V. 3 FAQ
The questions below are those that patients ask most often. The answers are short and easy to understand; on any individual question, your treating physician is the one to guide you.
Does the treatment hurt? No. DiffBiome is a capsule taken by mouth – there is no colonoscopy, no enema, no procedure. This is one of the great advantages of oral FMT[G] over the older methods.
How long does the course last? One bottle of DiffBiome contains 30 capsules, which corresponds to roughly a ten-day course, typically with 2–5 capsules a day depending on your classification. In more severe cases a longer or repeated course may be needed – this is determined by your physician. The entire programme of the book is 90 days, because recovery does not end with the course: building up your lifestyle and engraftment also take time.
What can I eat during the course? At the start of the course a gentle diet and plenty of fluids are recommended. As you improve, gradually move to a varied, fibre-rich, plant-based diet – this feeds the beneficial bacteria that are settling in (Koh et al., 2016 [111]). Fermented foods[G] (kefir, sauerkraut) can also support the flora (Dimidi et al., 2019 [161]).
Can I drink coffee or alcohol? Never take the capsule with alcohol or a hot drink, because these can harm the live bacteria. Half an hour after taking the capsule you can return to your usual routine. It is worth avoiding or minimising alcohol during the course; regarding coffee, ask your physician's advice, and do not drink it directly with the capsule.
What if I miss a dose? Don't panic. If you remember, take it as soon as you can, unless it is already close to the time of the next dose – in that case continue with your usual schedule and do not take a double dose. If you miss doses regularly, let your physician know. Keep the diary so you can see the pattern.
Can the infection return after recovery? Unfortunately, with recurrent CDI there is a chance of a repeated relapse, but the DiffBiome course is designed to reduce precisely this risk by restoring the balance of the flora: in a randomised trial, FMT cleared recurrent infection at a substantially higher rate than the antibiotic (van Nood et al., 2013 [029]), and the capsule form proved equivalent to colonoscopic delivery (Kao et al., 2017 [008]). A maintenance lifestyle – a diverse diet, antibiotic awareness – reduces the chance further. If symptoms appear again, turn to your physician; a repeat cycle is also possible.
Am I contagious to others during the course? DiffBiome itself does not make you contagious. C. difficile[G] itself, however, can spread, so thorough handwashing (with soap and water, not just hand sanitiser) is especially important, particularly after using the toilet. This protects both you and those around you.
Can I take antibiotics during the course? If you are still taking an antibiotic, finish it at least 48 hours before starting DiffBiome – otherwise the antibiotic will also destroy the freshly delivered flora; FMT protocols generally require a 1–3 day antibiotic washout before administration (Kelly et al., 2021 [005]). During the course, only take an antibiotic if your physician expressly prescribes it, and always mention to them that you are on a DiffBiome course.
Can I take probiotics during the course? During the course, probiotic[G] products generally have to be stopped, unless your physician says otherwise. DiffBiome delivers a live, diverse flora, and a probiotic can interfere with this in an undesirable way: in a perturbed gut ecosystem, probiotics can delay the reconstitution of your own microbiota (Suez et al., 2018 [018]).
Is it safe during pregnancy or in old age? In older age the treatment is often the only alternative when antibiotics do not work, but because of the several concurrent illnesses and medications, more cautious, closer medical supervision is needed. During pregnancy and breastfeeding there are not enough study data, so the guidelines give no separate recommendation for this situation – the decision must always be made together with your physician, on an individual basis.
What should I do if my immune system is weakened? The course can be considered in this case too, but with increased monitoring – in immunocompromised patients, a case series supports the safety of FMT performed under closer supervision (Kelly et al., 2014 [100]). Report any unusual symptom – even one that seems mild – and stay in closer contact with your physician.
Can I travel with the capsules? Yes. The capsules are products in the SoHO[G] (substances of human origin) category, intended for personal use, and a travel/customs certificate (Medical Recommendation) is available for them, certifying that this is not a medicine but a personal, non-commercial supply. While travelling, keep the capsules in the appropriate, cool storage conditions.
