II. Phase 1 – The acute course and foundations (days 4–24)

II. 5 What DiffBiome FMT is, and how it restores balance

You will understand what is in your capsule and how it works: the living, diverse gut flora of a healthy donor, which engrafts in your gut, restores balance, and pushes back C. difficile.

Summary

DiffBiome is the brand name of a so-called faecal microbiota transplant, better known as FMT: it delivers the living gut flora of a healthy, carefully screened donor into your gut – now in the convenient form of a capsule taken by mouth. The diverse bacterial community delivered engrafts in your gut, restores the depleted flora, and gives back the protection that keeps C. difficile^[G] in check. In recurrent infection, studies show this approach brings recovery in most cases. In this chapter you will understand what is in your capsule and how it works.

What is FMT, and what is in your capsule?

FMT^[G] – that is, faecal microbiota transplantation^[G] – rests on a simple core idea: if the infection and the antibiotics have emptied out your protective gut flora, then we replace it with the whole, diverse bacterial matrix of a healthy person. We do not give a single or a few bacterial strains, as conventional probiotics^[G] do: at best they improve individual microbiota measures, but rebuilding the diversity of the whole community and its missing functional groups cannot be entrusted to them (McFarland 2014 [104]). Instead we deliver an entire, functioning community – exactly what is needed to reverse dysbiosis^[G].

In the case of DiffBiome, this happens not through an uncomfortable procedure but through a simple capsule^[G]. The capsule contains gut flora from a healthy, thoroughly screened and verified donor^[G], in freeze-dried form. The freeze-drying (the technical term for it is lyophilisation) allows the living bacteria to be kept viable and stable for a long time, and to be concentrated into a small capsule that can be taken painlessly, without any procedure, even at home (Zain 2025 [833]; Reygner 2020 [832]).

This is an enormous advantage over the earlier, more uncomfortable methods: there is no need for a colonoscopy or an enema. The capsule form is convenient, can be used at home as an outpatient, and makes it easier to stick to the course. It is scalable and repeatable. The contents of your capsule are therefore not a medicine in the usual sense, but life itself – the whole, functioning ecosystem of a healthy gut.

How does it restore balance?

When you take the capsule, the living bacteria inside reach your gut and begin to settle in – this process is what we call engraftment^[G]. The diverse community delivered occupies the places that were emptied out by dysbiosis, and repopulates your gut with the rich flora that became depleted because of the infection and the antibiotics.

As this community engrafts, the natural protection – colonisation resistance^[G] – gradually returns: the restored flora^[G] takes up the space and the nutrients away from C. difficile, and creates an environment in which the pathogen's spores cannot germinate and multiply. The overgrowth of C. difficile recedes, toxin^[G] production falls, and your symptoms ease too.

This explains why this approach is more effective in recurrent infection than continuous courses of antibiotics: it does not merely attack the pathogen, but restores the fundamental balance whose absence was feeding the relapses. In your diary, over the coming days and weeks, you can follow for yourself how your symptom trend turns in the right direction in step with engraftment. Patience matters here: engraftment is a process, not a moment – but the process is working for you.

What to expect during engraftment

In the first days, engraftment may sometimes come with mild, transient discomfort: bloating, gassiness and abdominal discomfort can occur. This is mostly normal – a by-product of the gut flora rearranging itself – and usually eases on its own. Even so, continue the course as agreed, and watch in your diary how the complaints develop.

What is not normal is any of the red flags: severe, cramping abdominal pain, high fever, fresh blood in the stool, signs of dehydration. These always require urgent medical evaluation (McDonald LC 2018 [023]; Kelly 2021 [005]). The difference between transient, mild bloating and warning signs is precisely why daily diary-keeping and the conscious observation of symptoms are so useful – they help you too to judge what belongs to the course of recovery, and when you need to raise the alarm.

