-8 weeks. In this arm, participants will take the fiber supplements in the following order: Beta-Glucan, Arabinoxylan, Inulin, Resistant Starch.
Dietary supplement: Fiber cycles ARM 8

Participants will complete 4 cycles. For each cycle, they will take 20g per day fiber supplement for 3 weeks, followed by a washout period of at least 6-8 weeks.

On cycle 1, they will take 20g per day of Beta-Glucan. On cycle 2, they will take 20g per day of Arabinoxylan. On cycle 3, they will take 20g per day of Inulin. On cycle 4, they will take 20g per day of Resistant Starch.
Experimental: ARM 9: Beta-Glucan, Resistant Starch, Inulin, Arabinoxylan
Participants will complete 4 cycles. For each cycle they will take 20g per day fiber supplement for 3 weeks, followed by a washout period of at least 6-8 weeks. In this arm, participants will take the fiber supplements in the following order: Beta-Glucan, Resistant Starch, Inulin, Arabinoxylan.
Dietary supplement: Fiber cycles ARM 9

Participants will complete 4 cycles. For each cycle, they will take 20g per day fiber supplement for 3 weeks, followed by a washout period of at least 6-8 weeks.

On cycle 1, they will take 20g per day of Beta-Glucan. On cycle 2, they will take 20g per day of Resistant Starch. On cycle 3, they will take 20g per day of Inulin. On cycle 4, they will take 20g per day of Arabinoxylan.
Experimental: ARM 10: Beta-Glucan, Resistant Starch, Arabinoxylan, Inulin
Participants will complete 4 cycles. For each cycle they will take 20g per day fiber supplement for 3 weeks, followed by a washout period of at least 6-8 weeks. In this arm, participants will take the fiber supplements in the following order: Beta-Glucan, Resistant Starch, Arabinoxylan, Inulin.
Dietary supplement: Fiber cycles ARM 10

Participants will complete 4 cycles. For each cycle, they will take 20g per day fiber supplement for 3 weeks, followed by a washout period of at least 6-8 weeks.

On cycle 1, they will take 20g per day of Beta-Glucan. On cycle 2, they will take 20g per day of Resistant Starch. On cycle 3, they will take 20g per day of Arabinoxylan. On cycle 4, they will take 20g per day of Inulin.
Experimental: ARM 11: Beta-Glucan, Inulin, Arabinoxylan, Resistant Starch
Participants will complete 4 cycles. For each cycle they will take 20g per day fiber supplement for 3 weeks, followed by a washout period of at least 6-8 weeks. In this arm, participants will take the fiber supplements in the following order: Beta-Glucan, Inulin, Arabinoxylan, Resistant Starch.
Dietary supplement: Fiber cycles ARM 11

Participants will complete 4 cycles. For each cycle, they will take 20g per day fiber supplement for 3 weeks, followed by a washout period of at least 6-8 weeks.

On cycle 1, they will take 20g per day of Beta-Glucan. On cycle 2, they will take 20g per day of Inulin. On cycle 3, they will take 20g per day of Arabinoxylan. On cycle 4, they will take 20g per day of Resistant Starch.
Experimental: ARM 12: Beta-Glucan, Inulin, Resistant Starch, Arabinoxylan
Participants will complete 4 cycles. For each cycle they will take 20g per day fiber supplement for 3 weeks, followed by a washout period of at least 6-8 weeks. In this arm, participants will take the fiber supplements in the following order: Beta-Glucan, Inulin, Resistant Starch, Arabinoxylan.
Dietary supplement: Fiber cycles ARM 12

Participants will complete 4 cycles. For each cycle, they will take 20g per day fiber supplement for 3 weeks, followed by a washout period of at least 6-8 weeks.

