The Future of FMT in the Light of Regulation
Commercial products, synthetic consortia, and global harmonization: we sketch the directions regulation will push FMT over the coming decade.
In the early 1980s, as the AIDS epidemic spread, blood transfusion services had to fundamentally rethink donor selection protocols. Until then, blood donation had been almost unimpeded; the introduction of new safety requirements provoked sharp protests from donor communities and clinicians alike – "unnecessary bureaucracy", "obstructing patient care". Thirty years later, no one questions that HIV screening, hepatitis screening and detailed history-taking are basic requirements of blood supply. FMT regulation will likely follow a similar path: some of today's stricter requirements will be considered just as natural by future clinicians as today's blood donation protocols.
Expected directions of development
The future of FMT regulation will be shaped by four parallel processes:
- Spread of commercial products: [309], [319] The success of Rebyota and Vowst will likely stimulate the development of new commercial FMT products – not only for rCDI, but also for IBD, metabolic syndrome and other indications. These products will have genuine drug status, increasing industrial partners but narrowing the possibility of individual donor matching.
- SOHO regulation implementation: By 2027–2028, EU member states must apply [310], [315] the SOHO regulation's requirements. This will harmonise minimum donor bank requirements and the traceability system – but the drafting of detailed rules remains at member state level, where discrepancies may again emerge.
- Synthetic and modified FMT products: The next development direction is so-called "engineered microbiome therapeutics" – precisely defined, synthetically assembled microbial consortia that do not require a real donor. These products are more easily standardised and regulated, but their effectiveness compared to full microbiome-complexity FMT remains to be demonstrated.
- Global harmonisation: ISO, ISBT (International Society of Blood Transfusion) and other organisations have initiated global FMT standardisation efforts [316], [319]. The goal: minimum requirements enabling cross-recognition between accredited donor banks – similar to the global blood supply system.
The domestic situation and actions required
For Hungary, monitoring regulatory developments and proactive participation in the legislative process is particularly important [263], [314]. Implementation of the SOHO regulation will be a shared responsibility of OGYÉI, the Ministry of Human Resources, and professional organisations (Hungarian Gastroenterological Society). MicroBiome Bank and domestic FMT centres must engage actively in this process with professional contributions.
The most important domestic actions:
- Developing and publishing a uniform domestic donor safety protocol [316], [310] – a prerequisite for SOHO implementation and the foundation of patient safety.
- Establishing an accreditation system for FMT-performing institutions – ensuring not only donor quality, but also procedural quality is consistent.
- Participating in European FMT registries [319] – integrating domestic outcomes into the global evidence base increases the credibility of domestic FMT application and provides feedback for protocol development.
- Involving patient organisations in the regulatory process – those directly affected by FMT access are legitimate stakeholders in shaping regulation.
References
[263] EMA/HMA. Faecal Microbiota Transplantation – EU-IN Horizon Scanning Report. EMA/204935/2022/Rev. 1 (updated May 2025). 2022. Link
The 2022 (updated May 2025) EMA/HMA 'Faecal Microbiota Transplantation – EU-IN Horizon Scanning Report' (EMA/204935/2022/Rev. 1) is the official European Medicines Agency horizon-scanning analysis of FMT regulation. It maps the heterogeneous EU regulatory landscape (tissue, drug, blood-component or hybrid frameworks across member states), reviews clinical evidence by indication (CDI, IBD, hepatic encephalopathy, decolonisation of MDROs), and identifies harmonisation priorities. The report informs the EU SoHO Regulation 2024/1938 negotiations and proposes a coordinated approach to donor screening, stool-bank licensing, traceability, pharmacovigilance and clinical-trial registries. It is a key policy reference for EU FMT governance.
[309] FDA. Rebyota (fecal microbiota, live-jslm) approval. 2022. 2022. Link
This FDA news entry documents the 2022 approval of Rebyota (fecal microbiota, live-jslm) by Ferring Pharmaceuticals — the first FDA-approved fecal microbiota product. Rebyota is indicated for the prevention of recurrent Clostridioides difficile infection (rCDI) in adults following antibiotic treatment for rCDI. Administered as a single rectal dose, the product contains a standardised microbial consortium derived from screened human donor stool. The phase 3 PUNCH CD3 trial showed a treatment success rate of approximately 71% versus 58% with placebo at 8 weeks. The approval marked a regulatory milestone, transitioning FMT from enforcement-discretion clinical practice to a defined drug-pathway product.
