I. Phase 0 – Getting started now (days 1–3)

I. 2 Quickstart: triage and launching the first course

You don't have to understand everything before you can start getting better. This chapter gets you going within three days: where you stand right now, which course is right for you, and how to take the first capsules correctly.

Summary

With recurrent Clostridioides difficile^[G] infection, time is what really counts, which is why this book does not begin with the science but with action. The aim of the first three days is simple: to assess how severe your condition is right now, on that basis to start the appropriate DiffBiome course together with your treating physician, and to learn how to take the capsules correctly. The "why it works" and the full lifestyle change can wait for the coming weeks – for now the task is to get your recovery started. If you experience any of the warning signs listed at the end of the chapter, do not sit reading this book – turn to a doctor immediately!

How severe is it? – a quick assessment

The first step of treatment is to assess how severe your condition currently is, because this determines the intensity with which it must begin. For this, your treating physician uses a simple score (called the SIS^[G] – Symptom Importance Scale): a few questions about your symptoms, your previous relapses and your risk factors, from which a score between 0 and 100 and a classification emerge. That the score measures not only your current symptoms but also your risk of relapse is deliberate: the international guidelines have themselves moved in this direction – the treatment pathway is determined not by momentary severity alone, but also by individual recurrence risk (van Prehn 2021 [017]). If you already have the capsule in your hand, this classification has been made – from here your job is to know what it means. You don't need to know the score by heart; the key point is that the classification tells you where your condition can be treated and with what starting dose.

Broadly speaking, three situations can arise – and what distinguishes them is not the name of the severity but the care setting. Home treatment: the course runs at home, with the daily dose set by your treating physician, alongside fluid replacement and observation. Hospital assessment: treatment can continue at home, but first it must be checked in hospital whether that is safe. Hospital admission: the course starts in hospital, with a higher-density preparation and close medical follow-up – here referral is not an overreaction but the only acceptable, safe path.

The classification is always carried out by your treating physician, because they see the whole picture. Your job right now is simply to report your symptoms honestly – especially the daily number of stools, the consistency of the stool, and whether you have seen any blood – and to recognise those signs where you must not wait any longer but ask for help at once. If you would like to speed up the process, our own medical colleagues can help assess the severity of your condition: Link

Launching the course

Once the classification is done, your treating physician (or the MicroBiome Bank team) selects the DiffBiome preparation that suits you and its daily dose. The preparation for home treatment is DiffBiome 30(V)+: a dark glass bottle containing 30 capsules. The "30" indicates the number of capsules and the Roman numeral in brackets the density^[G] – the more concentrated a preparation is, the fewer capsules are needed for the same effect.

You are not choosing from a range here: according to your classification your doctor prescribes a specific starting dose, and raises it only if symptoms do not improve. How long the bottle lasts therefore depends on the daily dose: at 1 capsule a day 30 days, at 2 a day 15, at 3 a day 10, at 4 a day 7–8, at 6 a day 5 days. You can read more about capsule density here: Link

The key point is to launch the course with medical help: using DiffBiome capsules requires the supervision of a doctor experienced in FMT^[G], and the exact preparation, the daily number of capsules and the duration are tailored by them to your condition. The more severe the classification, the higher the starting dose and the longer restoration takes. If the daily number of stools does not decrease beyond 48 hours, your doctor may raise the dose up to the maximum of your band; if there is no improvement there either, the starting dose of the next level or a LOT change may come into play, and the classification must be taken again. This is always a medical decision – never change the daily dose on your own.

Don't be put off by the thought that it is "only" a capsule. The living gut flora^[G] it contains, sourced from a rigorously screened donor^[G], replaces exactly what the infection and the antibiotics wiped out – and what probiotics^[G] cannot restore – and this is precisely what durably pushes the pathogen back. In one study, after antibiotics the probiotic was not even neutral: it did colonise the gut mucosa, but it delayed the return of the patient's own flora, whereas the complete microbiota graft restored it within days (Suez 2018 [018]). The details are covered in the following chapters; for now the most important thing is that you start feeling better.