On cycle 1, they will take 20g per day of Beta-Glucan. On cycle 2, they will take 20g per day of Inulin. On cycle 3, they will take 20g per day of Resistant Starch. On cycle 4, they will take 20g per day of Arabinoxylan.
Experimental: ARM 13: Resistant Starch, Inulin, Beta-Glucan, Arabinoxylan
Participants will complete 4 cycles. For each cycle they will take 20g per day fiber supplement for 3 weeks, followed by a washout period of at least 6-8 weeks. In this arm, participants will take the fiber supplements in the following order: Resistant Starch, Inulin, Beta-Glucan, Arabinoxylan.
Dietary supplement: Fiber cycles ARM 13

Participants will complete 4 cycles. For each cycle, they will take 20g per day fiber supplement for 3 weeks, followed by a washout period of at least 6-8 weeks.

On cycle 1, they will take 20g per day of Resistant Starch. On cycle 2, they will take 20g per day of Inulin. On cycle 3, they will take 20g per day of Beta-Glucan. On cycle 4, they will take 20g per day of Arabinoxylan.
Experimental: ARM 14: Resistant Starch, Inulin, Arabinoxylan, Beta-Glucan
Participants will complete 4 cycles. For each cycle they will take 20g per day fiber supplement for 3 weeks, followed by a washout period of at least 6-8 weeks. In this arm, participants will take the fiber supplements in the following order: Resistant Starch, Inulin, Arabinoxylan, Beta-Glucan.
Dietary supplement: Fiber cycles ARM 14

Participants will complete 4 cycles. For each cycle, they will take 20g per day fiber supplement for 3 weeks, followed by a washout period of at least 6-8 weeks.

On cycle 1, they will take 20g per day of Resistant Starch. On cycle 2, they will take 20g per day of Inulin. On cycle 3, they will take 20g per day of Arabinoxylan. On cycle 4, they will take 20g per day of Beta-Glucan.
Experimental: ARM 15: Resistant Starch, Arabinoxylan, Inulin, Beta-Glucan
Participants will complete 4 cycles. For each cycle they will take 20g per day fiber supplement for 3 weeks, followed by a washout period of at least 6-8 weeks. In this arm, participants will take the fiber supplements in the following order: Resistant Starch, Arabinoxylan, Inulin, Beta-Glucan.
Dietary supplement: Fiber cycles ARM 15

Participants will complete 4 cycles. For each cycle, they will take 20g per day fiber supplement for 3 weeks, followed by a washout period of at least 6-8 weeks.

On cycle 1, they will take 20g per day of Resistant Starch. On cycle 2, they will take 20g per day of Arabinoxylan. On cycle 3, they will take 20g per day of Inulin. On cycle 4, they will take 20g per day of Beta-Glucan.
Experimental: ARM 16: Resistant Starch, Arabinoxylan, Beta-Glucan, Inulin
Participants will complete 4 cycles. For each cycle they will take 20g per day fiber supplement for 3 weeks, followed by a washout period of at least 6-8 weeks. In this arm, participants will take the fiber supplements in the following order: Resistant Starch, Arabinoxylan, Beta-Glucan, Inulin.
Dietary supplement: Fiber cycles ARM 16

Participants will complete 4 cycles. For each cycle, they will take 20g per day fiber supplement for 3 weeks, followed by a washout period of at least 6-8 weeks.

On cycle 1, they will take 20g per day of Resistant Starch. On cycle 2, they will take 20g per day of Arabinoxylan. On cycle 3, they will take 20g per day of Beta-Glucan. On cycle 4, they will take 20g per day of Inulin.
Experimental: ARM 17: Resistant Starch, Beta-Glucan, Inulin, Arabinoxylan
Participants will complete 4 cycles. For each cycle they will take 20g per day fiber supplement for 3 weeks, followed by a washout period of at least 6-8 weeks. In this arm, participants will take the fiber supplements in the following order: Resistant Starch, Beta-Glucan, Inulin, Arabinoxylan.
Dietary supplement: Fiber cycles ARM 17

Participants will complete 4 cycles. For each cycle, they will take 20g per day fiber supplement for 3 weeks, followed by a washout period of at least 6-8 weeks.

