Outcomes of Outpatients in an Gut Microbiota Clinic (Microfec)

July 23, 2026 updated by: IANIRO GIANLUCA, Fondazione Policlinico Universitario Agostino Gemelli IRCCS

Characteristics and Outcomes of Outpatients Referred to an Gut Microbiota Clinic

The gut microbiota plays a crucial role in human health, influencing metabolism, immunity, and pathogen resistance. Research has linked microbiome dysbiosis to various intestinal and extra-intestinal disorders, prompting interest in therapeutic strategies like fecal microbiota transplantation (FMT), which is now standard for recurrent Clostridioides difficile infection and shows promise for other conditions.

Despite its potential, the clinical integration of microbiome research remains limited due to biological complexity, lack of clinician awareness, and the absence of standardized guidelines. Meanwhile, patient demand for microbiome-based interventions is rising, leading some to seek non-scientific alternatives with potential health risks.

Since 2016, the Gut Microbiota Clinic at Fondazione Policlinico Gemelli has provided personalized microbiota-based treatments, collaborating with specialists across disciplines. The clinic primarily serves patients with gastrointestinal and extra-intestinal disorders and employs a multidisciplinary approach.

This study aims to characterize the clinical and microbiological and cytokine profiles of patients attending the clinic and establish a microbiological database. Primary and secondary endpoints include microbiota composition changes and clinical outcomes assessed through validated diagnostic tools.

Study Overview

Status

Recruiting

Conditions

Intervention / Treatment

Detailed Description

The gut microbiota is a key mediator of various human functions, including metabolism, the immune system, and resistance to pathogen colonization. A growing body of scientific research has demonstrated-initially through association studies and subsequently through mechanistic experiments-that gut microbiome dysbiosis is linked to a wide range of both intestinal and extra-intestinal disorders.

Recent evidence indicates that the gut microbiota is part of a complex network of interactions involving other host microbial communities and the immune system. In particular, the oral-gut axis has emerged as a key pathway through which the oral microbiota may influence gut microbial composition and function. Furthermore, host-microbiota interactions are mediated by immune mechanisms, including cytokine production and systemic inflammatory responses, linking microbiota composition to disease pathophysiology and clinical outcomes.

This body of evidence has led to the exploration of gut microbiome modulation as a therapeutic strategy, such as fecal microbiota transplantation (FMT), which has become a standard treatment for recurrent Clostridioides difficile infection and has also shown promise for several other indications, including ulcerative colitis, irritable bowel syndrome, and metabolic syndrome.

Furthermore, there is increasing interest in leveraging the gut microbiome as a diagnostic tool in clinical practice for various applications, including disease diagnosis, prognosis, and risk assessment; prediction of patient response to specific therapies; guidance and personalization of microbiome-targeted interventions such as probiotics or FMT; and monitoring the effectiveness of these treatments.

Despite this enthusiasm, however, the integration of microbiome research advancements into routine clinical practice remains generally limited. This gap can be attributed to several factors, primarily the complexity of microbiome biology, the limited knowledge of gut microbiota among most healthcare professionals, and the absence of established guidelines and infrastructures for the clinical application of microbiome research.

In contrast to the relatively slow adoption of microbiome research by clinicians, there is growing enthusiasm and high expectations among various patient groups for the rapid implementation of microbiota-related findings in clinical practice. This discrepancy poses the risk of patients seeking alternative, non-scientific solutions due to the lack of medical guidance. As a result, many individuals turn to non-medical sources, often found online, which may expose them to potential health risks and significant financial costs.

Since 2016, the Gut Microbiota Clinic has been active within the CEMAD (Center for Digestive Diseases) at Fondazione Policlinico Gemelli. This clinic was established to address the needs of patients with gut microbiota imbalances, offering personalized therapeutic approaches based on microbiota profiling, which is assessed using a commercially available test. In particular, Fondazione Policlinico Gemelli collaborates with the company XBIOGEM for the production and supply of gut microbiota tests.

The clinic primarily evaluates patients with gastrointestinal disorders (e.g., irritable bowel syndrome, inflammatory bowel diseases, and colitis induced by oncological treatments) as well as other conditions (e.g. patients with autoimmune disorders or patients undergoing oncological treatments). It operates through close collaboration with specialists from other medical fields, depending on the patient's condition (e.g., gastroenterologists, rheumatologists, dermatologists, infectious disease specialists, etc.), and follows a multidisciplinary approach involving dietitians and psychologists/psychiatrists as needed.

This clinic is highly specialized and innovative and, to the best of our knowledge, is the first dedicated clinic of its kind worldwide.

The aim of our study is to describe the characteristics of patients attending the Gut Microbiota Clinic at Fondazione Policlinico Gemelli and to establish a clinical and microbiological database. This initiative seeks to bridge the gap between the vast diagnostic and therapeutic potential of the gut microbiome and its practical application in routine clinical care.

OBJECTIVES

Primary Objective The primary objective is to describe the clinical and microbiological characteristics of patients attending the Gut Microbiota Clinic at Fondazione Policlinico Gemelli.

Secondary Objectives

  • To describe changes in microbiota composition in patients undergoing microbiota testing as part of routine clinical practice after receiving standard treatments.
  • To assess clinical changes by evaluating follow-up consultations with the referring specialist (e.g., rheumatologist or dermatologist) for patients with extra-intestinal conditions, or through the judgment of the responsible physician. When applicable, validated diagnostic scores specific to the relevant condition (e.g., Mayo Score for ulcerative colitis, CDAI for Crohn's disease, or IBS-SSS for irritable bowel syndrome, PFS and OS for oncological patients) will be used.
  • To establish a microbiological database.

