Microbiome transfer

The hospital considers microbiome transfer for four groups of patients, and the strength of the evidence differs sharply between them.

• Recurrent Clostridioides difficile infection after at least two antibiotic failures. This is the established indication, and the evidence is strong.
• Severe intestinal dysbiosis after prolonged antibiotic therapy, including the months-long courses many Lyme disease patients have received before they arrive. Evidence here is limited.
• Persistent gastrointestinal symptoms during or after Lyme treatment, and gut dysbiosis documented in Long COVID or chronic fatigue. Evidence is limited.
• Inflammatory bowel conditions with documented microbial disruption, in cooperation with the treating gastroenterologist. Evidence is emerging for ulcerative colitis.

Outside recurrent C. difficile infection, microbiome transfer is an individual treatment attempt decided with the patient after medical consultation. The decision rests on a stool analysis, not on the diagnosis alone: a patient with a normal microbiome does not receive a transfer, whatever the label on the referral letter.

Who is excluded: patients with a severely weakened immune system, for example during chemotherapy or after transplantation; patients with acute severe colitis or recent bowel surgery; patients who cannot safely undergo bowel preparation or sedation; and patients with a documented severe allergy to a food the donor eats. Oncology patients are reviewed by Dr. Martin Rößner and the clinical team before any decision.

For recurrent C. difficile infection the evidence is strong. In the first randomized trial, a single duodenal infusion of donor stool resolved the infection far more often than the standard vancomycin course, and the trial was stopped early because the difference was so large (van Nood et al., N Engl J Med, 2013). A Cochrane review of six randomized trials concluded that the transfer likely leads to a large increase in resolution compared with antibiotics in immunocompetent adults, while noting that the trials were too small to settle its safety profile (Minkoff et al., Cochrane Database Syst Rev, 2023).

For ulcerative colitis the evidence is emerging. An Australian trial of intensive, multidonor transfer achieved clinical remission and endoscopic improvement more often than placebo over eight weeks, and the authors described it as a promising option that still needs its dosing and donor matching defined (Paramsothy et al., Lancet, 2017).

For irritable bowel syndrome the trials disagree. A Norwegian colonoscopic trial found response in 65 percent of treated patients versus 43 percent on placebo at three months (Johnsen et al., Lancet Gastroenterol Hepatol, 2018), and a second Norwegian trial using a single well-characterized donor reported dose-dependent symptom improvement (El-Salhy et al., Gut, 2020). A Danish capsule trial found the opposite: the microbiome changed, but the placebo group felt better at three months (Halkjær et al., Gut, 2018). The lesson we draw is that donor, route and dose decide the result, which is why the hospital works with characterized donor lots and colonoscopic delivery wherever possible.

What the evidence does not show: no randomized trial has tested microbiome transfer in Lyme disease, Long COVID or chronic fatigue, and improvement in those conditions cannot be promised from the C. difficile data.

Safety rests on donor screening. The 2019 international consensus on stool banking sets the standard the hospital follows: donor questionnaire, blood serology, stool testing for pathogens and multidrug-resistant organisms, and traceable frozen lots (Cammarota et al., Gut, 2019), building on the earlier European practice consensus (Cammarota et al., Gut, 2017). The reason that screening is non-negotiable is documented: two patients in US trials developed bacteremia with an ESBL-producing E. coli traced to one donor, and one of them died (DeFilipp et al., N Engl J Med, 2019). Across published series, most adverse events are transient gastrointestinal symptoms; serious events were more frequent with lower-gastrointestinal routes and in sicker patients (Wang et al., PLoS One, 2016).

If a long antibiotic history or a stool analysis has left you with a gut that no longer works, write a short inquiry to the International Office, free of charge; it asks for your findings afterwards. A physician reads them before the video consultation and tells you whether a transfer belongs in your program.