How to take it correctly

Taking it correctly is just as important as the capsule itself. In the morning, on an empty stomach, take the prescribed number of capsules with plenty of water, swallowing them whole – do not chew or open them. Taking them on an empty stomach is not a whim: this is how the capsules were given in the clinical trials of capsule-based FMT as well (Youngster 2014 [019]). About thirty minutes later, drink another large glass of fluid; after that you can have breakfast, take your other medications and start your usual daily routine. Never take the capsules with alcohol or a hot drink, as these can harm the living bacteria.

Two things that matter a great deal: if you are still taking an antibiotic, finish it – on medical advice – at least 48 hours before starting DiffBiome, otherwise the antibiotic would also destroy the freshly delivered flora; the European professional consensus likewise prescribes such a wait before FMT (Cammarota 2017 [016]). And during the course, stop any probiotic preparations, unless your doctor advises otherwise. The capsules contain many thousands of strains, a probiotic at most a few to ten; these are not the same order of magnitude, and the probiotic – as discussed above – may actually slow the return of your own flora (Suez 2018 [018]). Storage follows two regimes: during the course keep the unopened bottle in the refrigerator, in a dark place, standing upright; if the preparation has to be kept for longer, that belongs in the freezer, again in the unopened bottle. This does not mean the capsules are ruined the moment they leave the refrigerator: for a short while – the trip home from the pharmacy, a journey or a working day – room temperature does them no harm either. The refrigerator is where they are stored, not the only environment they can tolerate; put them back as soon as you can. Protect them from moisture and direct sunlight, keep them out of the reach of children, and once opened use them as soon as possible.

🩺 Clinical block

The tool for classification is the SIS (Symptom Importance Scale): two independent subscores – A-SIS (acute severity, maximum 44 points) and P-SIS (prognostic/recurrence risk, maximum 56 points), totalling 0–100 points; 23 weighted variables from four domains (patient-reported symptoms and their severity, laboratory results, prior treatment data, risk factors).

The seven treatment levels directly specify the care setting, the preparation and the dosing. The starting dose is a mandatory initial value; the band maximum is an escalation value only in the case of non-response, not a freely chosen range. The daily density unit is given in brackets (starting → maximum):

Level 1 – SIS 0–24: home observation, fluid replacement; no capsule needed;
Level 2 – SIS 25–39: home course, DiffBiome 30(V)+, starting 1 capsule/day, band maximum 2/day (5 → 10);
Level 3 – SIS 40–49: home course with medical consultation, DiffBiome 30(V)+, starting 2/day, maximum 3/day (10 → 15);
Level 4 – SIS 50–59: home course with close supervision, DiffBiome 30(V)+, starting 3/day, maximum 4/day (15 → 20);
Level 5 – SIS 60–69: hospital assessment, may continue at home, DiffBiome 30(V)+, starting 4/day, maximum 6/day (20 → 30);
Level 6 – SIS 70–79: hospital treatment, HospBiome 5(XX), starting 3/day, maximum 5/day (60 → 100);
Level 7 – SIS 80–100: immediate hospital admission, HospBiome 5(L), 5 capsules/day, for a minimum of 3 days (250);
HospBiome override: regardless of the score, immediate hospital admission, HospBiome 5(L), 5 capsules/day.

Escalation and dose reduction: if the daily number of stools does not decrease beyond 48 hours → raise to the band maximum; if there is no response there either → the starting dose of the next level OR a LOT change (of equal rank), then re-administration of the SIS and reclassification. Dose reduction: a minimum of 10 days on the starting (or escalated) dose, then −1 capsule every 3–4 days, but only if every condition of the symptomatic gate is met — the Bristol value has moved durably from the baseline range towards 5–6 and then 4–5, the extreme daily stool count has decreased appreciably relative to baseline, and there is no blood in the stool. On relapse: back to the band maximum, hold, consider a LOT change. There is no fixed day-ladder.

