Question 1

Do probiotics work for Crohn's disease?

Accepted Answer

The evidence is weak, and this is where Crohn's differs sharply from ulcerative colitis. A 2020 Cochrane review found only two small trials (46 total participants) testing probiotics for CD induction, with very low certainty evidence showing no benefit. A 2024 meta-analysis of 45 RCTs confirmed probiotics are not effective for CD maintenance (OR 1.49, 95% CI 0.64-3.50). Saccharomyces boulardii is the single exception, with one positive CD maintenance RCT.

Question 2

What is the Crohn's Disease Exclusion Diet (CDED)?

Accepted Answer

The CDED is a whole-food diet developed by Prof. Arie Levine's team and designed to reduce exposure to dietary components that damage the microbiome and intestinal barrier. It excludes processed foods, emulsifiers, wheat, dairy (except aged cheeses), animal fats, red and processed meat, maltodextrins, sulfites, and carrageenan, and emphasizes chicken, fish, eggs, rice, potatoes, fruits, vegetables, and olive oil. It is paired with partial enteral nutrition supplying 25-50% of calories.

Question 3

Why can't I take Faecalibacterium prausnitzii as a supplement?

Accepted Answer

F. prausnitzii is an obligate anaerobe that dies on contact with oxygen, so it cannot currently be manufactured as a supplement. This protocol focuses on feeding and supporting the F. prausnitzii already present through prebiotics such as inulin and FOS, resistant starch, a Mediterranean-style diet, and avoidance of emulsifiers that damage its niche.

Question 4

How much vitamin D is suggested for Crohn's disease?

Accepted Answer

The protocol describes a starting dose of 2000-4000 IU/day of vitamin D3 (cholecalciferol), with a target 25(OH)D above 30 ng/mL and an optimal range of 40-60 ng/mL. If levels are severely deficient (below 20 ng/mL), a loading dose of 50,000 IU/week for 8 weeks followed by maintenance is described, coordinated with a doctor. Patients with ileal disease may need higher doses due to malabsorption.

Question 5

Why is fecal calprotectin the most important number to track?

Accepted Answer

Fecal calprotectin directly reflects intestinal inflammation and is more sensitive than symptoms alone. Many people with Crohn's feel fine while subclinical inflammation continues to cause stricturing or fistulizing damage. A rising calprotectin, even without symptoms, should prompt a discussion with a gastroenterologist. It is particularly useful for monitoring postoperative recurrence at the anastomotic site.

Question 6

Is fecal microbiota transplantation an option for Crohn's disease?

Accepted Answer

FMT is an emerging clinical treatment for IBD. A 2026 meta-analysis of 6 RCTs found FMT significantly improved clinical remission versus controls (OR 3.24, 95% CI 1.43-7.41, p=0.005) and endoscopic response (OR 6.80, 95% CI 2.96-15.63, p<0.0001). However, most of that evidence comes from ulcerative colitis trials and CD-specific RCT data remains limited. FMT is not a DIY intervention and is performed under medical supervision at specialized centers.

Crohn's Disease Microbiome Protocol: Diet & Supplements