High-Resolution Measurements of Diet-Microbiome Interactions

First-Principles Mapping of Regional Fermentation Physiology in the Human Intestine With Ingestible Capsules

The goal of this clinical trial is to characterize regional intestinal fermentation physiology and determine how the response to fermentable dietary fiber differs between healthy individuals and individuals with irritable bowel syndrome (IBS). The study will use ingestible capsule technologies to directly measure intestinal gases and regional microbiome composition following low-fiber and high-fiber meal challenges.

The main questions it aims to answer are:

Does the change in regional intestinal gas levels following a fermentable-fiber challenge differ between participants with IBS and healthy controls? How are regional intestinal gas dynamics associated with microbiome composition, breath gases, serum short-chain fatty acids, glucose dynamics, metabolites, and gastrointestinal symptoms?

Researchers will compare participants with IBS to healthy controls to determine whether intestinal fermentation responses to dietary fiber differ between these populations.

Participants will:

Complete two study visits approximately one week apart. At one visit, participants will receive a low-fiber control meal, and at the other visit, they will receive the same base meal containing 15 g of inulin. The order of the two meals will be assigned at random.

Swallow an Atmo gas-sensing capsule to measure intestinal H2, CO2, and O2 and a CapScan capsule to collect regional intestinal fluid for microbiome analysis.

Undergo serial blood and breath sampling and gastrointestinal symptom assessments during each 8-hour study visit.

Complete stool and urine collections, dietary assessment, and continuous glucose monitoring before and/or after the study visits.

Study Overview

• Status: Not yet recruiting
• Conditions: IBS (Irritable Bowel Syndrome)
• Intervention / Treatment: Dietary supplement: Inulin; Other: Low-fiber control breakfast shake; Device: Atmo Gas-Sensing Capsule; Device: CapScan Regional Fluid-Sampling Capsule

Detailed Description

Irritable Bowel Syndrome (IBS) affects an estimated 25-45 million people in the United States, accounts for roughly 20-40% of gastroenterology visits, and imposes a major societal burden, with annual U.S. costs estimated at approximately $1.7-$10 billion in direct medical spending and approximately $20 billion in indirect costs from lost productivity (Hulisz 2004; Leong et al. 2003; Canavan et al. 2014). Despite this burden, IBS remains poorly understood, and no validated biochemical diagnostic or curative therapy currently exists (Lacy et al. 2021; Kim et al. 2017).

In most individuals, a high-fiber diet supports a healthy microbiome and improves health outcomes without adverse symptoms (Fu et al. 2022). In patients with IBS, however, fermentable fiber is known to worsen symptoms such as bloating, flatulence, and abdominal pain; patients are often advised to restrict fermentable fiber intake (e.g., a low-FODMAP diet), and antibiotics are sometimes used therapeutically to suppress fermentation (Halmos et al. 2014; Lacy et al. 2021). These clinical observations motivate the mechanistic hypothesis underlying this protocol: that IBS symptoms may arise, at least in part, from disordered microbial fermentation and impaired intestinal gas handling.

Progress toward this goal has been limited by the absence of direct clinical tools capable of quantifying fermentation physiology in vivo and by intestinal region. Current clinical testing (e.g., hydrogen/methane breath testing) provides only an indirect, systemic proxy for fermentation and remains variably standardized (Rezaie et al. 2017; Pitcher et al. 2022).

The human intestine is more than 30 feet in length and is home to regionally distinct microbial communities that closely track local gut physiology (Martinez-Guryn et al. 2019). Recently developed non-invasive capsule-based microbiome sampling has shown that the small intestine and proximal colon harbor communities that are distinct from stool and disproportionately altered in IBS (Shalon et al. 2023; Leite et al. 2020; Chung et al. 2016).

This protocol leverages two complementary ingestible capsule technologies - a real-time gas-sensing capsule (Atmo) and a regional fluid/microbiome-sampling capsule (CapScan) - together with stool, urine, breath, and blood-based measurements, to establish regional gas production and consumption profiles in healthy individuals and patients with IBS.