Clinical override (independent of the calculated score): on detecting critical signs (suspected toxic megacolon, fulminant colitis, severe dehydration, sepsis criteria) → immediate hospital admission is required. The SIS is a decision-support, not a decision-making tool; automatic classification must not be carried out without medical review. Pathway reassignment (not band reassignment), three separate triggers: (1) the SIS falls below 40 in a patient on the CDI protocol → switch to the dysbiosis protocol, FindBiome compatibility test for the personalised TransferBiome treatment; (2) the SIS reaches or exceeds the 50–60 point band in a patient on the dysbiosis or IBS/IBD protocol → switch to the acute CDI protocol, DiffBiome or HospBiome according to the score, with close medical supervision; (3) the SIS remains persistently below 40 after a CDI episode → return to the original protocol, continuing the FindBiome/TransferBiome process and further SIS monitoring. (Source: SIS v7.1 severity scale, approved 2026-08-09 at 08:08.)

🩺 Clinical block

*Capsules in use (SIS v7.1):

at home exclusively DiffBiome 30(V)+ (pooled, fivefold density; at levels 2–5, i.e. SIS 25–69); there is no other home preparation;
in institutions – HospBiome 5(L) (50× lyophilised density, induction, min. 3 days; may be opened if needed and mixed into a neutral fluid – this is an option, not a requirement), 5(XX) (20× density, continuation if the stool count decreases), 5(V) and 15(V) (5× density, late phase – the same capsule, only the pack size differs).

The density system refers to the dry-matter content of a 150 g reference donation: 1 density unit = 1 capsule of density I = 1/1200 of the dry matter. I ≈ 1200, II ≈ 600, V ≈ 240, X ≈ 120, XX ≈ 60, L ≈ 24 capsules from one donation. Clinical anchor: 24 L capsules = 1200 units = the quantity equivalent to one complete conventional faecal transplant. Hyperbolic model: a more severe condition → a more concentrated and/or a higher number of capsules. The tools of the dysbiosis pathway: FindBiome (4×15 capsules, donor–recipient compatibility test) → TransferBiome (60, 2–5 capsules/day, min. 60 days, then dose reduction). Regulation: "Medical Laboratory Services (869015)", SoHO; tied to medical supervision. This is not a local peculiarity: internationally too, FMT is tied to medical supervision and to a controlled, institutional setting — in the United States it is regulated as a medicinal product, in the European Union within the framework for substances of human origin (SoHO) (Hoffmann 2025 [024]; Rodriguez 2025 [025]).*

Day 1 – Classification and the first dose

Today your treatment begins! Together with your treating physician, complete the necessary assessment, and take the first dose of capsules – correctly. Start keeping the diary too – it will be your guide to recovery over the next 90 days.

Classification with the treating physician (SIS); determining the preparation and the daily number of capsules;
The first dose in the morning, on an empty stomach, with plenty of water; more fluid 30 minutes later;
Antibiotic: if you took one, check that you finished it at least 48 hours before taking the first capsule;
Starting the diary: date, preparation and dose (capsules/day), LOT number^[G], daily number of stools, Bristol^[G] value (Lewis & Heaton 1997 [020]), bloating, fluid intake, well-being.

Day 2 – Continuing the course and fluids

Today the goal is continuity: the same intake routine and conscious fluid replacement, because diarrhoea entails the loss of a lot of fluid.

Taking the daily dose according to yesterday's routine (morning, on an empty stomach, with plenty of water);
Fluids: on top of your usual intake, an extra glass of clean, still water after every looser stool — according to the guideline on diarrhoeal infections, fluid and electrolyte replacement is not adjunctive but primary treatment (Riddle 2016 [026]);
Diary: recording the number of stools, the Bristol-scale rating, bloating, fluids, well-being;
Watch for the warning signs (see the box at the end of the chapter)!

Day 3 – A short assessment

Today, assess briefly: is your condition improving, holding steady or worsening? Share this with your treating physician too!

Taking the daily capsule dose;
Diary: the 3-day stool-count and Bristol trend in one place;
If the number of stools does not decrease beyond 48 hours, alert your doctor – the daily dose may then be raised up to the maximum of your band;
If any warning sign appears → see a doctor immediately;
Sleep from now on: keep a fixed wake-up time and get natural light within 10–15 minutes of waking – the composition and function of the gut flora follow a daily rhythm, and if that rhythm is upset, the flora is upset with it (Thaiss 2014 [021]).

