Gut Microbiome and Fasting

The human gut hosts more than 100 trillion microorganisms. This “community,” known as the gut microbiome, consists primarily of bacteria, but also includes viruses, fungi, and archaea. The role of the microbiome in our health is not merely supportive, but fundamental. The balance of the microbiome is closely linked to:

• the digestion and absorption of nutrients
• the regulation of the immune response
• protection against pathogenic microorganisms
• the production of metabolites with systemic effects, such as short-chain fatty acids (SCFAs)

Dysbiosis, meaning disruption of the microbiome’s balance, has been associated with conditions such as metabolic syndrome, obesity, depression, autoimmune diseases, and inflammatory bowel diseases.

We live in an era in which nutrition, gut health, and lifestyle practices are becoming central to our overall well-being. Among these practices, fasting, whether in the form of intermittent fasting or more traditional forms of food restriction, is increasingly discussed as a means of improving health, with potential benefits for inflammatory markers, weight regulation, and the long-term prevention of chronic diseases.

In the Greek population, fasting is not only a modern metabolic strategy but also a deeply rooted cultural and often religious practice, involving periods of abstinence from animal products and changes in dietary composition for weeks or even months. This means that its effects are related not only to time-restricted eating but also to qualitative changes in dietary composition.

Recent scientific evidence indicates that the type, duration, and frequency of fasting can alter the composition and function of gut bacterial populations, thereby directly influencing inflammatory mechanisms, insulin sensitivity, and even nervous system function. Thus, fasting is not merely a matter of calories, but also an issue of cellular and microbial regulation.

Understanding the biological mechanisms that define the relationship between fasting and the microbiome extends to investigating different fasting protocols, their impact on gut microbiome balance, and how this balance, in turn, affects overall health. Furthermore, such understanding is essential to properly use the diagnostic tools offered by the functional approach to ensure the safe and effective implementation of fasting strategies in daily life.

How Does Fasting Affect the Microbiome?

The effects on the microbiome vary depending on the type of fasting. In intermittent fasting, the primary factor is time-restricted eating. In traditional religious fasting, the key determinant is a change in dietary composition, with increased consumption of plant-based foods and reduced consumption of animal products.

Different forms of fasting appear to directly influence the composition and function of the gut microbiome in the following ways:

• Reduction of pathogenic microbes and enhancement of beneficial species. In intermittent fasting, the periodic absence of food appears to modify the gut metabolic environment, thereby limiting bacteria associated with inflammatory processes. In traditional fasting, increased consumption of plant-based foods and reduced intake of saturated fats may promote the growth of species with anti-inflammatory effects, such as Akkermansia muciniphila and Faecalibacterium prausnitzii, thereby contributing to improved intestinal epithelial integrity.
• Increased production of short-chain fatty acids (SCFAs). The production of SCFAs, such as butyric acid, primarily depends on the fermentation of dietary fibers. In traditional fasting, in which the diet consists of legumes, vegetables, fruits, and whole grains, the availability of substrates for microbial fermentation increases. In intermittent fasting, the effect depends more on the composition of the diet during eating windows. If these meals are rich in fiber, overall SCFA production may be enhanced, with positive effects on inflammation and blood glucose regulation.
• Resetting of the gut circadian rhythm. The microbiome exhibits daily fluctuations that synchronize with the feeding–fasting cycle. Time-restricted eating appears to enhance synchronization between the intestinal clock and glucose metabolism. In traditional fasting, although there is not always strict time restriction, meal consistency and dietary simplicity may also contribute to improved metabolic regulation.
• Enhancement of intestinal integrity and reduction of permeability. Alternating phases of feeding and fasting may activate cellular renewal mechanisms, such as autophagy, that support intestinal epithelial health. At the same time, a more plant-centered diet, as followed during traditional fasting, may increase the production of butyric acid, which exerts protective effects on intestinal epithelial cells and strengthens intercellular connections.
• Reduction of systemic inflammatory markers. Clinical studies indicate that both intermittent fasting and dietary patterns with an increased plant-based focus are associated with reductions in markers such as C-reactive protein (CRP) and interleukin-6 (IL-6).

The above mechanisms highlight that fasting does not function in isolation but interacts with an individual’s metabolic and microbial profile, necessitating a more personalized, functional approach.

The Functional Approach to the Microbiome and Fasting

Functional medicine does not merely seek to diagnose a symptom, but to understand the “why” behind each dysfunction. At the same time, it adopts a multifactorial approach to health, accounting for interactions among genes, environment, and lifestyle.

Within this framework, fasting is evaluated not only as a dietary pattern but also as a metabolic stressor or regulatory factor. Its implementation is approached as a targeted regulatory intervention, provided that an individualized assessment has first been conducted.

Questions raised in a functional assessment include:

• What is the condition of the intestinal barrier? Are there any signs of increased permeability?
• Is there dysbiosis or overgrowth of specific bacterial populations?
• What are the body’s needs? Are there subclinical deficiencies? This is particularly important during prolonged periods of traditional fasting, when the intake of animal proteins, iron, vitamin B12, and omega-3 fatty acids is restricted.
• How does the body respond to glucose? Are there indications of insulin resistance?
• What is the function of the stress axis? Are cortisol levels properly regulated?