The Healthy and IBS cohorts are defined by baseline clinical status and are not randomized. Within each cohort, participants undergo a randomized two-period crossover of meal order. Each participant receives both the low-fiber control meal and the 15 g inulin meal, with the order assigned at random.

• Study Type: Interventional
• Enrollment (Estimated): 40
• Phase: Not Applicable

Contacts and Locations

• Study Contact: Name: Roujheen Sabetan, MPH; Phone Number: 925-963-7021; Email: rsabetan@stanford.edu
• Study Contact Backup: Name: Jacob T Hizon, BS; Phone Number: 619-874-4562; Email: jthizon@stanford.edu

Study Locations

• United States
  • California
    • Stanford, California, United States, 94305
      • Stanford University
      • Contact: Sean P Spencer, MD, PhD; Phone Number: 608-469-5076; Email: seanspen@stanford.edu

Participation Criteria

Eligibility Criteria

• Ages Eligible for Study: 18 years to 75 years (Adult, Older Adult)
• Accepts Healthy Volunteers: Yes
• Genders Eligible for Study: All

Description

Inclusion Criteria:

1. Age 18-75 years.
2. Able to provide written informed consent.
3. Able and willing to swallow capsules and complete all study procedures.
4. For the Healthy cohort: no history of a diagnosed chronic GI disorder and no ongoing GI symptoms warranting clinical evaluation.
5. For the IBS cohort: meets Rome IV diagnostic criteria for IBS, with a prior clinical hydrogen/methane breath test on record sufficient to assign a breath-test subtype.
6. Willing and able to complete a virtual (Zoom) screening visit and two in-clinic study visits approximately one week apart.

Exclusion Criteria:

1. Known or suspected gastrointestinal stricture or physiological/mechanical gastrointestinal obstruction.
2. Gastrointestinal fistula.
3. Dysphagia or other swallowing disorder affecting the ability to swallow food, pills, or capsules.
4. Gastrointestinal surgery within the past 3 months.
5. Prior gastrointestinal surgery that alters luminal anatomy (e.g., bowel resection or bariatric surgery).
6. Diverticulitis.
7. Gastric bezoar.
8. Radiation enteritis.
9. Pacemaker or other implanted or portable electromechanical medical device.
10. Pregnancy or breastfeeding.
11. BMI ≥40 kg/m².
12. Use of antibiotics, probiotics, or prebiotics within 4 weeks prior to enrollment.
13. Use of proton-pump inhibitors (e.g., omeprazole, lansoprazole, esomeprazole [Nexium®]) within 7 days prior to the study procedure.
14. Use of histamine blockers, motility-altering medications, narcotic analgesics, or anticholinergic medications within 3 days prior to the study procedure.
15. Use of antiemetics/5-HT3 antagonists, macrolide antibiotics, or 5-HT4-modulating medications within 2 days prior to the study procedure.
16. Use of antacids (e.g., Gaviscon®, Mylanta®, TUMS) within 1 day prior to the study procedure.
17. Diabetes or use of medications affecting glucose handling.
18. Known allergy or intolerance to inulin or other study meal components.
19. Current participation in another interventional study.

Study Plan

How is the study designed?

Design Details

• Primary Purpose: Basic Science
• Allocation: Randomized
• Interventional Model: Crossover Assignment
• Masking: Double