🍽️ Eating during these days

The first three days are about classification, the safe launching of the course and fluid replacement – and your eating serves the same purpose. Since at this point diarrhoea and dehydration are the main danger, a gentle, firming diet is what belongs on your table now: plenty of fluids, easily digestible foods and soluble fibre. Soluble fibre^[G] forms a gel in water, which slows the passage of bowel contents and thus supports a firmer stool – the evidence most strongly supports precisely this kind of soluble, gel-forming fibre (psyllium, for example), while coarse, insoluble fibre tends to increase bloating (Eswaran 2013 [022]); and plenty of fluids replace what the looser stool takes away. Your concrete tasks during these three days: on the first day take the first dose in the morning, on an empty stomach, with plenty of water, and 30 minutes later drink another large glass of fluid; on the second and third days keep to this routine, and after every looser stool drink an extra glass.

In this early phase there is not yet a daily plant – the Plant Calendar only starts from day 15. For now the goal is for your bowel to settle, so stay with easily digestible, gentle foods (for example boiled, steamed or peeled), and avoid raw, coarse, strongly gas-forming foods. Building up a varied, diverse diet can wait for the coming weeks, when your symptoms settle.

📊 Data

In the first three days, record these daily:

DiffBiome dose (capsules/day) and the LOT number;
daily number of stools;
stool Bristol scale (1–7);
bloating (0–5);
bloody stool (yes/no);
fluid intake (litres);
well-being (1–5);
Movement: type + minutes, step count (target/actual);
Stress level (1–5) and mood (1–5);
Sleep (hours + quality 1–5).

⚠️ Red flags – with these, see a doctor immediately

Don't wait if you experience any of the following warning signs^[G]: strong, cramping abdominal pain or a tense, tender abdomen; high fever; signs of dehydration (you barely pass urine, dizziness, weakness, confusion); fresh blood in the stool; or if you feel so unwell that you cannot get up. These situations require urgent medical care – the DiffBiome course does not replace the hospital at such times. The international guideline treats these very signs – circulatory collapse, ileus and toxic megacolon – as the hallmarks of the severe, fulminant form, which require institutional care (McDonald 2018 [023]).

Why does this matter?

These three days are about getting your recovery started: about the right classification, the safe beginning of the course, and starting the diary. Understanding and the lifestyle change build up step by step over the coming weeks – for now your job is to make a start!

References

[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.

[017] van Prehn J, Reigadas E, Vogelzang EH, Bouza E, Kuijper EJ et al. European Society of Clinical Microbiology and Infectious Diseases: 2021 update on the treatment guidance document for Clostridioides difficile infection in adults. Clinical Microbiology and Infection. 2021. Link

ESCMID 2021 treatment guidance for C. difficile infection in adults. Metronidazole is no longer recommended where fidaxomicin or vancomycin is available; fidaxomicin is the preferred agent for an initial episode and for the first recurrence; for a second or further recurrence, faecal microbiota transplantation (FMT) or bezlotoxumab in addition to standard-of-care antibiotics is preferred. Compared with the previous edition, emphasis shifts from disease severity to risk of recurrence: treatment strategy is determined by the individual patient's recurrence risk. This supports triage that measures prognostic risk alongside current symptoms.

[018] Suez J, Zmora N, Zilberman-Schapira G, Mor U, Dori-Bachash M et al. Post-Antibiotic Gut Mucosal Microbiome Reconstitution Is Impaired by Probiotics and Improved by Autologous FMT. Cell. 2018. Link

Human and mouse study of what happens to the gut mucosal microbiome after a course of antibiotics. Three routes were compared: spontaneous recovery, an 11-strain probiotic preparation, and autologous faecal transplantation, that is, return of the person's own flora frozen before the antibiotic. The probiotic colonised the mucosa but delayed the return of the indigenous microbiome and of host mucosal gene expression, and the difference persisted for months. Autologous transplantation, by contrast, produced near-complete recovery within days. Conclusion: after antibiotics a probiotic is not a neutral supplement but may slow the return of the native flora; it is a full microbiota graft that replaces the missing community.

