Integrative Personal Omics Profiling for Dynamic Molecular Phenotypes Monitoring During Fiber Supplementation

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.

Study Overview

• Status: Completed
• Conditions: Prebiotics
• Intervention / Treatment: Dietary supplement: Dietary fiber supplementation

Detailed Description

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. 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 (Actual): 18
• Phase: Not Applicable

Contacts and Locations

Study Locations

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

Participation Criteria

Eligibility Criteria

• Ages Eligible for Study: 18 years to 65 years (Adult, Older Adult)
• Accepts Healthy Volunteers: Yes
• Genders Eligible for Study: All

Description

Inclusion Criteria:

• Good general health

Exclusion Criteria:

• Fasting Blood Sugar >126 mg/dL
• Triglycerides >400 mg/dL
• Uncontrolled hypertension
• Vascular disease
• Chronic inflammatory conditions
• Major organ disease
• Heavy alcohol use
• Pregnancy/lactation
• Prior bariatric surgery
• Active psychiatric disease
• Use of medication known to affect carbohydrate or lipid metabolism
• Active eating disorder

Study Plan

How is the study designed?

Design Details

• Primary Purpose: Basic Science
• Allocation: N/A
• Interventional Model: Sequential Assignment
• Masking: Single

What is the study measuring?

Primary Outcome Measures

Outcome Measure	Measure Description	Time Frame
Mapping of microbiota changes in response to prebiotic intervention	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
Lipid profile changes in response to prebiotic intervention	Analysis of changes in the the lipid profile of participants on the prebiotic intervention. Measured lipids in mg/dL include total cholesterol, LDL cholesterol, HDL cholesterol, and triglycerides.	3 years

Secondary Outcome Measures

Outcome Measure	Measure Description	Time Frame
Comprehensive metagenome profile during prebiotic intervention	Changes in host (human) metagenome profile during the prebiotic intervention will be determined. Stool DNA Sequences are analyzed using the Humann2 and Metaphlan pipelines to generate pathway coverage values, gene families abundances, and taxa abundances {Franzosa, 2018}. These are mapped to the Human Microbiome Project database for alignment.	3 years
Comprehensive transcriptome profile during prebiotic intervention	Changes in host (human) transcriptome profile during the prebiotic intervention will be determined. RNA isolated from PBMC samples reads are aligned to hg38 using the program Spliced Transcripts Alignment to a Reference (STAR). Transcript abundance is calculated using RNA-Seq by Expectation Maximization (RSEM). Normalization of transcript frequency and pairwise statistics measuring differences in transcript frequency between time points are calculated using the software package for R from Bioconductor (DESeq2).	3 years
Comprehensive metabolome profile during prebiotic intervention	Changes in host (human) metabolome profile during the prebiotic intervention will be determined. Plasma metabolites are run in mass spectrometers columns (HILIC and RPLC separation in both positive and negative ionization modes). MetID and our MS/MS data are used to identify 12740 metabolites with confidence levels ranging from 1-3, where 1 matches MS/MS, retention time and m/z from standards on our platform, 2 has MS/MS and m/z matches from a database, and 3 matches the m/z of a database.	3 years
Comprehensive cytokine profile during prebiotic intervention	Changes in host (human) cytokine profile during the prebiotic intervention will be determined. Cytokines are profiled using a Luminex xMAP cytokine profiling system at the Stanford Human Immune Monitoring Center. This involves attaching antibodies specific to cytokines to beads using a capture molecule. The fluorescent molecules are attached to the cytokines, and fluorescence is used as the measure of cytokine abundance.	3 years

Collaborators and Investigators

• Sponsor: Stanford University

Study record dates

Study Major Dates

• Study Start (Actual): October 15, 2014
• Primary Completion (Actual): August 11, 2017
• Study Completion (Actual): August 11, 2017

Study Registration Dates

• First Submitted: December 3, 2020
• First Submitted That Met QC Criteria: January 9, 2021
• First Posted (Actual): January 13, 2021

Study Record Updates

• Last Update Posted (Actual): January 13, 2021
• Last Update Submitted That Met QC Criteria: January 9, 2021
• Last Verified: January 1, 2021

More Information

Terms related to this study

• Other Study ID Numbers: 1636

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