Gut Microbiome-Metabolome Profiling in H. Pylori-SIBO Comorbidity

March 21, 2026 updated by: Yucheng Zhu, Zhongshan Hospital (Xiamen), Fudan University

Characterization of Gut Microbiota and Metabolic Profiles in Patients With Helicobacter Pylori Infection and Small Intestinal Bacterial Overgrowth Based on Metagenomic and Metabolomic Analyses

Patients with concurrent Helicobacter pylori infection and small intestinal bacterial overgrowth (SIBO) represent a clinically challenging subgroup, often experiencing refractory gastrointestinal symptoms and diminished treatment responses. Current evidence indicates that individuals infected with H. pylori may related SIBO as a comorbidity; however, the synergistic effects of these conditions on gut ecosystem homeostasis remain poorly understood. To address this knowledge gap, we employed a dual-omics approach that combined shotgun metagenomic sequencing with liquid chromatography-mass spectrometry (LC-MS) metabolomic profiling. This methodology allowed for a comprehensive mapping of microbial community structures, including species-level taxonomy and functional pathways, as well as host-microbiota co-metabolism signatures in fecal samples.

Study Overview

Status

Completed

Conditions

Intervention / Treatment

Detailed Description

Patients presenting with concurrent Helicobacter pylori infection and small intestinal bacterial overgrowth (SIBO) constitute a clinically challenging subgroup characterized by refractory gastrointestinal symptoms and diminished responses to standard therapeutic interventions. Current evidence supports an association between H. pylori infection and an increased prevalence of SIBO as a comorbidity. However, the synergistic effects of these two conditions on the fundamental mechanisms governing gut ecosystem homeostasis - particularly concerning microbial community dynamics, functional metabolic output, and host-microbial interactions - remain poorly understood, representing a significant knowledge gap.

To systematically address this gap and elucidate the complex interplay, we implemented an integrated dual-omics analytical approach. This methodology combined shotgun metagenomic sequencing of fecal samples with liquid chromatography-mass spectrometry (LC-MS) metabolomic profiling. This powerful combination enables a comprehensive mapping of the gut ecosystem by simultaneously characterizing: Host-Microbiota Co-Metabolism Signatures: Revealing the metabolic landscape through the detection and quantification of metabolites derived from microbial activity, host metabolism, and crucially, their interactions (co-metabolism) within the fecal metabolome.

This multimodal strategy offers an unprecedented, holistic view of the perturbations induced by the co-occurrence of H. pylori infection and SIBO, moving beyond singular aspects to capture the integrated functional and compositional state of the gut ecosystem.

Study Type

Observational

Enrollment (Actual)

42

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

  • China
    • Fujian
      • Xiamen, Fujian, China, 361015
        • Zhongshan Hospital (Xiamen), Fudan 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

  • Adult
  • Older Adult

Accepts Healthy Volunteers

No

Sampling Method

Probability Sample

Study Population

A prospective observational cohort of adult patients (aged 18-65 years) with concomitant Helicobacter pylori infection and small intestinal bacterial overgrowth (SIBO) was enrolled at Zhongshan Hospital (Xiamen), Fudan University.

Description

Inclusion Criteria:

  • Age from 18 to 65 years;
  • All enrolled patients underwent both the 13C-urea breath test (13C-UBT) and hydrogen-methane breath test (HMBT).

Exclusion Criteria:

  • Coexistence of significant concomitant illnesses, including heart disease, renal failure, hepatic disease, previous abdominal surgery, lactation, or pregnancy;
  • Patients who had used probiotics and antibiotics in the past 12 weeks;
  • Unwillingness to participate in this study.