Number of Arms

2

Arms and Interventions

Participant Group / Arm	Intervention / Treatment
Experimental: Healthy controls; The Healthy cohort consists of individuals without a diagnosed chronic gastrointestinal disorder or ongoing gastrointestinal symptoms warranting clinical evaluation. Participants complete two study visits approximately one week apart and receive both meal conditions in randomized order: low-fiber control followed by 15 g of inulin, or 15 g of inulin followed by low-fiber control. At each visit, participants consume the assigned standardized breakfast shake with the Atmo gas-sensing capsule at t=0 and ingest the CapScan regional sampling capsule at t=4 hours.	Dietary supplement: Inulin; Participants consume a standardized breakfast shake containing 15 g of inulin at one of the two study visits, according to the randomized meal sequence. At the other visit, they consume the same base shake without added inulin as the low-fiber control. Visits occur approximately one week apart.; Other: Low-fiber control breakfast shake; Participants consume the standardized low-fiber base breakfast shake without added inulin at one of the two study visits, according to the randomized meal sequence. This condition serves as the within-participant control. Visits occur approximately one week apart.; Device: Atmo Gas-Sensing Capsule; At each of the two study visits, participants will swallow one Atmo gas-sensing capsule with the assigned standardized breakfast shake at t=0. As it transits the gastrointestinal tract, the wireless capsule records regional luminal hydrogen (H2), carbon dioxide (CO2), oxygen-related signals, temperature, and transit-related data. Data are transmitted by radiofrequency to a wearable receiver for analysis. Capsule passage will be monitored after each visit.; Other Names: Atmo Gas Capsule System; Device: CapScan Regional Fluid-Sampling Capsule; At each of the two study visits, participants will swallow one CapScan capsule at t=4 hours. CapScan is a single-use, passive ingestible device that collects regional gastrointestinal luminal fluid as it transits the intestine. The collected samples will be used for ex vivo microbiome and multiomic analyses. The device passes in the stool and is retrieved by the participant using the provided retrieval materials for subsequent processing.; Other Names: CapScan; Envivo Bio Collection Device
Experimental: Irritable Bowel Syndrome (IBS); The IBS cohort consists of individuals who meet Rome IV diagnostic criteria for irritable bowel syndrome. Participants complete two study visits approximately one week apart and receive both meal conditions in randomized order: low-fiber control followed by 15 g of inulin, or 15 g of inulin followed by low-fiber control. At each visit, participants consume the assigned standardized breakfast shake with the Atmo gas-sensing capsule at t=0 and ingest the CapScan regional sampling capsule at t=4 hours.	Dietary supplement: Inulin; Participants consume a standardized breakfast shake containing 15 g of inulin at one of the two study visits, according to the randomized meal sequence. At the other visit, they consume the same base shake without added inulin as the low-fiber control. Visits occur approximately one week apart.; Other: Low-fiber control breakfast shake; Participants consume the standardized low-fiber base breakfast shake without added inulin at one of the two study visits, according to the randomized meal sequence. This condition serves as the within-participant control. Visits occur approximately one week apart.; Device: Atmo Gas-Sensing Capsule; At each of the two study visits, participants will swallow one Atmo gas-sensing capsule with the assigned standardized breakfast shake at t=0. As it transits the gastrointestinal tract, the wireless capsule records regional luminal hydrogen (H2), carbon dioxide (CO2), oxygen-related signals, temperature, and transit-related data. Data are transmitted by radiofrequency to a wearable receiver for analysis. Capsule passage will be monitored after each visit.; Other Names: Atmo Gas Capsule System; Device: CapScan Regional Fluid-Sampling Capsule; At each of the two study visits, participants will swallow one CapScan capsule at t=4 hours. CapScan is a single-use, passive ingestible device that collects regional gastrointestinal luminal fluid as it transits the intestine. The collected samples will be used for ex vivo microbiome and multiomic analyses. The device passes in the stool and is retrieved by the participant using the provided retrieval materials for subsequent processing.; Other Names: CapScan; Envivo Bio Collection Device

What is the study measuring?

Primary Outcome Measures

Outcome Measure	Measure Description	Time Frame
Successful Acquisition of a Complete Regional Multiomic Fermentation-Physiology Dataset	To successfully obtain a complete regional multiomic fermentation-physiology dataset - defined as paired Atmo gas capsule data (H2, CO2, O2), CapScan regional microbiome/fluid sampling, stool microbiome sequencing, and breath testing (H2, CH4, H2S) with serum SCFA measurements - from at least 30 of the 40 enrolled participants (15 healthy, 15 IBS), across both study visits. Primary outcome measure: the number and proportion of enrolled participants from whom a complete multiomic dataset is successfully obtained across both study visits.	up to 12 months