How should I store the capsules? Keep the unopened bottle in the refrigerator, in a dark place, standing upright — the refrigerator is where it is stored (+4 to +8 °C, up to 24 months). For long-term storage, use the freezer (<−20 °C, up to 20 years). Room temperature (≤25 °C) is a transient tolerance, not a storage mode: the capsules stay stable for up to 6 months, but put them back in the fridge as soon as you can. Open the bottle rarely, so that the contents stay protected.
How is DiffBiome different from an ordinary probiotic? Shop-bought probiotics contain a few selected bacterial strains whose colonisation is individual and often only transient (Zmora et al., 2018 [034]). DiffBiome, by contrast, delivers a whole, diverse bacterial community – the flora of a rigorously screened, healthy donor[G] – of which those donor strains persist that have somewhere to settle in your own community (Smillie et al., 2018 [108]), and which thereby restores colonisation resistance[G], the protection that keeps C. difficile in check (Britton and Young, 2014 [002]). That is why it can help where a probiotic alone is not enough.
Why can FMT work where antibiotics fail? An antibiotic “empties out”: it suppresses C. difficile but does not rebuild the missing, diverse flora, and treatment-resistant spores[G] can reactivate once the drug is stopped. FMT “repopulates”: it replaces the missing community and restores colonisation resistance, so the pathogen has no room left. That is why it can break the cycle of recurrence[G] where antibiotics repeatedly fail.
Why does the infection keep coming back? Behind recurrent CDI is a disrupted gut flora[G]: C. difficile spores resist the antibiotic, and because the competing flora is not there, they multiply again after treatment. Each relapse raises the odds of the next (Chilton et al., 2018 [007]) – this spiral is broken by restoring the flora (FMT + lifestyle).
How long until I see results? Symptoms often begin to ease in the first days of the course, but durable remission[G] develops over weeks as the delivered flora settles in: the composition of the transplanted community shifts towards the healthy range within days (Weingarden et al., 2015 [048]), though the exact time course here reflects DiffBiome protocol experience. In the first days, transient bloating or changes in stool are common, and usually mild and self-limiting (Marcella et al., 2021 [015]). The book’s 90-day programme is this long precisely because engraftment and lifestyle-building also take time.
What clinical evidence is there behind DiffBiome? In recurrent C. difficile infection, FMT is among the most effective, best-evidenced treatments (van Nood et al., 2013 [029]), and it is recommended by international clinical guidelines (Cammarota et al., 2017 [016]; Johnson et al., 2021 [028]). Studies have shown that FMT given orally in capsules clears the infection at rates comparable to delivery by colonoscopy – in the randomised comparison, freedom from recurrence was 96% on both routes (Kao et al., 2017 [008]) – so the least burdensome route is also one of the most effective.
What is in a DiffBiome capsule? A thoroughly, multi-step screened whole gut-flora graft from a healthy donor – not a few isolated strains, but a diverse bacterial community. The product is supplied lyophilised, in capsules.
Can DiffBiome cause an allergic reaction? The common side effects are mild and transient: bloating, gas, a temporary change in stool (Marcella et al., 2021 [015]). An allergic reaction is rare but possible – if you notice a rash, itching, breathing difficulty or another unusual, sudden symptom, stop taking it and see a doctor immediately.
Do I need a prescription, and how do I obtain it? Everywhere, the use of FMT is tied to medical supervision and requires the involvement of a physician experienced in FMT – the treatment and dosing are always determined by a doctor. DiffBiome belongs to the substances-of-human-origin (SoHO) category; it is not an ordinary, freely purchasable medicine. Discuss exactly how to obtain it with your treating physician.
When is DiffBiome NOT suitable? In certain conditions – severe immunodeficiency, an active IBD[G] flare, pregnancy, active oncological treatment – the treatment can only be considered with heightened caution and your physician’s approval: the European FMT consensus requires an individual risk–benefit assessment in these cases (Cammarota et al., 2017 [016]), and in immunocompromised patients a case series supports the safety of FMT performed under closer supervision (Kelly et al., 2014 [100]). This is why it is important to tell your doctor about every chronic illness and medication before treatment.
How is C. difficile infection diagnosed? The diagnosis combines symptoms (typically several watery stools a day) and a stool test: the laboratory detects the presence of C. difficile and its toxins[G]. It is important that only diarrhoeal, unformed stool be tested and that the test be interpreted alongside symptoms – asymptomatic carriage of the bacterium does not on its own require treatment (McDonald et al., 2018 [023]). Your doctor always makes the definitive diagnosis.
