SH-DS01 on Fecal Metagenomic Stability

January 29, 2026 updated by: Judy Nee, Beth Israel Deaconess Medical Center

A Randomized, Double Blind, Placebo-controlled Study to Evaluate the Impact of a Multi-strain Synbiotic on Fecal Metagenomic Stability, Gut Barrier Integrity, and Metabolic Output of the Gut Microbiota

This is a randomized, double blind, Phase 1 study. There will be a 12-week comparison of the safety of DS-01 versus placebo with a secondary outcome measure of the efficacy in a cohort of 100 men or women with IBS with constipation. 50 IBS-C or IBS-M patients will receive DS-01 (Daily Synbiotic, once daily) for 12 weeks, while 50 IBS-C or IBS-M patients will receive the placebo (once daily). Safety is a paramount concern in the study design and will be monitored carefully throughout the study. Study subjects will also receive extensive education on use of the synbiotic.

Study Overview

Status

Status

Indicates the current recruitment status or the expanded access status.
Completed

Conditions

Conditions

The disease, disorder, syndrome, illness, or injury that is being studied. On ClinicalTrials.gov, conditions may also include other health-related issues, such as lifespan, quality of life, and health risks.

Intervention / Treatment

Intervention / Treatment

A process or action that is the focus of a clinical study. Interventions include drugs, medical devices, procedures, vaccines, and other products that are either investigational or already available. Interventions can also include noninvasive approaches, such as education or modifying diet and exercise.

Detailed Description

Irritable bowel syndrome (IBS) is a chronic functional gastrointestinal disorder that generates a significant health care burden and is the most commonly diagnosed gastrointestinal condition. Nearly 12% of all patients in the United States seek medical care in primary care practice for IBS and it accounts for 3.1 million ambulatory care visits and 5.9 million prescriptions annually.

The pathophysiology of IBS is distinctly broad compared to other gastrointestinal conditions and includes abnormalities involving motility, visceral sensation, brain-gut interaction, and distress. Though patients with IBS often have a heterogeneous symptom profile, the predominant theme is the presence of abdominal pain or discomfort that is usually relieved by defecation. Host factors such as genetics, immune function, and psychological status, as well as environmental factors such as stress, recent infection, or treatment with antibiotics, could predispose to the development of chronic IBS symptoms. Due to a myriad of contributing factors, a single cause of IBS remains enigmatic. Despite the urgent need to develop better therapies, the high range of placebo response has made clinical trials challenging, ranging from 16.0 to 71.4% with a population-weighted average of 40.2%.

Recent studies have also shown alterations in gut immune response, and a disrupted intestinal and colonic microbiome in association with IBS. The current working hypothesis is that abnormal microbiota activate mucosal innate immune responses, which increase epithelial permeability, activate nociceptive sensory pathways, and dysregulate the enteric nervous system. Targeting the microbiota and gastrointestinal tract with live organisms is a promising approach, yet previous trials have yielded limited success due to empiric strain selection, small population size, and inadequate trial design to control for a high placebo response.

This protocol aims to assess the impact of a multi-strain consortia of 24 commensal organisms across 12 species with extensive strain-specific in vivo data, assessing a range of gastrointestinal symptoms without negatively altering the naive gut microbiota. High-throughput shotgun DNA sequencing will provide opportunity for '-omics'-based analyses of the gut microbiota, which can be augmented by the metabolite profiles resulting from total microbial activity in the gut. Since many of these metabolites are bioeffector molecules acting upon the host, such analysis can provide a direct measure of the consequences of microbial activity in the gut and provide a novel integrated data set for patients with IBS. Recruited subjects will also use a smart-phone application to report day to day gastrointestinal symptoms, a patient-centric hallmark of this chronic gut condition.

Probiotics are live microorganisms with a vast array of therapeutic potential for gastrointestinal disease. Several probiotics strains have shown beneficial outcomes in constipation-predominant IBS (IBS-C) patients, especially as an adjunct to conventional treatment. However, a number of controversial issues regarding the roles of probiotics in pathogenesis of IBS-C remain to be clarified, including precise mechanism of action.

This protocol aims to assess the impact of a mix of 24-beneficial strains on individual subjects with IBS-C or IBS-M.

