XVII. 6 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: The success of Rebyota and Vowst will likely stimulate the development of new commercial FMT products [738] – 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: From 7 August 2027, EU member states must apply the requirements of Regulation (EU) 2024/1938 on substances of human origin [733], [729]. 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 [735], [738]. The goal: minimum requirements enabling cross-recognition between accredited donor banks – similar to the global blood supply system.
National implementation and the actions required
Wherever FMT is practised, monitoring regulatory developments and participating proactively in the legislative process is particularly important [728], [733]. Within the EU, implementation of Regulation (EU) 2024/1938 is a shared responsibility of the SoHO national authority designated by each member state, the competent authorities operating alongside it and the professional societies; the Regulation applies from 7 August 2027 and explicitly brings intestinal microbiota within its scope [733]. Stool banks and FMT centres must engage actively in this process with professional contributions.
The most important national actions:
- Developing and publishing a uniform national donor safety protocol [735], [733] – 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 – integrating national outcomes into the global evidence base increases the credibility of national FMT practice 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
[728] 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.
[729] 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.
[733] . Regulation (EU) 2024/1938 of the European Parliament and of the Council of 13 June 2024 on standards of quality and safety for substances of human origin intended for human application and repealing Directives 2002/98/EC and 2004/23/EC. Official Journal of the European Union, OJ L, 2024/1938, 17.7.2024. 2024. Link
Regulation (EU) 2024/1938 on substances of human origin (SoHO) was adopted on 13 June 2024 and published in the Official Journal on 17 July 2024, repealing Directive 2002/98/EC (blood) and Directive 2004/23/EC (tissues and cells). It entered into force on 6 August 2024, with the large majority of its provisions applying from 7 August 2027. Compared with the earlier directive framework, its scope is extended to further substances of human origin, including human breast milk and intestinal microbiota — the first binding European legal framework covering FMT.
[735] 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.
[738] Khanna S, Pardi DS. Clostridioides difficile infection: curbing a difficult menace. Therap Adv Gastroenterol. 2022. Link
Khanna and Pardi's 2022 Therapeutic Advances in Gastroenterology review 'Clostridioides difficile infection: curbing a difficult menace' provides a comprehensive update on CDI epidemiology, pathogenesis, diagnosis and modern management. The authors cover the shift toward fidaxomicin and bezlotoxumab over vancomycin as preferred therapies, the role of FMT for recurrent CDI, and the emergence of microbiota-based products (Rebyota, Vowst). Risk factors (antibiotics, PPIs, hospitalisation, advanced age, comorbidity) are reviewed alongside infection control. The article situates CDI within the broader microbiome-disruption paradigm and discusses prevention, diagnostic stewardship, and the evolving therapeutic algorithm. A key reference for current CDI clinical practice.