🩺 Clinical block

DiffBiome is a standardised, lyophilised human colonic microbiota graft, from a screened donor, in oral capsule form, primarily for recurrent/refractory/therapy-resistant CDI, for home use. Mechanism of action: the living, diverse community of microorganisms colonises the recipient's^[G] gut and restores diversity^[G] – within days the composition of the engrafted community moves from the dysbiotic state back into the healthy range (Weingarden 2015 [048]) – and with it metabolic balance: SCFA^[G] production and bile acid metabolism, which underpin the colonisation resistance that suppresses the overgrowth of C. difficile (Khoruts & Sadowsky 2016 [487]; Reed & Theriot 2021 [003]). Processing: pathogen clearance → bacterial suspension → lyophilisation → encapsulation, with LOT identification and GMP-level quality control. The packaging unit in a dark glass bottle is 30 capsules = roughly a 6-day dose (the amount needed for the full course depends on the severity of the condition); storage at room temperature ≤25°C for 6 months, refrigerated at +4 to +8°C for 24 months, deep-frozen at <−20°C for up to 20 years; room temperature is a transient tolerance, not a storage mode. The evidence base is randomised: in recurrent CDI the cure rate of FMT in the van Nood trial was 81% after the first infusion and 94% overall with a repeat infusion, versus 31% for vancomycin alone (van Nood 2013 [029], NEJM), and the capsule route proved equivalent to colonoscopic delivery in a randomised comparison (Kao 2017 [008]); the rate of serious adverse events is likewise low according to a systematic review of FMT-related adverse events (4,241 patients) (Marcella et al. 2021 [015]); multiple recurrence^[G] is an FMT indication: the ESCMID treatment guidance names FMT as the primary option in multiple recurrence (van Prehn 2021 [017]), which is confirmed by the European FMT consensus (Cammarota 2017 [016]) and by IDSA/SHEA 2021 [028]. Advantages over the conventional delivery routes: non-invasive (no colonoscopy/enema) and ready-to-use; in the randomised comparison a greater proportion of patients rated capsule delivery as not unpleasant at all than colonoscopic delivery (Kao 2017 [008]) – home/outpatient use and better adherence to the course are practical consequences that the trial itself did not measure.

Day 16 – What is in my capsule?

Today, make yourself aware of what you are taking: the living, diverse flora of a healthy donor, which engrafts and restores the balance of your gut. Meanwhile, you continue the usual routine.

Take the daily DiffBiome dose according to the usual routine (in the morning, on an empty stomach, with plenty of water);
Observe whether transient bloating appears, and note it down;
Hydration: an extra glass after every looser stool;
Diary: stool count, Bristol, bloating, bloody stool, fluids, wellbeing.

Day 17 – Support engraftment

Today, work on making the flora feel more at home: enough fluids, rest, and avoiding the unnecessary things that damage the flora help engraftment.

Take the daily DiffBiome dose;
Do not take probiotics or antibiotics on your own initiative;
Build in some rest; regeneration is engraftment's ally;
Diary: stool count, Bristol, bloating, fluids, sleep, wellbeing.

Day 18 – In the mirror of the trend

Today, look back: are the complaints easing, is the consistency of the stool normalising? Engraftment is a process – the trend is your friend.

Take the daily DiffBiome dose;
Diary: review the stool-count and Bristol trend for days 16–18 (the goal is heading towards a Bristol value of 3–4);
If the stool count is not falling, let your treating physician know (a higher DiffBiome capsule count may be needed);
In the event of any red flag → see a doctor immediately;
Sleep enough and regularly: disruption of the daily rhythm also affects gut function – motility, the mucosal barrier and the microbiota itself – and during engraftment this matters especially (Bishehsari 2025 [105]).

🍽️ Eating during these days

In these three days you come to understand what is in your capsule and how the new flora engrafts – and your diet supports this engraftment, still on the gentle, firming line. Your tasks are simple: take the daily dose according to the usual routine, drink an extra glass of water after every looser stool, and do not start a probiotic or antibiotic course on your own that would disturb the freshly arrived flora.

For these days, the Plant Calendar recommends sources high in pectin that are traditionally stool-firming: on day 16 quince (stewed or as a compote), on day 17 grated or stewed apple, and on day 18 blueberries (which contain tannin in addition to pectin). Pectin is a soluble fibre: it forms a gel in water, slows the passage of the gut contents, and so supports a firmer stool while your symptoms settle. Build the plant of the day into at least one meal, prepared gently; if you do not tolerate one of them, leave it out and return to it later.

📊 Data

In these days, record daily:

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

Why does this matter?

If you understand that DiffBiome is not a simple medicine but the whole, living flora of a healthy donor, which engrafts and restores colonisation resistance, then you also understand why it can bring durable recovery where antibiotics failed again and again. Your job now is patience and consistent intake – engraftment is working for you.

References

[003] Reed AD, Theriot CM. Contribution of Inhibitory Metabolites and Competition for Nutrients to Colonization Resistance against Clostridioides difficile by Commensal Clostridium**. Microorganisms. 2021. Link

This review examines how commensal *Clostridium* species mediate colonization resistance against C. difficile. Commensal *Clostridia* modify primary bile acids into secondary bile acids that suppress C. difficile spore germination and vegetative outgrowth. They additionally produce antimicrobial peptides and short-chain fatty acids that directly inhibit C. difficile and compete for limiting nutrients such as proline, important for C. difficile growth via Stickland fermentation. Loss of commensal *Clostridia* after broad-spectrum antibiotics is a key mechanistic step toward CDI susceptibility. The authors conclude from this that new therapies against CDI are urgently needed; the clinical validation of defined *Clostridium* consortia comes not from this review but from the VE303 phase 2 trial [56].