Study Type

Study Type

Describes the nature of a clinical study. Study types include interventional studies (also called clinical trials), observational studies (including patient registries), and expanded access.
Interventional

Enrollment (Actual)

Enrollment

The number of participants in a clinical study. The "anticipated" enrollment is the target number of participants that the researchers need for the study.
48

Phase

Phase

The stage of a clinical trial studying a drug or biological product, based on definitions developed by the U.S. Food and Drug Administration (FDA). The phase is based on the study's objective, the number of participants, and other characteristics. There are five phases: Early Phase 1 (formerly listed as Phase 0), Phase 1, Phase 2, Phase 3, and Phase 4. Not Applicable is used to describe trials without FDA-defined phases, including trials of devices or behavioral interventions.
  • Phase 2

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
    • Massachusetts
      • Boston, Massachusetts, United States, 02215
        • Beth Israel Deaconess Medical Center

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

Eligibility Criteria

The key requirements that people who want to participate in a clinical study must meet or the characteristics they must have. Eligibility criteria consist of both inclusion criteria (which are required for a person to participate in the study) and exclusion criteria (which prevent a person from participating). Types of eligibility criteria include whether a study accepts healthy volunteers, has age or age group requirements, or is limited by sex.

Ages Eligible for Study

18 years and older (Adult, Older Adult)

Accepts Healthy Volunteers

No

Description

Inclusion Criteria:

  • Patient must be willing and able to give informed assent/ consent for participation in the study
  • Patient must be willing and able (in the PI's opinion) to comply with all study requirements.
  • Patient must be a premenopausal female or male aged 18 and older.
  • Patient must have a documented history of IBS that is not completely controlled by current IBS drugs.
  • Patient must have a score of ≥150 on the IBS-SSS at screening.
  • Patient must have no clinically relevant (in the judgment of the PI) abnormal blood laboratory levels at screening or randomization.
  • The clinician will assess eligibility as per the Rome IV criteria (Recurrent abdominal pain or discomfort at least 1 day/week in the last 3 months associated with two or more of the following: Improvement with defecation. Onset associated with a change in frequency of stool).

Exclusion Critieria:

  • Patient has clinically significant unstable medical conditions other than IBS.
  • Patient has had clinically relevant symptoms or a clinically significant illness in the four weeks prior to screening or randomization.
  • Patient has clinically significant laboratory values (in the PI's opinion).
  • Patient is currently using or has in the past used recreational or medicinal cannabis, or synthetic cannabinoid based medications (including Sativex®) or supplements (including hemp oil/extracts) within one month prior to study entry and is unwilling to abstain for the duration for the study.
  • Patient has consumed any probiotic product three days prior to screening and/or is unwilling to abstain from consuming these during the study.
  • Intake of antibiotics in the past 1-month (i.e. penicillin, amoxicillin, cephalexin (Keflex), erythromycin (E-Mycin), clarithromycin (Biaxin), azithromycin (Zithromax), ciprofloxacin (Cipro), levofloxacin (Levaquin), ofloxacin (Floxin), co-trimoxazole (Bactrim), trimethoprim (Proloprim), tetracycline (Sumycin or Panmycin), doxycycline (Vibramycin), gentamicin (Garamycin), or tobramycin (Tobrex). The supplement in the present study may have a minor interaction with these medications.
  • Patient has any known or suspected hypersensitivity to pomegranate, pine, or mushrooms, or any of the excipients of the Supplement Synbiotic Product (SSP).
  • Patients of child bearing potential unless willing to ensure that they use effective contraception, for example, oral contraception, double barrier, intra-uterine device, during the study and for three months thereafter.
  • Patients who are pregnant, lactating, or planning pregnancy during the course of the study and for three months thereafter.
  • Patients who have been part of a clinical trial involving any investigational product in the previous six months.
  • Any other significant disease or disorder which, in the opinion of the PI, may either put the patient at risk because of participation in the study, may influence the result of the study, or affect the patient's ability to participate in the study.
  • Patient has significantly impaired hepatic function at Visit 1 (Alanine aminotransferase (ALT) >5 × upper limit of normal (ULN) or bilirubin >2 × ULN) OR the ALT or Aspartate aminotransferase (AST) >3 × ULN and the bilirubin >2 × ULN (or international normalized ratio >1.5).
  • Obesity (BMI > 30)
  • Implantable device such as heart pacemaker.
  • Patients unwilling to abstain from donation of blood during the study.
  • History of inflammatory bowel disease.
  • History of diverticulosis.
  • History of cardiovascular disease.
  • History of kidney/liver/serious infection.
  • History of diabetes or other hormone diseases.
  • History of abdominal surgery.
  • Currently suffering from high blood pressure.
  • Following a physical examination, the patient has any abnormalities that, in the opinion of the investigator would prevent the patient from safe participation in the study.
  • There are plans for the patient to travel outside the USA during the 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

  • Primary Purpose: Treatment
  • Allocation: Randomized
  • Interventional Model: Parallel Assignment
  • Masking: Quadruple

