The goal of this clinical trial is to learn if oral capsules containing lyophilized fecal microbiota transplantation (FMT) can safely and effectively treat refractory irritable bowel syndrome (IBS) in adults aged 18-65 years. The main questions it aims to answer are:

Does treatment with lyophilized FMT capsules reduce IBS symptom severity compared with placebo?

Does treatment with lyophilized FMT capsules improve quality of life, anxiety, and depression in patients with IBS?

Are there differences in the frequency of adverse events between participants receiving FMT capsules and those receiving placebo?

Researchers will compare lyophilized FMT capsules to placebo capsules to see if FMT reduces IBS symptoms and improves quality of life and mental health.

Participants will:

Be randomly assigned to receive either lyophilized FMT capsules or placebo capsules for three consecutive days.

Take the capsules under supervision after receiving a proton pump inhibitor before the first dose.

Complete questionnaires assessing symptom severity, quality of life, anxiety, and depression at baseline, 4 weeks, and 12 weeks after treatment.

Attend follow-up visits at 4 weeks and 12 weeks after treatment and receive a telephone follow-up call 10 days after capsule ingestion.

Report any adverse events and have vital signs and medical information monitored during follow-up.

This study will help determine whether oral lyophilized FMT capsules are a safe and effective treatment option for adults with refractory IBS.

Irritable bowel syndrome (IBS) is a common functional gastrointestinal disorder affecting approximately 7-21% of the population in Western countries. In Croatia, the estimated prevalence is up to 28%. IBS is a symptom-based condition with a chronic course that significantly affects quality of life, social functioning, and work productivity. It is characterized by disturbances in gastrointestinal motility, altered intestinal secretion, and visceral hypersensitivity in the absence of identifiable structural or biochemical abnormalities.

The exact etiology and pathophysiology of IBS remain incompletely understood. Current evidence suggests that IBS develops through a complex interaction of multiple mechanisms rather than a single underlying cause. These mechanisms include abnormal gastrointestinal motility, visceral hypersensitivity, low-grade intestinal inflammation, psychosocial factors, alterations in the brain-gut axis, and environmental influences. Increasing attention has been directed toward the role of intestinal microbiota, as changes in the composition and diversity of gut microorganisms have been observed in patients with IBS.

IBS symptoms vary widely between individuals and can significantly impair daily functioning and overall well-being. According to the Rome IV diagnostic criteria, IBS can be classified into four subtypes based on predominant bowel habits: diarrhea-predominant (IBS-D), constipation-predominant (IBS-C), mixed type (IBS-M), and unclassified IBS (IBS-U). Studies have demonstrated differences in intestinal microbiota composition between these subtypes, suggesting that microbial imbalance may contribute to the development and persistence of symptoms.

Management of IBS remains challenging. Current treatment strategies include dietary modifications, antidepressants, pro- and anti-motility drugs, serotonin receptor agonists and antagonists, antibiotics, and probiotics. However, these approaches often provide limited or temporary relief, and many patients continue to experience persistent symptoms despite treatment.

Considering the growing evidence that alterations in gut microbiota play an important role in IBS pathogenesis, fecal microbiota transplantation (FMT) has emerged as a potential therapeutic option for gastrointestinal disorders associated with dysbiosis. FMT involves the transfer of processed stool from a healthy donor to a recipient with the goal of restoring a balanced intestinal microbiota. The effectiveness of FMT has been well established in the treatment of recurrent Clostridioides difficile infection. However, the efficacy of FMT in IBS remains under investigation, with clinical trials producing mixed results. Some studies have reported improvements in IBS symptoms after FMT, while others have not demonstrated significant benefits.

FMT can be delivered using several routes, including colonoscopy, nasoenteric tubes, enemas, or oral capsules. Capsule-based administration has gained interest because it is non-invasive, safer, more accessible, and generally more acceptable to patients than endoscopic methods. Previous studies have demonstrated that capsules containing frozen donor stool can be effective and comparable to other delivery methods in certain conditions such as Clostridioides difficile infection.

One limitation of capsules containing fresh or frozen stool is that patients often need to ingest a large number of capsules to receive an adequate therapeutic dose, sometimes several dozen capsules. This can reduce patient acceptance and complicate treatment administration. Recent advances in stool processing have introduced lyophilization techniques that enable concentration of fecal microbiota while significantly reducing the volume of fecal material required.

Lyophilization, also known as freeze-drying, is a dehydration process performed at low temperatures that preserves microbial viability while removing water content. This method allows the preparation of concentrated fecal microbiota products that require a smaller number of capsules while maintaining therapeutic potential. As a result, lyophilized FMT capsules may represent a more practical and patient-friendly method of microbiota transfer.

Although several randomized controlled trials and meta-analyses have investigated FMT for the treatment of IBS, most studies have used capsules containing frozen stool. Currently, there is limited evidence regarding the use of lyophilized FMT capsules for this indication. Therefore, additional studies are needed to evaluate their safety and therapeutic effectiveness in patients with IBS.