[310] European Commission. Proposal for a Regulation on standards of quality and safety for substances of human origin intended for human application (SOHO Regulation). 2022. 2022. Link
The 2022 European Commission 'Proposal for a Regulation on standards of quality and safety for substances of human origin intended for human application (SOHO Regulation)' is the EU's draft replacement for the 2002/98/EC Blood and 2004/23/EC Tissues and Cells Directives. The proposal creates a unified, future-proof framework for blood, tissues, cells, reproductive cells, breast milk, fecal microbiota and any future SoHO. It establishes the EU SoHO Coordination Board, the SoHO Platform, harmonised authorisation pathways for SoHO preparations and entities, donor protection rules, and vigilance/traceability requirements. The proposal was adopted as Regulation (EU) 2024/1938 in June 2024 and applies from August 2027. It is the central EU regulatory instrument for FMT and stool banks.
[314] Ministry of Interior (BM). Professional clinical guideline on conventional intestinal microbiota transplantation procedures. Identifier: 002338. Published: 15 August 2025. Valid until: 15 August 2028. (Replaces: EMMI 002080/2020.). 2025. Link
The 2025 Ministry of Interior (BM) of Hungary professional clinical guideline (Identifier 002338, published 15 August 2025, valid until 15 August 2028, replacing EMMI 002080/2020) on conventional intestinal microbiota transplantation procedures defines Hungarian standards for FMT practice. The document specifies donor screening, stool processing, storage and traceability requirements aligned with the EU SoHO Regulation; defines indications (primarily recurrent and refractory CDI, with research framework for other indications); specifies delivery routes (capsule, nasogastric/duodenal, colonoscopic, enema); and outlines pharmacovigilance, follow-up and registry obligations. The guideline is the operative national standard for hospital-based FMT services in Hungary and aligns domestic practice with European consensus.
[315] Keller JJ, Vehreschild MJ, Stallmach A et al. FMT regulation: the EU perspective. United European Gastroenterol J. 2023. Link
This cross-sectional questionnaire study screened 434 patients with inflammatory bowel disease (IBD) at a nutrition clinic between November 2021 and April 2022 for prevalence of exclusion diets and fasting. Total exclusion was complete avoidance of a food category; partial exclusion was most-of-the-time avoidance. Patients also reported total, intermittent or partial fasting practices. The prevalence and risk factors for exclusion diets and fasting were characterized. The findings document widespread dietary self-restriction practices in IBD patients with implications for nutritional management.
[316] Cammarota G, Ianiro G, Kelly CR et al. International consensus conference on stool banking for faecal microbiota transplantation in clinical practice. Gut. 2019. Link
This international consensus from FMT experts in Europe, North America and Australia provides statements on stool banking for FMT, covering general principles, organization, donor selection and screening, stool collection/preparation/storage, services and clients, registries, outcome monitoring, ethics and FMT's evolving clinical role. Consensus was achieved through Delphi rounds plus plenary discussion, with statements supported by best available evidence. The document guides global stool-bank development to promote safe, equitable FMT access for recurrent C. difficile infection.
[319] Peery AF, Kelly CR, Kao D et al. AGA Clinical Practice Guideline on Fecal Microbiota-Based Therapies for Select Gastrointestinal Diseases. Gastroenterology. 2024. Link
This American Gastroenterological Association (AGA) guideline, developed using GRADE methodology, makes 7 recommendations on faecal microbiota-based therapies (FMT, fecal microbiota live-jslm, fecal microbiota spores live-brpk) in adults. In immunocompetent adults with recurrent C. difficile infection, the AGA suggests selective use of these therapies after completion of standard antibiotics to prevent recurrence. The guideline also addresses severe-to-fulminant CDI, IBD including pouchitis and irritable bowel syndrome. The findings establish evidence-based clinical guidance for faecal microbiota-based therapy use across multiple GI conditions.