Welcome to the DiffBiome programme

Beating recurrent C. difficile infection is not a matter of willpower; it is about restoring a collapsed gut ecosystem. This short introduction shows what to expect during the 90-day DiffBiome programme.

This handbook is your companion through the 90-day oral microbiota transplantation (FMT^[G]) treatment for recurrent Clostridioides difficile^[G] infection. In plain language – but without sacrificing scientific accuracy – it explains what happens in your gut and how you can actively support your own recovery.

The core idea is simple: antibiotics strip the gut flora^[G], while FMT restores it – which is why it can work where antibiotics repeatedly fail (Seekatz 2022 [001]). Over the next 90 days we move step by step: from getting started immediately, through understanding the disease, to stabilisation and preventing relapse.

The treatment, however, is not just about taking a capsule. The 90-day programme has two parts of equal weight: the capsule, which puts back the missing bacterial community, and the change in the way you live, which gives that community a home. The delivered flora needs nourishment – above all fibre and plant diversity^[G] – along with fluids, sleep, movement and stress kept within bounds, if it is to settle in and stay. If you only take the capsule, you have done half the treatment. That is why the chapters on diet, hydration, sleep, movement and stress run alongside the capsule schedule throughout this book – they are not add-ons, they are the other half of the treatment.

You don't have to understand everything before you can start getting better. If time is pressing, begin with the Quickstart – in the most critical window it sets you on the right course within three days. You can read the "why" afterwards; the book's layered structure means everyone, from patient to treating physician, will find something useful to them.

FMT must be used under medical supervision (Cammarota 2017 [016]; Hoffmann 2025 [024]; Rodriguez 2025 [025]). This book does not replace consultation with your treating physician – it helps you become an informed, active participant in your own recovery.

References

[001] Seekatz A, Safdar N, Khanna S. The role of the gut microbiome in colonization resistance and recurrent. Therapeutic advances in gastroenterology. 2022. Link

Colonization resistance of the gut microbiota and FMT therapy in rCDI — A healthy microbiota inhibits C. difficile colonization (nutrient competition, bile acids, SCFAs, bacteriocins). Antibiotics → dysbiosis → CDI. FMT restores diversity. Monoclonal antibodies do not treat dysbiosis.

[016] Cammarota G, Ianiro G, Tilg H et al. European consensus conference on faecal microbiota transplantation in clinical practice. Gut. 2017. Link

European consensus conference developing evidence-based recommendations on FMT for clinical practice, with 28 experts from 10 countries collaborating in working groups. Statements were generated through evidence-based review, evaluated electronically via a Delphi process, and finalized in a plenary consensus session. Recommendations cover FMT indications, donor selection, faecal material preparation, clinical management, faecal delivery, and minimum requirements for establishing an FMT centre. Provides the European standardization framework for safe and governed FMT delivery.

[024] Hoffmann DE, Javitt GH, Kelly CR, Keller JJ, Baunwall SMD, Hvas CL. Fecal microbiota transplantation: a tale of two regulatory pathways. Gut Microbes. 2025. Link

A joint analysis by lawyers and clinicians of how faecal microbiota transplantation came to sit on two divergent regulatory pathways. In the United States it is handled as a drug (investigational new drug, or licensed product); in Europe it falls under the framework for substances of human origin (SoHO). The authors work through what this means for donor screening, traceability, access and liability. What both pathways share: FMT is not a freely available preparation but a procedure tied to medical supervision and a controlled institutional setting — whichever legal route a given country follows.

[025] Rodriguez J, Cordaillat-Simmons M, Pot B, Druart C. The regulatory framework for microbiome-based therapies: insights into European regulatory developments. npj Biofilms and Microbiomes. 2025. Link

Review of the European regulatory framework for microbiome-based therapies. The paper separates live biotherapeutic products (LBPs), which can be authorised as medicines, from donor-derived substances, which fall under the EU framework for substances of human origin (SoHO) — faecal microbiota transplantation among them. It stresses that donor screening, traceability and clinical oversight are minimum requirements, and that member-state practice can differ within the common frame. This is the international background to which the book's phrasing „tied to medical supervision and an institutional setting" is aligned.