Updated 15Jan2026

The Harmonize project

The Harmonize project, co-funded by the European Union, is dedicated to supporting the implementation of the new Regulation on Substances of Human Origin (SoHO) within the European stool banks. The primary goal is to improve the quality and safety of faecal microbiota transplantations across Europe.

The Harmonize project builds on existing activities in the EurFMT network and contains five main sub-objectives, including the creation of 1) expert forums, 2) guidelines, 3) a training programme, 4) a EurFMT data registry, and 5) a dialogue with industry stakeholders and regulators. Each of these sub-objectives is implemented into four work packages with an assigned responsible partner allocated, as illustrated in the figure below.

A brief overview of the Harmonize project can be obtained by reading this Leaflet (Link).The project was initiated in January 2025 and runs for 18 months, being co-funded by the European Union.

The partners of the Harmonize project include:

1. Johann Wolfgang Goethe University, Frankfurt am Main, Germany
2. Academic University of Leiden, Leiden, The Netherlands
3. Aarhus University Hospital, Aarhus, Denmark
4. Pharmabiotic Research Institute, France
5. European Helicobacter and Microbiota Study Group (EHMSG)

Guideline development

Two complementary guidelines are being developed as part of the Harmonize project: one technical guideline focusing on the manufacturing, processing, storage, and delivery of FMT preparations, and a second guideline dedicated to donor selection and screening procedures. Together, these guidelines aim to harmonise FMT protocols in Europe and help further implementation and compliance with the new EU SoHO regulation, which now includes FMT.

Harmonisation is essential to unify clinical and regulatory practices, ensuring that FMT products are of consistently high quality, regardless of the laboratory or country where they are prepared. Establishing minimum technical standards for donor screening, processing of FMT preparations, and storage will further safeguard patient safety and support reproducible treatment efficacy. Furthermore, it will provide a framework for structured collaboration among key stakeholders, including academic institutions, regulators, patients, and industry, using shared protocols. Ultimately, the guideline will establish a foundation for a sustainable, expert-driven approach to maintaining and updating best practices as science and regulations continue to evolve.

The objectives of these guidelines are: (1) to define minimum standards for donor selection and screening, and technical and procedural standards for the manufacturing and handling of FMT preparations, 2) to support compliance with the 2027 EU regulations on SoHO, and 3) to promote harmonised practices across Member States. Additionally, it aims to foster cross-sectoral collaboration and expert consensus, while improving institutional implementation through a clear and practical technical framework.

Training programme

A core element in reaching the goal of improving the quality and safety of faecal microbiota transplantations in Europe is the development and implementation of a structured training programme for stool banks in Europe. The training programme is organised by the Harmonize project partner at Aarhus University Hospital, Denmark.

Eligibility for the training programme requires prior experience with faecal microbiota transplantation (FMT). Each participating centre should have at least one EurFMT network member and aim to become a SoHO establishment by 2027, undertaking activities such as donor screening, processing, storage, distribution, or follow-up.

The training programme introduces the essential aspects of running a stool bank within the framework of the SoHO Regulation. It will guide the participants through several important areas, including donor recruitment, donor screening, faeces procurement, FMT processing, clinical application, and biovigilance. Each of these topics will be addressed by different means during three training phases, including 1) a self-study phase, 2) an on-site or virtual visit to the stool bank at Aarhus University Hospital, and 3) a follow-up phase, all briefly described and shown visually below. The content will build on the SoHO Regulation and the “Guide to the Quality and Safety of Tissues and Cells for Human Application”, issued by the EDQM.

1) Self-studying phase
Participants in the training programme are encouraged to read some specified material before visiting the FMT centre at Aarhus University Hospital. Besides the reading material, participants are also highly encouraged to watch four training videos explicitly produced for the training programme within the Harmonize project. The self-studying material for the training programme can be accessed here:

2) Visit a stool bank
The visit requires a full day of participation, during which we have prepared a program to guide the participants through the key facilities in the stool bank at Aarhus University Hospital. These facilities include the donor screening area, the faeces processing laboratory, the distribution laboratory, and the outpatient clinic where patients receive the treatment. Each stop in a key facility will be accompanied by one or two presentations with pre-prepared teaching materials to provide further context and associate the regulatory framework with the FMT system implemented at Aarhus University Hospital.

3) Follow-up phase
Three months after the visit, a one-hour virtual meeting will be scheduled. The primary purpose of this meeting is to ensure the availability for answering questions that may have arisen at the trained FMT centres following the implementation of potential changes in their own FMT practices. We will also be available for responding to questions sent by email for up to 12 months after the visit.

Peer audit

The Harmonize project will also focus on identifying key shortcomings in the current landscape of faecal microbiota transplantation. This includes assessing gaps in treatment availability, compliance with procurement/processing standards, and monitoring the quality and safety of treatments. To address these issues, an audit plan and a European EurFMT Registry will be developed and implemented, providing a structured approach to strengthen quality, safety, and access across participating centres.

Audit concept
Within the framework of the Harmonize project, an audit concept will be developed to support establishments in meeting the regulatory requirements for Substances of Human Origin (SoHO). This will include the creation of an implementation and audit plan designed to ensure compliance not only with technical guidelines but also with the regulatory oversight. This oversight encompasses entity and establishment authorisations, preparation process authorisations, inspections, as well as vigilance and traceability obligations.

The development of the implementation and audit plans will be guided by the European Committee on Organ Transplantation’s Guide to the Quality and Safety of Tissues and Cells for Human Application, alongside the specific guidelines produced within the Harmonize project. As part of this process, initial audit visits will be conducted, providing a practical test of the concept and laying the groundwork for future audits.

EurFMT Registry

As part of the Harmonize project, the EurFMT Registry will be further developed as a central European database to monitor the efficacy and safety of faecal microbiota transplantation (FMT). Established in 2022, the registry addresses the limitations of fragmented national registries, which often provide only small sample sizes, use different variables and endpoints, and therefore hinder comparison and large-scale analysis. By harmonising data collection across European centres, the EurFMT Registry enables robust assessments of clinical efficacy, safety, and technical procedures, while also allowing the detection of rare adverse events and supporting effective biovigilance.

A central ethics vote has already been obtained, and participating members will be supported in securing local ethical and data protection approvals. The registry will provide comprehensive data management, annual analyses, and detailed reports for both regulators and scientific publications. Participation will not only improve the quality of FMT procedures and strengthen patient safety but also connect individual stool banks within the EurFMT network, ensuring collaboration and continuity beyond the duration of the project. Ultimately, the EurFMT Registry will deliver Europe-wide insights that inform future guidelines, regulations, and scientific advancement in the field of FMT.