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

Not Applicable

Completed

• Conditions: Prebiotics

• Registration Number: NCT04706858
• Lead Sponsor: Stanford University

Brief Summary

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.

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 Timeline

• Study Start: 2014-10-15
• Primary Completion: 2017-08-11
• Study Completion: 2017-08-11
• Study First Submitted: 2020-12-03
• Status Verified: 2021-01
• Study First Submitted QC: 2021-01-09
• Last Update Submitted: 2021-01-09
• Study First Posted: 2021-01-13
• Last Update Posted: 2021-01-13

Recruitment & Eligibility

• Status: COMPLETED
• Sex: All
• Target Recruitment: 18

Inclusion Criteria

• Good general health

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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

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Study & Design

• Study Type: INTERVENTIONAL
• Study Design: SEQUENTIAL

Primary Outcome Measures

Name	Time	Method
Mapping of microbiota changes in response to prebiotic intervention	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.
Lipid profile changes in response to prebiotic intervention	3 years	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.

Secondary Outcome Measures

Name	Time	Method
Comprehensive cytokine profile during prebiotic intervention	3 years	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.
Comprehensive transcriptome profile during prebiotic intervention	3 years	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).
Comprehensive metabolome profile during prebiotic intervention	3 years	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.
Comprehensive metagenome profile during prebiotic intervention	3 years	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.

Trial Locations

Locations (1)

Stanford University; 🇺🇸 Stanford, California, United States