Secondary Outcome Measures

Outcome Measure	Measure Description	Time Frame
Change in Regional Intestinal Gas Concentrations Following Inulin Challenge	Regional hydrogen (H2), carbon dioxide (CO2), and oxygen (O2) concentration-time profiles will be measured using the Atmo gas-sensing capsule. Changes in gas concentrations between the low-fiber control visit and the 15 g inulin visit will be compared within participants and between healthy and IBS groups, including regional differences between the small intestine and colon.	Through completion of both study visits, 2 week
Regional Intestinal Microbiome Composition Following Dietary Fiber Challenge	Microbial composition will be characterized from regional intestinal fluid samples collected using the CapScan capsule and from stool samples. Microbiome profiles will be evaluated across intestinal regions and compared between the low-fiber and inulin visits and between healthy and IBS participants.	Through completion of sample collection, up to 72 hours after each study visit
Change in Breath H2, CH4, and H2S Concentrations Following Inulin Challenge	Breath hydrogen (H2), methane (CH4), and hydrogen sulfide (H2S) concentrations will be measured every 30 minutes during each 8-hour study visit. Concentration-time profiles will be compared between the low-fiber and inulin visits and between healthy and IBS participants.	8 hours during each study visit
Change in Serum Short-Chain Fatty Acid Concentrations Following Inulin Challenge	Serum short-chain fatty acid (SCFA) concentrations will be measured from serial blood samples collected every 30 minutes during each 8-hour study visit. SCFA concentration-time profiles will be compared between the low-fiber and inulin visits and between healthy and IBS participants.	8 hours during each study visit
Change in Gastrointestinal Symptom Severity Following Inulin Challenge	Participant-reported gastrointestinal symptoms, including bloating/distention, abdominal pain/cramping, flatulence, nausea, and urgency, will be assessed throughout each study visit. Symptom trajectories will be compared between the low-fiber and inulin visits and between healthy and IBS participants.	8 hours during study visit
Glucose Response Following Dietary Fiber Challenge	Continuous glucose monitor (CGM)-derived glucose profiles will be evaluated following the low-fiber and inulin meal challenges. Glucose responses will be compared within participants across study visits and between healthy and IBS groups.	Through CGM monitoring throughout 2 weeks including both study visits.
Atmo Capsule Gastrointestinal Transit Time	Quantify the gastrointestinal transit time of the Atmo capsule after participant ingestion.	From capsule ingestion through passage, confirmation up to 72 hours after clinic visit.

Collaborators and Investigators

• Sponsor: Stanford University
• Investigators: Study Director: Michael Fischbach, PhD, Stanford University; Principal Investigator: Sean P Spencer, MD PhD, Stanford University; Study Director: Benjamin Good, PhD, Stanford University; Study Director: Jonas Cremer, PhD, Stanford University

Study record dates

Study Major Dates

• Study Start (Estimated): October 1, 2026
• Primary Completion (Estimated): October 1, 2028
• Study Completion (Estimated): December 1, 2028

Study Registration Dates

• First Submitted: September 28, 2026
• First Submitted That Met QC Criteria: September 28, 2026
• First Posted (Actual): October 5, 2026

Study Record Updates

• Last Update Posted (Actual): October 5, 2026
• Last Update Submitted That Met QC Criteria: September 28, 2026
• Last Verified: September 1, 2026

More Information

Terms related to this study

• Keywords: Irritable Bowel Syndrome; IBS; Dietary Fiber; Inulin; Intestinal Microbiome; Intestinal Fermentation; Regional Microbiome
• Additional Relevant MeSH Terms: Intestinal Diseases; Digestive System Diseases; Gastrointestinal Diseases; Colonic Diseases; Colonic Diseases, Functional; Irritable Bowel Syndrome; Therapeutics; Drug Therapy; Dietary Carbohydrates; Carbohydrates; Polymers; Macromolecular Substances; Polysaccharides; Starch; Glucans; Biopolymers; Fructans; Drug Delivery Systems; Inulin
• Other Study ID Numbers: 87591

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: Yes
• product manufactured in and exported from the U.S.: No