Is there a vaccine against C. difficile? There is currently no widely available, approved vaccine against C. difficile. The best protection is restoring and maintaining the balance of the flora, avoiding unnecessary antibiotics, and proper hygiene.
How long does C. difficile survive on surfaces, and what should I disinfect with at home? C. difficile spores stay viable on surfaces for a long time and resist alcohol-based hand sanitiser. So after contact with stool, handwashing with soap and water is the preferred method (the friction washes the spores off), and for surfaces a sporicidal, chlorine-based cleaner (bleach, 1:10 diluted sodium hypochlorite) is recommended, especially in the bathroom and around the toilet (McDonald et al., 2018 [023]).
Can my family or my pet catch it? DiffBiome itself is not infectious. C. difficile, however, can spread via its spores, so thorough handwashing and keeping surfaces clean protect those living around you. Healthy people with an intact gut flora rarely fall ill, because an intact microbiota provides colonisation resistance against C. difficile (Britton and Young, 2014 [002]); on current data the risk of catching it from pets is low, but it cannot be ruled out entirely – hygiene matters here too.
Do “natural” remedies (garlic, honey, essential oils, fasting) help? There is no reliable evidence that garlic, honey, essential oils or fasting cure C. difficile infection – these should not be relied on as treatment, and fasting in particular should be avoided, because recovery needs nutrients and plenty of fluids. The proven path is restoring the flora (FMT) and a gradual, varied, fibre-rich diet.
Does stress or mental state affect the infection? The gut and the brain are closely connected (the gut–brain axis[G]), so sustained stress can heighten abdominal sensitivity and symptoms (Cryan et al., 2019 [445]) – but it does not cause the infection on its own. Managing stress, rest and a predictable daily routine support recovery; if the emotional burden is persistently heavy, talk about it with your treating physician.
When should I see a doctor immediately? If you experience strong or tense abdominal pain, a high fever, confusion, severe dehydration (you barely pass urine, dizziness, weakness), or fresh blood in the stool, do not wait – see a doctor immediately, and in a severe case go to the emergency department. These are the red flags, and they require urgent care (Kelly et al., 2021 [005]; McDonald et al., 2018 [023]).
References
[002] Britton R, Young V. Role of the intestinal microbiota in resistance to colonization by Clostridium. difficile. Gastroenterology. 2014. Link
Intestinal microbiota and C. difficile colonization resistance — fundamental mechanisms — The native microbiota inhibits germination and growth of C. difficile spores. Antibiotics impair this defense. Key mechanisms: bile acid metabolism, nutrient competition. FMT restores colonization resistance.
[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.
[007] Chilton C, Pickering D, Freeman J. Microbiologic factors affecting Clostridium. difficile recurrence. Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases. 2018. Link
Microbiological causes of C. difficile recurrence — spore persistence and dysbiosis — Low bacterial diversity correlates with clinical rCDI. Spore persistence + germination is the key to recurrence. FMT and microbiota therapies are increasingly investigated. Targeted antibiotics (fidaxomicin) + microbiota restoration form the combined approach.
[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.
[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.
[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.
[034] Zmora N, Zilberman-Schapira G, Suez J, Mor U, Dori-Bachash M, Bashiardes S, Kotler E, Zur M, Regev-Lehavi D, Brik RB, Federici S, Cohen Y, Linevsky R, Rothschild D, Moor AE, Ben-Moshe S, Harmelin A, Itzkovitz S, Maharshak N, Shibolet O, Shapiro H, Pevsner-Fischer M, Sharon I, Halpern Z, Segal E, Elinav E. Personalized Gut Mucosal Colonization Resistance to Empiric Probiotics Is Associated with Unique Host and Microbiome Features. Cell. 2018. Link
Companion paper to Suez et al. (2018) demonstrating that probiotic colonisation of the gut mucosa is highly person-specific: some individuals are 'permissive' colonisers, while others are 'resistant', and oral probiotic intake exerted a transient and individually variable effect on mucosal community structure and the gut transcriptome. Stool sampling alone fails to detect this heterogeneity – direct mucosal sampling was required. The result undermines the case for empiric probiotic use as a generic intervention. It also provides the conceptual basis for personalised, compatibility-tested microbiota therapy of the kind operationalised by FindBiome.