[019] Youngster I, Russell GH, Pindar C, Ziv-Baran T, Sauk J, Hohmann EL. Oral, capsulized, frozen fecal microbiota transplantation for relapsing Clostridium. difficile infection. JAMA. 2014. Link

Twenty patients with relapsing C. difficile infection received encapsulated stool from prescreened donors, stored frozen at -80 degrees C: 15 capsules on each of 2 consecutive days. No serious adverse event attributable to the treatment occurred. Diarrhoea resolved in 14 patients (70 percent) after a single course; after re-treatment of the six non-responders the overall figure was 90 percent (18/20). The daily number of bowel movements fell from a median of 5 before treatment to 2 by day 3 and 1 by week 8. This was the first study to obtain results comparable to procedural delivery using frozen, capsulised, orally administered FMT — without sedation or endoscopy.

[020] Lewis SJ, Heaton KW. Stool form scale as a useful guide to intestinal transit time. Scandinavian Journal of Gastroenterology. 1997. Link

The original validation of the Bristol Stool Form Scale. Whole-gut transit time was measured with radio-opaque marker pellets in 66 volunteers, who kept a diary of stool form on a 7-point scale and of defecation frequency. Transit time correlated most closely with stool form (r = -0.54), more strongly than with stool frequency or stool output. When transit time was altered with senna and with loperamide, stool form tracked the change (r = -0.65). Conclusion: recording stool form is a simple and responsive way to monitor change in bowel function — which is why it is suitable for the patient's own diary.

[021] Thaiss CA, Zeevi D, Levy M, Zilberman-Schapira G, Elinav E et al. Transkingdom control of microbiota diurnal oscillations promotes metabolic homeostasis. Cell. 2014. Link

The composition and function of the gut microbiota follow a daily rhythm: bacterial abundance and metabolic activity oscillate across the light-dark cycle, and this oscillation is driven chiefly by the host's feeding rhythm. When the rhythm is disrupted — modelled here in mice and in human samples after intercontinental flight — microbiota oscillation is abolished and dysbiosis develops; transferring the arrhythmic flora into germ-free mice induces metabolic disturbance. Conclusion: a regular daily rhythm is one precondition of microbiota stability — hence the value of a fixed wake time and morning light from the first days of treatment.

[022] Eswaran S, Muir J, Chey WD. Fiber and functional gastrointestinal disorders. American Journal of Gastroenterology. 2013. Link

Review of the role of fibre in functional bowel disorders. The authors organise fibres by solubility and fermentability and stress that these two properties decide which fibre suits a given patient. Fibre ferments partly or completely in the distal small bowel and colon, producing short-chain fatty acids and gas, and thereby affecting gut function and sensation. Where fibre is recommended for functional bowel disease, the evidence best supports a soluble, gel-forming supplement (ispaghula, psyllium). Even when used judiciously, however, fibre can worsen abdominal distension, flatulence, constipation and diarrhoea, so the dose should be built up gradually.

[023] McDonald LC, Gerding DN, Johnson S, Bakken JS, Carroll KC et al. Clinical Practice Guidelines for Clostridium. difficile Infection in Adults and Children: 2017 Update by the Infectious Diseases Society of America (IDSA) and Society for Healthcare Epidemiology of America (SHEA). Clinical Infectious Diseases. 2018. Link

Comprehensive IDSA/SHEA clinical practice guideline on the diagnosis, treatment and prevention of C. difficile infection in adults and children. It defines severity categories (non-severe, severe, fulminant) and characterises fulminant disease by hypotension or shock, ileus or toxic megacolon — findings that require inpatient care, intravenous therapy and surgical consultation. For multiply recurrent infection in which antibiotic therapy has repeatedly failed, faecal microbiota transplantation is recommended. This document provides the international frame to which the book's red flags and hospital-referral signs are aligned.

[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.

[026] Riddle MS, DuPont HL, Connor BA. ACG Clinical Guideline: Diagnosis, Treatment, and Prevention of Acute Diarrheal Infections in Adults. American Journal of Gastroenterology. 2016. Link

American College of Gastroenterology clinical guideline on the diagnosis, treatment and prevention of acute diarrhoeal infection in adults. The foundation of care in every form is fluid and electrolyte replacement: oral, with generous fluid and salt intake, in mild and moderate cases, and intravenous in severe dehydration. The guideline sets out the signs by which dehydration is recognised and the groups at risk, and stresses that rehydration is not adjunctive but primary treatment — which is what supports deliberate fluid replacement after every loose stool during the course.