On cycle 1, they will take 20g per day of Resistant Starch. On cycle 2, they will take 20g per day of Beta-Glucan. On cycle 3, they will take 20g per day of Inulin. On cycle 4, they will take 20g per day of Arabinoxylan.
Experimental: ARM 18: Resistant Starch, Beta-Glucan, Arabinoxylan, Inulin
Participants will complete 4 cycles. For each cycle they will take 20g per day fiber supplement for 3 weeks, followed by a washout period of at least 6-8 weeks. In this arm, participants will take the fiber supplements in the following order: Resistant Starch, Beta-Glucan, Arabinoxylan, Inulin.
Dietary supplement: Fiber cycles ARM 18

Participants will complete 4 cycles. For each cycle, they will take 20g per day fiber supplement for 3 weeks, followed by a washout period of at least 6-8 weeks.

On cycle 1, they will take 20g per day of Resistant Starch. On cycle 2, they will take 20g per day of Beta-Glucan. On cycle 3, they will take 20g per day of Arabinoxylan. On cycle 4, they will take 20g per day of Inulin.
Experimental: ARM 19: Inulin, Resistant Starch, Arabinoxylan, Beta-Glucan
Participants will complete 4 cycles. For each cycle they will take 20g per day fiber supplement for 3 weeks, followed by a washout period of at least 6-8 weeks. In this arm, participants will take the fiber supplements in the following order: Inulin, Resistant Starch, Arabinoxylan, Beta-Glucan.
Dietary supplement: Fiber cycles ARM 19

Participants will complete 4 cycles. For each cycle, they will take 20g per day fiber supplement for 3 weeks, followed by a washout period of at least 6-8 weeks.

On cycle 1, they will take 20g per day of Inulin. On cycle 2, they will take 20g per day of Resistant Starch. On cycle 3, they will take 20g per day of Arabinoxylan. On cycle 4, they will take 20g per day of Beta-Glucan.
Experimental: ARM 20: Inulin, Resistant Starch, Beta-Glucan, Arabinoxylan
Participants will complete 4 cycles. For each cycle they will take 20g per day fiber supplement for 3 weeks, followed by a washout period of at least 6-8 weeks. In this arm, participants will take the fiber supplements in the following order: Inulin, Resistant Starch, Beta-Glucan, Arabinoxylan.
Dietary supplement: Fiber cycles ARM 20

Participants will complete 4 cycles. For each cycle, they will take 20g per day fiber supplement for 3 weeks, followed by a washout period of at least 6-8 weeks.

On cycle 1, they will take 20g per day of Inulin. On cycle 2, they will take 20g per day of Resistant Starch. On cycle 3, they will take 20g per day of Beta-Glucan. On cycle 4, they will take 20g per day of Arabinoxylan.
Experimental: ARM 21: Inulin, Beta-Glucan, Resistant Starch, Arabinoxylan
Participants will complete 4 cycles. For each cycle they will take 20g per day fiber supplement for 3 weeks, followed by a washout period of at least 6-8 weeks. In this arm, participants will take the fiber supplements in the following order: Inulin, Beta-Glucan, Resistant Starch, Arabinoxylan.
Dietary supplement: Fiber cycles ARM 21

Participants will complete 4 cycles. For each cycle, they will take 20g per day fiber supplement for 3 weeks, followed by a washout period of at least 6-8 weeks.

On cycle 1, they will take 20g per day of Inulin. On cycle 2, they will take 20g per day of Beta-Glucan. On cycle 3, they will take 20g per day of Resistant Starch. On cycle 4, they will take 20g per day of Arabinoxylan.
Experimental: ARM 22: Inulin, Beta-Glucan, Arabinoxylan, Resistant Starch
Participants will complete 4 cycles. For each cycle they will take 20g per day fiber supplement for 3 weeks, followed by a washout period of at least 6-8 weeks. In this arm, participants will take the fiber supplements in the following order: Inulin, Beta-Glucan, Arabinoxylan, Resistant Starch.
Dietary supplement: Fiber cycles ARM 22

Participants will complete 4 cycles. For each cycle, they will take 20g per day fiber supplement for 3 weeks, followed by a washout period of at least 6-8 weeks.