In addition to gastrointestinal symptoms, IBS is frequently associated with psychological symptoms such as anxiety and depression. The gut-brain axis represents a bidirectional communication system between the gastrointestinal tract and the central nervous system involving neural, immune, endocrine, and metabolic pathways. Changes in gut microbiota induced by fecal microbiota transplantation may influence mental health and quality of life through mechanisms such as immune modulation, production of microbial metabolites (e.g., short-chain fatty acids), and neuroendocrine signaling.

The aim of this study is to evaluate the safety and efficacy of oral lyophilized fecal microbiota transplantation capsules compared with placebo for the treatment of refractory IBS. The study also aims to assess whether this intervention can improve symptom severity, quality of life, and psychological well-being.

This study is designed as a monocentric, prospective, randomized, placebo-controlled, double-blind clinical trial. Participants will be adults aged 18-65 years with an established diagnosis of IBS according to Rome IV criteria and moderate to severe disease activity defined by an IBS Symptom Severity Score (IBS-SSS) greater than 175. Only patients whose symptoms are refractory to conventional medical therapy will be eligible for inclusion.

Participants will be randomly assigned in a 1:1 ratio to receive either capsules containing lyophilized fecal microbiota or placebo capsules. Participants in the experimental group will ingest three capsules per day during three consecutive days. The total dose of lyophilized microbiota corresponds to approximately 80 grams of original donor stool. Participants in the control group will receive placebo capsules identical in appearance and weight.

Capsule ingestion will be supervised by a member of the research team. Capsules will be administered two hours after breakfast. Participants will be instructed not to consume food between breakfast and capsule administration and for two hours after capsule ingestion.

Because placebo responses are common in IBS clinical trials, participants' treatment expectations will be assessed using the Stanford Expectations of Treatment Scale (SETS). All participants will be followed for a total of 12 weeks after the intervention.

Follow-up will include a telephone contact approximately 10 days after capsule ingestion and two in-person visits at 4 weeks and 12 weeks after the intervention. During follow-up visits, concomitant medications will be reviewed, vital signs will be recorded, and participants will be asked to report any adverse events. Participants will also complete validated questionnaires assessing symptom severity, quality of life, anxiety, and depression, including IBS-SSS, IBS-QoL, and the Hospital Anxiety and Depression Scale (HADS). Participants will additionally be asked whether they believe they received the active treatment or placebo in order to evaluate the success of study blinding.

Donor stool used for the preparation of FMT capsules will be obtained from carefully screened healthy donors according to established European consensus guidelines. Lyophilization and preparation of the fecal microbiota product will be conducted in collaboration between the Faculty of Medicine and the Teaching Institute of Public Health of Primorsko-Goranska County, while the manufacturing of both FMT capsules and placebo capsules will be supported by Jadran-Galenski Laboratorij d.d.

This study is expected to provide important evidence regarding the clinical effectiveness and safety of lyophilized FMT capsules as a novel therapeutic approach for patients with refractory IBS. If successful, this treatment could represent a non-invasive and more acceptable option for microbiota-based therapy and may further contribute to understanding the role of gut microbiota in IBS and related conditions.

Inclusion Criteria:

• 18-65 years of age
• disease activity defined by an IBS-Symptom Severity Score (IBS-SSS) of more than 175
• symptoms refractory to conservative medical therapy (hyoscine salts, osmotic laxatives such as polyethylene glycol, loperamide, rifaximin, tricyclic antidepressants, SSRIs or other antidepressants, peppermint oil)
• negative evaluation for coeliac disease
• signed informed consent

Exclusion Criteria:

• pregnant or breastfeeding women
• women of childbearing potential who are unwilling to use an acceptable method of birth control
• severely immunocompromised or immunosuppressed (organ transplant recipients, those with neutropenia with an absolute neutrophil count of <500 cells per mm3, those receiving current treatment with antineoplastic drugs, HIV positive)
• gastrointestinal symptoms explained by an alternative diagnosis (underlying IBD, infectious enteritis)
• severe allergy to capsule components
• therapy with new antidepressants or had a change in antidepressant dose within previous 3 months
• serious medical comorbidities (including neurological or psychiatric comorbidities)
• treatment with antibiotics 3 months before enrolment
• previous history of FMT at any time in the past
• unwillingness to ingest the capsules

De-identified individual participant data (IPD) that underlie the results resported in the publication (e.g. adverse events, changes in IBS-SSS, IBS-QoL, and HADS questionnaires) will be made available upon reasonable request. Data will be shared with qualified researchers for academic purposes under a data use agreement. Requests should be directed via e-mail.

Beginning 3 months and ending 3 years after the publications of results.

Data will be shared with qualified researchers for academic purposes under a data use agreement. Requests should be directed via e-mail.