ENDPOINTS

Primary Endpoint The primary endpoint is the assessment of the clinical and microbiological characteristics of patients attending the Gut Microbiota Clinic at Fondazione Policlinico Gemelli.

Secondary Endpoints Changes in gut microbiota composition and cytokine profile in patients undergoing the test as part of routine clinical practice, following treatment administered according to standard clinical care.

Study Type

Observational

Enrollment (Estimated)

400

Contacts and Locations

This section provides the contact details for those conducting the study, and information on where this study is being conducted.

Study Contact

Study Contact Backup

Study Locations

  • Italy
    • RM
      • Rome, RM, Italy, 00168
        • Recruiting
        • Policlinico Universitario Agostino Gemelli IRCCS
        • Contact:

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

Non-Probability Sample

Study Population

Outpatients attending the Gut Microbiota Clinic at Fondazione Policlinico Universitario "A. Gemelli" IRCCS

Description

Inclusion Criteria

  • Age ≥18 years.
  • Patients attending the Microbiota Outpatient Clinic at Fondazione Policlinico Universitario "A. Gemelli" IRCCS.
  • Ability to understand the study procedures and provide written informed consent.
  • Patients for whom gut microbiota testing has been requested as part of routine clinical care.

Exclusion Criteria

  • Age <18 years.
  • Severe psychiatric disorders that may interfere with study participation or informed consent.
  • Inability to provide written informed consent.

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
Cohort
The study cohort will consist of patients attending the Gut Microbiota Clinic at Policlinico Gemelli in Rome. Patients with all inclusion criteria and none of the exclusion criteria will be considered for this study. N=400 patients will be enrolled. Since the study is interventional and the primary objective is descriptive, the sample size justification is based on the precision of confidence intervals. This sample size will allow the calculation of 95% confidence intervals for the considered point estimates; these intervals will have a precision of at least 5% for categorical variables and a precision equal to one-tenth of the standard deviation for quantitative variables.
Other: Microbiome testing and Cytokine profiling
  • Gut microbiome testing for the characterization of the patient gut microbiome
  • Oral microbiota profiling using saliva samples collected with DNA/RNA Shield Collection Tubes with Swabs.
  • Cytokine profiling using peripheral venous blood samples.

What is the study measuring?

Primary Outcome Measures

Outcome Measure
Measure Description
Time Frame
Microbiological Characteristics of Patients at the Gut Microbiota Clinic
Time Frame: 24 months

The microbiome test results that patients will bring to the visit will be analyzed, including:

Alpha and beta diversity Taxonomic Composition (proportion of different bacterial phyla, genera, and species)
24 months

Secondary Outcome Measures

Outcome Measure
Measure Description
Time Frame
Changes in Microbiota Composition in Patients Undergoing Routine Clinical Microbiota Testing After Standard Treatments
Time Frame: 24 months
To describe changes in microbiota composition in patients undergoing microbiome testing as part of routine clinical practice after receiving standard treatments (Alpha and beta diversity, Taxonomic Composition - Proportion of different bacterial phyla, genera, and species).
24 months
Assessment of CDAI Scores
Time Frame: 24 months
Crohn's Disease Activity Index (CDAI) for Crohn's disease (Range: 0-600; higher scores indicate worse disease activity)
24 months
Assessment of IBS-SSS
Time Frame: 24 months
IBS Severity Scoring System (IBS-SSS) for irritable bowel syndrome (Range: 0-500; higher scores indicate worse symptoms).
24 months
Assessment of PFS Scores
Time Frame: 24 months
Variation of of Progression-Free Survival (PFS) in cancers patients treated with immunotherapy or targeted therapies: In selected patients with a sustained response, PFS can exceed 24 to 48 months.
24 months
Pain intensity
Time Frame: 24 months
The Visual Analog Scale (VAS) for Pain is a continuous scale, usually 10 cm long, where the patient marks the point that best represents their pain intensity. Scores range from 0 (no pain) to 10 (worst possible pain).
24 months
Assessment of OS scores
Time Frame: 24 months
Description: Variation of Overall Survival (OS) in cancers patients treated with immunotherapy or targeted therapies: In selected patients with a sustained response, PFS can exceed 24 to 48 months.
24 months

Collaborators and Investigators

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

Sponsor

Fondazione Policlinico Universitario Agostino Gemelli IRCCS

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)

March 13, 2025

Primary Completion (Estimated)

March 10, 2027

Study Completion (Estimated)

March 10, 2027

Study Registration Dates

First Submitted

February 6, 2025

First Submitted That Met QC Criteria

February 24, 2025

First Posted (Actual)

February 25, 2025

Study Record Updates

Last Update Posted (Actual)

July 24, 2026

Last Update Submitted That Met QC Criteria

July 23, 2026

Last Verified

July 1, 2026

More Information

Terms related to this study

Keywords

Additional Relevant MeSH Terms

Other Study ID Numbers

  • ID 6778

Plan for Individual participant data (IPD)

Plan to Share Individual Participant Data (IPD)?

YES

IPD Plan Description

The individual data of patients will be shared

IPD Sharing Access Criteria

Data will be given upon reasonable request to the PI

IPD Sharing Supporting Information Type

  • STUDY_PROTOCOL
  • SAP
  • ICF

Drug and device information, study documents

Studies a U.S. FDA-regulated drug product

No

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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