[005] Kelly C, Fischer M, Allegretti J, LaPlante K, Stewart D, Limketkai B, Stollman N. ACG Clinical Guidelines: Prevention, Diagnosis, and Treatment of Clostridioides difficile Infections. The American journal of gastroenterology. 2021. Link

According to the 2021 ACG guideline, FMT is part of standard care for rCDI; strongly recommended after ≥2 recurrences — American College of Gastroenterology's latest CDI guidelines: FMT strongly recommended after ≥2 CDI recurrences; capsule and colonoscopic administration are equivalent; detailed donor screening and storage protocol; COVID-era updates regarding FMT safety also incorporated.

[008] Kao D, Roach B, Silva M et al. Effect of Oral Capsule– vs Colonoscopy-Delivered Fecal Microbiota Transplantation on Recurrent Clostridium. difficile Infection: A Randomized Clinical Trial. JAMA. 2017. Link

Noninferiority randomized trial in 116 adults with recurrent CDI across three Canadian academic centres comparing oral capsule FMT with colonoscopy-delivered FMT (enrolment 2014–2016; noninferiority margin 15%). The study tested whether less invasive capsule delivery matches colonoscopy in preventing further CDI recurrence. Results support clinical equivalence between routes, enabling broader and lower-burden access to FMT for recurrent CDI.

[015] Marcella C, Cui B, Kelly CR, Ianiro G, Cammarota G, Zhang F. Systematic review: the global incidence of faecal microbiota transplantation-related adverse events from 2000 to 2020. Aliment Pharmacol Ther. 2021. Link

Systematic review of FMT safety summarizing adverse events (AEs) over 20 years from 129 studies including 4,241 patients and 5,688 FMT courses (search of EMBASE, MEDLINE, Cochrane, CNKI, Wanfang from 2000 to 2020). AEs were classified as delivery-related or microbiota-related. The review provides the largest aggregate FMT safety dataset to date and supports the overall favourable safety profile of FMT for recurrent CDI, while flagging that complications may be under-reported in the literature.

[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.

[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.

[028] Johnson S, Lavergne V, Skinner AM, Gonzales-Luna AJ, Garey KW, Kelly CP, Wilcox MH. Clinical Practice Guideline by the Infectious Diseases Society of America (IDSA) and Society for Healthcare Epidemiology of America (SHEA): 2021 Focused Update Guidelines on Management of Clostridioides difficile Infection in Adults. Clinical Infectious Diseases. 2021. Link

A focused update of the 2017 IDSA/SHEA guideline, limited to treatment recommendations. The principal change is that fidaxomicin is now preferred over vancomycin for an initial episode — a conditional recommendation with moderate certainty — because although initial cure is similar, sustained cure is better. For recurrent episodes fidaxomicin is likewise preferred, as is a tapered and pulsed vancomycin regimen. Bezlotoxumab is offered as an adjunct for patients at high risk of recurrence. The guideline states explicitly that vancomycin remains an acceptable choice where fidaxomicin is unavailable, and metronidazole has receded even for mild disease. For the SIS the guideline matters because it confirms that the treatment decision depends not only on current severity but on the risk of recurrence — the duality that underlies the acute and prognostic subscores of the SIS.

[029] van Nood E, Vrieze A, Nieuwdorp M, Fuentes S, Zoetendal EG, de Vos WM, Visser CE, Kuijper EJ, Bartelsman JF, Tijssen JG, Speelman P, Dijkgraaf MG, Keller JJ. Duodenal infusion of donor feces for recurrent Clostridium. difficile. The New England Journal of Medicine. 2013. Link

The first randomised controlled trial comparing faecal microbiota transplantation with standard antibiotic therapy in recurrent *Clostridioides difficile* infection. Patients were assigned to three arms: donor faeces given through a duodenal tube after a short course of vancomycin, vancomycin alone, or vancomycin with bowel lavage. The trial was stopped early because the difference was so large: in the transplantation arm 81 percent of patients were cured after the first infusion and 94 percent including repeat infusions, against 31 and 23 percent in the two vancomycin arms. After treatment the diversity of the patients' faecal flora came to resemble that of the donors. This paper turned microbiota transplantation into an evidence-based treatment and is the starting point for the dosing regimen of the present protocol.