Arms and Interventions

Participant Group / Arm

Participant Group / Arm

A group or subgroup of participants in a clinical trial that receives a specific intervention/treatment, or no intervention, according to the trial's protocol.
Intervention / Treatment

Intervention / Treatment

A process or action that is the focus of a clinical study. Interventions include drugs, medical devices, procedures, vaccines, and other products that are either investigational or already available. Interventions can also include noninvasive approaches, such as education or modifying diet and exercise.
Experimental: microbial consortia (DS-01)
DS-01 is a rationally defined microbial consortia consisting of 24 strains across 12 species, with polyphenolic and phenolic prebiotic bioactive compounds. Participants will be instructed to take 2 capsules daily for the duration of the trial.
Drug: DS-01
synbiotic
Other Names:
  • SEED synbiotic
Placebo Comparator: placebo
Placebo capsules for DS-01 will contain rice flour matched for color and texture in an identical outer capsule shell. Participants will be instructed to take 2 capsules daily for the duration of the trial.
Drug: DS-01
synbiotic
Other Names:
  • SEED synbiotic

What is the study measuring?

Primary Outcome Measures

Primary Outcome Measures

In a clinical study's protocol, the planned outcome measure that is the most important for evaluating the effect of an intervention/treatment. Most clinical studies have one primary outcome measure, but some have more than one.
Outcome Measure
Measure Description
Time Frame
Safety and Tolerability of DS-01 Treatment vs Placebo
Time Frame: 12 weeks
measure of reported adverse events during the study period
12 weeks

Secondary Outcome Measures

Secondary Outcome Measures

In a clinical study's protocol, a planned outcome measure that is not as important as the primary outcome measure for evaluating the effect of an intervention but is still of interest. Most clinical studies have more than one secondary outcome measure.
Outcome Measure
Measure Description
Time Frame
Maintenance or increase of diversity within the DS-01 treatment group [baseline-Day 84]
Time Frame: 12 weeks
Microbiota composition will be identified through fecal samples for total genomic DNA extraction in participants supplemented with DS-01 or placebo. Metagenomic sequencing will yield a total observable species count and maintenance will be defined as a change in total observed species less than or equal to 20% as compared to the total observed species count at baseline.
12 weeks
Improvement by ≥ 15% in one or more individual IBS symptoms: abdominal pain, bloating, bowel movement difficulty, or stool consistency.
Time Frame: 12 weeks
Self-reported in a Symptom Tracker app to track disease progression in real-time
12 weeks
Abdominal pain responder
Time Frame: 12 weeks
Percentage of responders in the intervention group who report a ≥ 20% reduction in average daily worst abdominal pain scores compared to placebo.
12 weeks
CSBM Responder
Time Frame: 12 weeks
Percentage of responders in subjects with IBS-C receiving DS-01 who report an increase from baseline of 1 complete spontaneous bowel movement (CSBM) per week for at least 6 weeks compared to placebo
12 weeks
Global Improvement in IBS
Time Frame: 12 weeks
Measured with one question with 7 possible answers: (1) much worse, (2) moderately worse, (3) slightly worse, (4) unchanged, (5) slightly better, (6) moderately better, or (7) much better.
12 weeks
Adequate Relief
Time Frame: 12 weeks
A higher proportion of subjects in the DS-01 intervention group with Adequate Relief of Global IBS Symptoms for ≥ 30% in the intervention duration compared to the placebo group
12 weeks
VSI responder
Time Frame: 12 weeks
A higher proportion of subjects with improvement ≥ 30% in Visceral Sensitivity Index score in the DS-01 intervention group compared to the placebo group.
12 weeks
Metagenomic Signature Change in Synbiotic group 1
Time Frame: 12 weeks
Participants displaying a change in metagenomic signatures resulting in increased representation from baseline of Bifidobacterium longum, or Prevotella intermedia or Bacteroides helcogenes or Akkermansia muciniphila or decreased representation of Blautia hansenii in subjects with IBS-C receiving DS-01 as greater than placebo treated subjects.
12 weeks
Metagenomic Signature Change in Synbiotic group 2
Time Frame: 12 weeks
Participants displaying a change in metagenomic signatures resulting in an increased representation from baseline of Alistipes finegoldii or Faecalibacterium prausnitzii or Akkermansia muciniphila or decreased representation from baseline of Blautia obeum in subjects with IBS-M receiving DS-01 greater than placebo treated subjects.
12 weeks

