FMT and Nutrition: 9 Habits That Enhance Outcomes

Proper nutrition alongside Fecal Microbiota Transplantation (FMT) is a critical topic for your health. Following an FMT performed with rigorously screened donor material (fresh stool), your daily diet creates the environment that determines whether this new microbiota will become a “permanent resident.”

This article serves as a scientific literature-based “roadmap” and is not a substitute for medical advice. You must consult with your EnvaBiome medical team and dietitian to make decisions regarding your personal health status, medications, and FMT protocol.

FMT and Nutrition: Why Is It So Important?

FMT is not a “miraculous solution” on its own. The newly introduced bacteria need a suitable living environment within the gut to achieve both engraftment and long-term maintenance.

Recent Studies Highlight:

• High-fiber, Mediterranean-type, or minimally processed diets can increase microbiota diversity and help sustain the diversity of donor bacteria for a longer period following FMT.
• In some studies, however, the impact of dietary interventions on the clinical outcome has been found to be weaker or uncertain.

In Summary: Nutrition does not replace FMT, but it is a crucial component that strengthens the process by providing a supportive environment for the microbiota.

EnvaBiome Perspective: Fresh Stool + Personalized Support

EnvaBiome adopts an approach that aims to work solely with fresh fecal material, coupled with rigorous donor screening and personalized FMT protocols. This type of fresh stool-focused model seeks to introduce a diverse and vibrant microbiota into the gut flora.

These “guests” must be nourished by elements that are also of crucial importance:

• Your daily meals,
• Your activity levels,
• Your sleep and stress management.

9 Nutritional Habits That Can Enhance FMT Outcomes

1. Gradually Increase Fiber Intake

Fiber is the essential fuel source (prebiotic) for your gut bacteria. Studies show that diets incorporating higher consumption of the following can support microbial diversity during and after the FMT process:

• Whole Grains (oats, brown rice, bulgur, buckwheat),
• Legumes (lentils, chickpeas, beans),
• Vegetables and Fruits

Note: If you experience issues such as IBS, bloating, or SIBO, the increase in fiber must be done gradually and under the supervision of a doctor or dietitian, not abruptly.

2. Sprinkle Fermented Foods Into Each Day in Small Doses

Fermented foods (despite the variability in their probiotic content) can help both increase microbiota diversity and support the production of short-chain fatty acids (SCFAs). Recent clinical and intervention studies, in particular, have shown that a diet rich in fermented foods can increase gut microbial diversity and reduce inflammatory markers over a period of a few weeks.

Examples from Turkish Cuisine:

• Homemade/Labneh-style yogurt & kefir
• Sauerkraut (controlling the salt content)
• Fermented Turnip and Carrot Juice (unsweetened options)

Note: Individuals with histamine intolerance, severe kidney disease, or salt restrictions must consult a doctor before consumption.

3. Minimize Ultra-Processed Foods

Recent data indicates that Ultra-Processed Foods (UPFs):

• Can reduce microbiota diversity.
• Are associated with low-grade chronic inflammation and certain chronic diseases.

Examples of UPFs:

• Packaged snacks, chips, biscuits
• Sugary drinks, flavored sodas
• Ready-made sauces, pre-packaged frozen meals
• Highly refined breakfast cereals

Switching back to “real food cooked in the kitchen” as much as possible provides a far more predictable environment for the microbiota to establish itself after FMT.

4. Limit Refined Sugar and Sugary Beverages

The gut microbiota is more susceptible to imbalance in environments high in simple sugars and low in fiber and complex carbohydrates. Some studies indicate that high-sugar, low-fiber patterns are associated with dysbiosis and inflammation.

Therefore:

• Carbonated drinks,
• Fruit-flavored sugary drinks,
• Excessively sugary desserts

should be the “exception,” not the routine.

5. Prioritize Mediterranean Fats and Fish

The Mediterranean diet (rich in olive oil, abundant in vegetables, and containing adequate fish) has been repeatedly associated with:

• A more balanced microbiota profile,
• Lower levels of inflammation.

Habit Recommendations:

• Use extra virgin olive oil as the main fat source,
• Eat oily fish (salmon, mackerel, sardines, etc.) at least 1–2 times a week,
• Significantly reduce (though not necessarily eliminate) butter intake.

6. Increase Plant Proteins, Reduce Red/Processed Meat

High consumption of red and processed meat can be associated with more pro-inflammatory profiles in the gut microbiota, whereas legumes and plant protein sources provide more fiber and polyphenols.

Actionable Steps:

• Make legumes (such as chickpeas, lentils, and dry beans) the main protein source for at least 2–3 meals per week.
• Relegate processed meats like sucuk, salam, and sausage to the status of an “exception.”

7. Maintain a Regular Meal Rhythm and Eat Slowly

Gut bacteria are influenced not only by what you eat but also by how regularly you eat. Very long periods of fasting followed by very large meals can trigger:

• The diarrhea/constipation cycle in some individuals,
• Bloating and reflux.

During the FMT process:

• Having 2–3 main meals + 1–2 small snacks per day,
• Chewing bites well and eating without rushing,

can support gut motility and digestion. While specific FMT studies on this are limited, this approach is frequently utilized in general gastroenterology practice.

8. Do Not Neglect Fluid Intake

Sufficient water is essential for fiber to pass through the intestines in a healthy manner. When high fiber is combined with low water intake, undesirable levels of constipation may occur during the post-FMT period.

General Rule:

• 1.5–2 liters of water per day is a good starting point for most adults; however, if you have heart/kidney disease or other restrictions, you must follow your doctor’s advice.

9. Do Not Make Supplement Decisions on Your Own

Probiotic capsules, prebiotic powders, vitamin-mineral supplements… These may be beneficial for some patients. However:

• Not every probiotic is suitable for every FMT patient.
• Unnecessary probiotic use can be risky, especially in individuals who are immunocompromised.

Therefore, discuss all supplements first with the medical team managing your FMT. This article provides general information only; do not attempt self-treatment.

Before and After FMT: Who Needs to Be Careful?

You must consult and coordinate closely with your EnvaBiome team and your doctor in the following situations:

• If you are elderly or immunocompromised.
• If you have severe heart, kidney, or liver disease.
• If you have an active flare-up of inflammatory bowel disease (Crohn’s, ulcerative colitis).
• If you are required to follow a specific protocol such as a low FODMAP diet, gluten-free diet, etc.

References:

1. Clancy AK, et al. Dietary Management for Faecal Microbiota Transplant. Nutrients. 2021.
2. Teigen LM, et al. Nutritional optimization of fecal microbiota transplantation. Gut Microbes. 2025.
3. Park I, et al. Fermented Foods as Functional Systems: Microbial, Metabolomic, and Immunologic Aspects. Foods. 2025.
4. Wastyk HC, et al. Gut-microbiota-targeted diets modulate human immune status. Cell. 2021.
5. Khavandegar A, et al. Adherence to the Mediterranean diet can beneficially affect gut microbiota. BMC Med Genomics. 2024. 
6. Perrone P, et al. Gut Microbiota Modulation Through Mediterranean Diet. 2025.
7. Whelan K, et al. Ultra-processed foods and food additives in gut health and disease. Nat Rev Gastroenterol Hepatol. 2024. 
8. Chen X, et al. The Potential Hazards of Ultra-Processed Foods on Gut Health. 2025.