On cycle 1, they will take 20g per day of Inulin. On cycle 2, they will take 20g per day of Beta-Glucan. On cycle 3, they will take 20g per day of Arabinoxylan. On cycle 4, they will take 20g per day of Resistant Starch.
Experimental: ARM 23: Inulin, Arabinoxylan, Beta-Glucan, Resistant Starch
Participants will complete 4 cycles. For each cycle they will take 20g per day fiber supplement for 3 weeks, followed by a washout period of at least 6-8 weeks. In this arm, participants will take the fiber supplements in the following order: Inulin, Arabinoxylan, Beta-Glucan, Resistant Starch.
Dietary supplement: Fiber cycles ARM 23

Participants will complete 4 cycles. For each cycle, they will take 20g per day fiber supplement for 3 weeks, followed by a washout period of at least 6-8 weeks.

On cycle 1, they will take 20g per day of Inulin. On cycle 2, they will take 20g per day of Arabinoxylan. On cycle 3, they will take 20g per day of Beta-Glucan. On cycle 4, they will take 20g per day of Resistant Starch.
Experimental: ARM 24: Inulin, Arabinoxylan, Resistant Starch, Beta-Glucan
Participants will complete 4 cycles. For each cycle they will take 20g per day fiber supplement for 3 weeks, followed by a washout period of at least 6-8 weeks. In this arm, participants will take the fiber supplements in the following order: Inulin, Arabinoxylan, Resistant Starch, Beta-Glucan.
Dietary supplement: Fiber cycles ARM 24

Participants will complete 4 cycles. For each cycle, they will take 20g per day fiber supplement for 3 weeks, followed by a washout period of at least 6-8 weeks.

On cycle 1, they will take 20g per day of Inulin. On cycle 2, they will take 20g per day of Arabinoxylan. On cycle 3, they will take 20g per day of Resistant Starch. On cycle 4, they will take 20g per day of Beta-Glucan.

What is the study measuring?

Primary Outcome Measures

Outcome Measure
Measure Description
Time Frame
Mapping of microbiota changes in response to prebiotic intervention
Time Frame: 3 years

A detailed map of microbes and microbial gene expression changes during the intervention will be developed.

Microbiota complexity in fecal samples will be determined by shotgun metagenomic sequencing. Novel microbes and gene pathways will be identified by de novo assemble of whole fecal metagenomes.
3 years
Comprehensive phenotyping of host profile during prebiotic intervention
Time Frame: 4 years

Changes in host (human) phenotypic profile during the prebiotic intervention will be determined.

Profile will include the metagenome, transcriptome, metabolome and cytokines of participants during the prebiotic intervention.
4 years
Biological signatures identified from the integration of microbiome-host omes
Time Frame: 4 years
Biological signatures will be developed from the integration of the omics data with microbial metabolite levels.
4 years

Collaborators and Investigators

This is where you will find people and organizations involved with this study.

Sponsor

Stanford University

Collaborators

National Center for Complementary and Integrative Health (NCCIH)

Investigators

  • Principal Investigator: Michael P Snyder, PhD, Stanford University

Study record dates

These dates track the progress of study record and summary results submissions to ClinicalTrials.gov. Study records and reported results are reviewed by the National Library of Medicine (NLM) to make sure they meet specific quality control standards before being posted on the public website.

Study Major Dates

Study Start (Actual)

January 21, 2020

Primary Completion (Estimated)

August 31, 2025

Study Completion (Estimated)

August 31, 2025

Study Registration Dates

First Submitted

December 20, 2018

First Submitted That Met QC Criteria

April 23, 2019

First Posted (Actual)

April 24, 2019

Study Record Updates

Last Update Posted (Actual)

March 26, 2025

Last Update Submitted That Met QC Criteria

March 22, 2025

Last Verified

April 1, 2024

More Information

Terms related to this study

Other Study ID Numbers

  • 23602
  • 5R01AT010232 (U.S. NIH Grant/Contract)

Plan for Individual participant data (IPD)

Plan to Share Individual Participant Data (IPD)?

NO

Drug and device information, study documents

Studies a U.S. FDA-regulated drug product

No

Studies a U.S. FDA-regulated device product

No

This information was retrieved directly from the website clinicaltrials.gov without any changes. If you have any requests to change, remove or update your study details, please contact register@clinicaltrials.gov. As soon as a change is implemented on clinicaltrials.gov, this will be updated automatically on our website as well.

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