[048] Weingarden A, González A, Vázquez-Baeza Y, Weiss S, Humphry G, Berg-Lyons D, Knights D, Unno T, Bobr A, Kang J, Khoruts A, Knight R, Sadowsky MJ. Dynamic changes in short- and long-term bacterial composition following fecal microbiota transplantation for recurrent Clostridium. difficile infection. Microbiome. 2015. Link

Longitudinal microbiome characterisation following FMT in four patients with recurrent CDI, sampling daily for 28 days and weekly to 84 days post-treatment, over a total of 151 days. The recipient microbiota rapidly normalised from a markedly dysbiotic state to a healthy-range composition within days. Composition continued to change thereafter, diverging from the original donor implant material and fluctuating dynamically over both the short and the long term – while remaining throughout within the cloud of healthy microbiota. The paper supports the framing in this Guide that successful MTT produces a self-sustaining recipient ecology, not a permanent donor-tracked imprint.

[104] McFarland, L. V. Use of probiotics to correct dysbiosis of normal microbiota following disease or disruptive events: a systematic review. BMJ Open. 2014. Link

Systematic review of the extent to which probiotics can restore normal microbiota disrupted by disease or antibiotic treatment, covering 63 studies. The result is twofold: individual probiotic strains measurably improved certain microbiota indices, but restoration of the whole community — rebuilding diversity and the missing functional groups — was not achieved in most studies, and the effect was strain-, dose- and baseline-dependent. The paper therefore does not argue against probiotics but for delimiting their scope precisely: delivering a few strains is not the same as replacing a complete, diverse microbiota community. Chapter II.5 of the handbook uses this distinction when separating probiotics from a whole microbiota graft.

[105] Bishehsari F, Post Z, Swanson GR, Keshavarzian A. Circadian Rhythms in Gastroenterology: The Biological Clock's Impact on Gut Health. Gastroenterology. 2025. Link

Review of the role of circadian rhythm in normal gastrointestinal function. The central clock in the hypothalamus and the peripheral clocks in GI organs together orchestrate gut function in response to environmental cycles; this clock is set by cues including light, **sleep** and eating times. Disruption of the rhythm — night-time light exposure, travel across time zones, shift work, mistimed eating, social jet lag — affects GI processes directly: digestion, absorption, **motility**, intestinal barrier function, immune function and the **microbiome**. The paper also discusses circadian-based interventions. Important for the handbook: the article links rhythm disruption to motility and the microbiome — it does NOT claim that sleep deprivation as such accelerates intestinal transit.

[487] Khoruts A, Sadowsky MJ. Understanding the mechanisms of faecal microbiota transplantation. Nat Rev Gastroenterol Hepatol. 2016. Link

Mechanistic review of FMT in recurrent C. difficile infection summarizing the proposed mechanisms of action: direct competition between C. difficile and commensals introduced by FMT, restoration of secondary bile acid metabolism (which inhibits C. difficile germination), and repair of the gut barrier through mucosal immune stimulation. The review consolidates the mechanistic basis for FMT in CDI and highlights translational implications for engineered microbial therapeutics targeting these pathways.

[832] Reygner J, Charrueau C, Delannoy J, Mayeur C, Robert V, Cuinat C, Meylheuc T, Mauras A, Augustin J, Nicolis I, Modoux M, Joly F, Waligora-Dupriet A, Thomas M, Kapel N. Freeze-dried fecal samples are biologically active after long-lasting storage and suited to fecal microbiota transplantation in a preclinical murine model of. Gut microbes. 2020. Link

Lyophilized FMT inocula can be stored for 12 months with stable viability; oral hard-capsule formulation is feasible with 0.5% glidant excipient — Lyophilized and frozen FMT samples retain viability, SCFA concentrations, and anti-C. difficile activity after 12 months of storage. The lyophilized powder can be filled into oral hard capsules; in a murine model, 70% survival rate (vs. 53–60% frozen, 20% untreated). Supports the feasibility of oral capsule formulation.

[833] Zain N, Merrick B, Martin-Lilley T, Edwards L, Ter Linden D, Tsoka S, Mason A, Hatton G, Allen E, Royall P, Lilley A, Bruce K, Shawcross D, Goldenberg S, Forbes B. Bacterial diversity, viability and stability in lyophilised faecal microbiota capsules support ongoing clinical use. International journal of pharmaceutics. 2025. Link

Bacterial diversity and viability of lyophilized enteric-coated FMT capsules are stable at −80°C for 36 weeks, at −20°C and 2–8°C for 24 weeks — supporting cold-chain-flexible clinical application — Lyophilized FMT capsules manufactured under King's College London GMP protocol (5 donors, 16S rRNA sequencing + live-dead separation): species diversity remained stable after manufacturing and 36 weeks of storage at −80°C. No significant viability loss at −20°C and 2–8°C for 24 weeks. Anaerobes survive aerobic processing with minimal loss. Confirms clinical applicability of the lyophilized capsule form with efficacy comparable to other formulations.