Other Outcome Measures

Other Outcome Measures

For clinical trials, a planned measurement described in the protocol that is used to determine the effect of an intervention/treatment on participants. For observational studies, a measurement or observation that is used to describe patterns of diseases or traits, or associations with exposures, risk factors, or treatment. Types of outcome measures include primary outcome measure and secondary outcome measure.
Outcome Measure
Measure Description
Time Frame
Exploratory endpoint 1
Time Frame: 12 weeks
Increase in tryptamine, SCFA, and hypoxanthine production in IBS-C, changes in serine protease, LPS, or calprotectin in the DS-01 intervention group compared to the placebo group.
12 weeks
Exploratory endpoint 2
Time Frame: 12 weeks
Change in plasma intestinal fatty acid binding protein (I-FABP), zonulin, LPS-binding protein, soluble CD14, cytokines
12 weeks

Collaborators and Investigators

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

Sponsor

Sponsor

The organization or person who initiates the study and who has authority and control over the study.
Beth Israel Deaconess Medical Center

Collaborators

Collaborators

An organization other than the sponsor that provides support for a clinical study. This support may include activities related to funding, design, implementation, data analysis, or reporting.
Seed Health

Investigators

Investigators

A researcher involved in a clinical study. Related terms include site principal investigator, site sub-investigator, study chair, study director, and study principal investigator.
  • Principal Investigator: Anthony J Lembo, MD, Beth Israel Deaconess Medical Center

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)

Study Start

The actual date on which the first participant was enrolled in a clinical study. The "anticipated" study start date is the date that the researchers think will be the study start date.
October 20, 2020

Primary Completion (Actual)

Primary Completion

The date on which the last participant in a clinical study was examined or received an intervention to collect final data for the primary outcome measure. Whether the clinical study ended according to the protocol or was terminated does not affect this date. For clinical studies with more than one primary outcome measure with different completion dates, this term refers to the date on which data collection is completed for all the primary outcome measures. The "anticipated" primary completion date is the date that the researchers think will be the primary completion date for the study.
October 17, 2022

Study Completion (Actual)

Study Completion

The date on which the last participant in a clinical study was examined or received an intervention/treatment to collect final data for the primary outcome measures, secondary outcome measures, and adverse events (that is, the last participant's last visit). The "anticipated" study completion date is the date that the researchers think will be the study completion date.
October 26, 2022

Study Registration Dates

First Submitted

First Submitted

The date on which the study sponsor or investigator first submitted a study record to ClinicalTrials.gov. There is typically a delay of a few days between the first submitted date and the record's availability on ClinicalTrials.gov (the first posted date).
August 31, 2020

First Submitted That Met QC Criteria

First Submitted That Met QC Criteria

The date on which the study sponsor or investigator first submits a study record that is consistent with National Library of Medicine (NLM) quality control (QC) review criteria. The sponsor or investigator may need to revise and submit a study record one or more times before NLM's QC review criteria are met. It is the responsibility of the sponsor or investigator to ensure that the study record is consistent with the NLM QC review criteria.
October 20, 2020

First Posted (Actual)

First Posted

The date on which the study record was first available on ClinicalTrials.gov after National Library of Medicine (NLM) quality control (QC) review has concluded. There is typically a delay of a few days between the date the study sponsor or investigator submitted the study record and the first posted date.
October 22, 2020

Study Record Updates

Last Update Posted (Actual)

Last Update Posted

The most recent date on which changes to a study record were made available on ClinicalTrials.gov. There may be a delay between when the changes were submitted to ClinicalTrials.gov by the study's sponsor or investigator (the last update submitted date) and the last update posted date.
February 17, 2026

Last Update Submitted That Met QC Criteria

Last Update Submitted That Met QC Criteria

The most recent date on which the study sponsor or investigator submitted changes to a study record that are consistent with National Library of Medicine (NLM) quality control (QC) review criteria. It is the responsibility of the sponsor or investigator to ensure that the study record is consistent with the NLM QC review criteria.
January 29, 2026

Last Verified

Last Verified

The most recent date on which the study sponsor or investigator confirmed the information about a clinical study on ClinicalTrials.gov as accurate and current. If a study with a recruitment status of recruiting; not yet recruiting; or active, not recruiting has not been confirmed within the past 2 years, the study's recruitment status is shown as unknown.
January 1, 2026

More Information

Terms related to this study

Additional Relevant MeSH Terms

Other Study ID Numbers

Other Study ID Numbers

Identifiers or ID numbers other than the NCT number that are assigned to a clinical study by the study's sponsor, funders, or others. These numbers may include unique identifiers from other trial registries and National Institutes of Health grant numbers.
  • 2019P-000274

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

Yes

Studies a U.S. FDA-regulated device product

No

product manufactured in and exported from the U.S.

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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