[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.
[100] Kelly CR, Ihunnah C, Fischer M, Khoruts A, Surawicz C, Afzali A, Aroniadis O, Barto A, Borody T, Giovanelli A, Gordon S, Gluck M, Hohmann EL, Kao D, Kao JY, McQuillen DP, Mellow M, Rank KM, Rao K, Ray A, Schwartz MA, Singh N, Stollman N, Suskind DL, Vindigni SM, Youngster I, Brandt L. **. American Journal of Gastroenterology. 2014. Link
Clostridium difficile infection (CDI) is especially dangerous in immunocompromised patients, yet the safety of fecal microbiota transplantation (FMT) in this group had been uncertain. This 16-centre retrospective series studied 80 immunocompromised patients (75 adults, 5 children) whose CDI was recurrent (55%), refractory (11%) or severe/overlapping (34%); causes of immunocompromise included HIV/AIDS, solid-organ transplant, oncologic disease, inflammatory bowel disease immunosuppression and other conditions. The CDI cure rate after a single FMT was 78%, and the procedure was generally safe: serious adverse events within 12 weeks were uncommon and did not indicate FMT-transmitted infection. The authors conclude that FMT is an effective and safe option for CDI even in immunocompromised patients.
[108] Smillie CS, Sauk J, Gevers D, Friedman J, Sung J, Youngster I, Hohmann EL, Staley C, Khoruts A, Sadowsky MJ, Allegretti JR, Smith MB, Xavier RJ, Alm EJ. Strain Tracking Reveals the Determinants of Bacterial Engraftment in the Human Gut Following Fecal Microbiota Transplantation. Cell Host Microbe. 2018. Link
Strain-level tracking after FMT: the authors examined what determines whether a given donor strain engrafts in the recipient. The strongest predictor is the **composition of the recipient's own community** — a strain engrafts when a relative is already present, or when a free ecological niche exists; donor strain richness and strain abundance also matter. Engraftment therefore follows ecological rules rather than chance, and is modifiable from the recipient's side. Important: the paper describes strain-level determinants; it does not prove fibre availability as a modifiable factor in an RCT.
[111] Koh A, De Vadder F, Kovatcheva-Datchary P, Bäckhed F. From Dietary Fiber to Host Physiology: Short-Chain Fatty Acids as Key Bacterial Metabolites. Cell. 2016. Link
Mechanistic review of short-chain fatty acids (SCFAs), produced by bacterial fermentation of dietary fibre. Fermentable fibre is the primary energy source for the colonic microbiota; the main fermentation products are **acetate, propionate and butyrate**. **Butyrate is the principal energy substrate of colonocytes**; SCFAs also influence barrier integrity, immune function and, once in the circulation, host metabolism, partly via G-protein-coupled receptors (GPR41/43) and histone deacetylase inhibition. This entry is the source for the textbook-level claims of III.2 (S-0302-01, -02). Important: a **review**, not original experimental data.
[161] Dimidi E, Cox SR, Rossi M, Whelan K. Fermented Foods: Definitions and Characteristics, Impact on the Gut Microbiota and Effects on Gastrointestinal Health and Disease. Nutrients. 2019. Link
Review defining fermented foods as products of controlled microbial growth and enzymatic substrate conversion, characterizing common items (kefir, kombucha, sauerkraut, tempeh, natto, miso, kimchi, sourdough bread) and their proposed mechanisms — including microbiota effects. The review summarizes evidence for fermented-food impact on human gastrointestinal health and disease, supporting selective incorporation into health-promoting dietary patterns.
[445] Cryan JF, O'Riordan KJ, Cowan CSM et al. The Microbiota-Gut-Brain Axis. Physiol Rev. 2019. Link
A comprehensive review (Cryan et al., Physiol Rev 2019) of the microbiota-gut-brain axis. It details the communication routes linking the gut microbiota and the brain, including the immune system, tryptophan metabolism, the vagus nerve and enteric nervous system, and microbial metabolites (short-chain fatty acids, branched-chain amino acids, peptidoglycans). The article surveys animal and human evidence for the axis's physiological and behavioral/neurological significance.