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

Cohorts and Interventions

Group / Cohort
Intervention / Treatment
Group A
H. pylori-positive and SIBO-positive group
Diagnostic test: 13C-Urea Breath Test
Participants underwent the 13C-urea breath test following a standardized protocol to detect active Helicobacter pylori (H. pylori) infection. After an overnight fast (≥8 hours), baseline breath samples were collected by exhaling gently through a straw. Participants then ingested 75 mg of 13C-labeled urea dissolved in 50 mL of citric acid solution to delay gastric emptying and maximize urease exposure. A second breath sample was collected 30 minutes post-ingestion using identical procedures.
Diagnostic test: Hydrogen-Methane Breath Test
Participants underwent a standardized hydrogen-methane breath test to evaluate for small intestinal bacterial overgrowth (SIBO) or carbohydrate malabsorption. After a 12-hour overnight fast, baseline breath samples were collected via controlled end-expiratory exhalation. Participants then ingested a substrate solution.
Group B
H. pylori-negative and SIBO-positive group
Diagnostic test: 13C-Urea Breath Test
Participants underwent the 13C-urea breath test following a standardized protocol to detect active Helicobacter pylori (H. pylori) infection. After an overnight fast (≥8 hours), baseline breath samples were collected by exhaling gently through a straw. Participants then ingested 75 mg of 13C-labeled urea dissolved in 50 mL of citric acid solution to delay gastric emptying and maximize urease exposure. A second breath sample was collected 30 minutes post-ingestion using identical procedures.
Diagnostic test: Hydrogen-Methane Breath Test
Participants underwent a standardized hydrogen-methane breath test to evaluate for small intestinal bacterial overgrowth (SIBO) or carbohydrate malabsorption. After a 12-hour overnight fast, baseline breath samples were collected via controlled end-expiratory exhalation. Participants then ingested a substrate solution.
Group C
H. pylori-positive and SIBO-negative group
Diagnostic test: 13C-Urea Breath Test
Participants underwent the 13C-urea breath test following a standardized protocol to detect active Helicobacter pylori (H. pylori) infection. After an overnight fast (≥8 hours), baseline breath samples were collected by exhaling gently through a straw. Participants then ingested 75 mg of 13C-labeled urea dissolved in 50 mL of citric acid solution to delay gastric emptying and maximize urease exposure. A second breath sample was collected 30 minutes post-ingestion using identical procedures.
Diagnostic test: Hydrogen-Methane Breath Test
Participants underwent a standardized hydrogen-methane breath test to evaluate for small intestinal bacterial overgrowth (SIBO) or carbohydrate malabsorption. After a 12-hour overnight fast, baseline breath samples were collected via controlled end-expiratory exhalation. Participants then ingested a substrate solution.
Group D
H. pylori-negative and SIBO-negative group
Diagnostic test: 13C-Urea Breath Test
Participants underwent the 13C-urea breath test following a standardized protocol to detect active Helicobacter pylori (H. pylori) infection. After an overnight fast (≥8 hours), baseline breath samples were collected by exhaling gently through a straw. Participants then ingested 75 mg of 13C-labeled urea dissolved in 50 mL of citric acid solution to delay gastric emptying and maximize urease exposure. A second breath sample was collected 30 minutes post-ingestion using identical procedures.
Diagnostic test: Hydrogen-Methane Breath Test
Participants underwent a standardized hydrogen-methane breath test to evaluate for small intestinal bacterial overgrowth (SIBO) or carbohydrate malabsorption. After a 12-hour overnight fast, baseline breath samples were collected via controlled end-expiratory exhalation. Participants then ingested a substrate solution.

What is the study measuring?

Primary Outcome Measures

Outcome Measure
Measure Description
Time Frame
13C-Urea Breath Test
Time Frame: day 0, Patient baseline levels at enrollment
The 13C-Urea Breath Test (13C-UBT) is a non-invasive, highly specific diagnostic assay used to detect active Helicobacter pylori (H. pylori) infection in the gastric mucosa. It leverages the bacterium's unique enzymatic activity-urease production-to metabolize ingested labeled urea, resulting in measurable changes in exhaled breath CO₂ isotopic composition.
day 0, Patient baseline levels at enrollment
Hydrogen-Methane Breath Test
Time Frame: day 0, Patient baseline levels at enrollment
The Hydrogen-Methane Breath Test (HMBT) is a non-invasive, gold-standard diagnostic tool for detecting small intestinal bacterial overgrowth (SIBO) and carbohydrate malabsorption disorders . It quantifies microbial fermentation activity in the gut by measuring gaseous metabolic end-products (H₂ and CH₄) in exhaled breath following substrate administration.
day 0, Patient baseline levels at enrollment

Collaborators and Investigators

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

Sponsor

Zhongshan Hospital (Xiamen), Fudan University

Investigators

  • Study Director: Wei Jiang, M.D., Zhongshan Hospital (Xiamen), Fudan University

Publications and helpful links

The person responsible for entering information about the study voluntarily provides these publications. These may be about anything related to the study.

General Publications

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 31, 2024

Primary Completion (Actual)

December 30, 2024

Study Completion (Actual)

February 28, 2025

Study Registration Dates

First Submitted

August 6, 2025

First Submitted That Met QC Criteria

August 12, 2025

First Posted (Actual)

August 14, 2025

Study Record Updates

Last Update Posted (Actual)

March 25, 2026

Last Update Submitted That Met QC Criteria

March 21, 2026

Last Verified

March 1, 2026

More Information

Terms related to this study

Additional Relevant MeSH Terms

Other Study ID Numbers

  • ZYC-SIBO2025

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.

Clinical Trials on Helicobacter Pylori Infection

Clinical Trials on 13C-Urea Breath Test

Search Similar Trials

Sponsors and Collaborators

Medical Conditions

Drug Interventions

CROs by country

CROs in India

Conditions

Rare Diseases

Drug Interventions

Dietary Supplements

Sponsor/Collaborators

Locations

Subscribe