Through this systematic analysis, fasting can be incorporated as a targeted intervention rather than a general recommendation.

When Further Investigation Is Needed
Each body is different. Two individuals may present similar symptoms (e.g., bloating, fatigue, weight gain) yet have different underlying causes. It is worth investigating deeper mechanisms, especially if, during fasting, you experience:

• Severe bloating, gas, or bowel irregularities
• Hypoglycemic episodes, dizziness, or pronounced fatigue
• Worsening of autoimmune or inflammatory symptoms
• Inability to lose weight despite adherence (if fasting is being used for this purpose)
   

How the Evaluation Is Conducted
The foundation of functional intervention is individualized assessment and diagnosis through specialized testing. Using the tools of functional medicine, this evaluation may include, depending on medical history:

• EnteroScan®: a specialized assessment of the gut microbiome, providing detailed analysis of its composition, along with evaluation of functional markers of digestion, intestinal permeability, and inflammation.
• NutriScan®: a panel of tests designed to detect deficiencies in vitamins and micronutrients that are essential for metabolism and proper gut function.
• Insulin Resistance, HOMA-IR: used to evaluate metabolic profile and metabolic sensitivity prior to implementing fasting.
• AdrenalScan®: hormonal testing to assess adrenal function and the stress axis.
• ImmuneScan®: assessment of systemic inflammatory markers that reflect the body’s internal inflammatory state.

Assessment of the above parameters allows for personalization of the nutritional strategy. For some individuals, a mild time-restricted eating approach may be beneficial. For others, restoration of gut balance is required before implementing any fasting protocol. The functional approach does not impose general guidelines; rather, it designs recovery pathways based on each person’s profile.

Practical Nutritional Strategies: What to Consider During Fasting

Fasting, whether involving time-restricted eating or abstinence from specific food groups, does not automatically function as a therapeutic intervention. It is a metabolic tool whose outcome depends on the overall dietary framework, the duration of implementation, and the individual's biological condition.

To meaningfully support the gut microbiome and metabolic balance, strategies and personalization are required. The following points deserve particular attention:

1. Adequate intake of dietary fiber and prebiotics. Microbiome health depends on the availability of appropriate substrates. Soluble and insoluble fibers, legumes, vegetables, fruits, and whole grains nourish beneficial bacteria, thereby promoting the production of short-chain fatty acids, including butyrate. In traditional fasting, increased consumption of plant-based foods can significantly enhance this process, provided that the diet is qualitatively balanced and not overloaded with refined carbohydrates. In intermittent fasting, emphasis should be placed on meal quality during eating windows to ensure that overall fiber intake is not reduced.

2. Adequate and high-quality protein intake. Prolonged abstinence from animal products or frequent fasting without adequate replenishment may result in insufficient protein intake. This affects muscle mass, basal metabolic rate, and immune competence. During religious fasting, it is important to use alternative plant-based protein sources, such as legumes, nuts, and soy products, and to combine them appropriately to achieve a complete amino acid profile. In intermittent fasting, meals must contain sufficient protein to prevent metabolic dysregulation and sharp fluctuations in blood glucose.

3. Adequate micronutrient coverage. During prolonged abstinence from animal-based foods, attention must be given to nutrients such as vitamin B12, iron, zinc, and omega-3 fatty acids. Deficiencies in these nutrients may affect immune function, intestinal integrity, and overall energy levels. Similarly, among individuals who consistently practice intermittent fasting, fewer meals may lead to subclinical deficiencies if the diet is not properly planned. Assessment of micronutrient status through specialized testing can help prevent such conditions.

4. Fat quality and inflammation control. The fats consumed during fasting periods directly influence the inflammatory profile and the microbiome. Emphasis on olive oil, fatty fish, and nuts contributes to anti-inflammatory effects and supports intestinal epithelial stability. In contrast, excessive consumption of fried foods, processed vegetable fats, and simple sugars may promote metabolic endotoxemia and negate the potential benefits of fasting.

5. Meal regulation, hydration, and stress management. In time-restricted eating, meal consistency and avoidance of overeating during eating windows are critical. In traditional fasting, organizing balanced meals prevents excessive intake of simple carbohydrates. At the same time, adequate hydration and proper electrolyte balance are essential, especially during periods of caloric restriction. Chronic stress may negate the benefits of fasting by disrupting the hypothalamic–pituitary–adrenal axis and affecting intestinal permeability.

6. The Role of Personalization. The duration, frequency, and intensity of fasting must be adapted to each individual’s metabolic and hormonal profile. For example, individuals with irritable bowel syndrome or a history of SIBO may require modifications in the intake of specific carbohydrates. Similarly, women with hormonal imbalances may not tolerate prolonged fasting without careful monitoring.
Particularly regarding intermittent fasting, not all protocols are suitable for everyone. Following appropriate laboratory assessment, its implementation can be designed with greater precision.
A mild protocol, such as 12 or 14 hours of fasting, may be sufficient to improve circadian synchronization and glycemic regulation in individuals without significant disorders. In contrast, more demanding protocols, such as the 16:8 model or occasional 24-hour fasts, require careful selection in individuals with:

• insulin resistance
• elevated inflammatory markers
• thyroid or adrenal disorders
• symptoms and indications of intestinal dysbiosis

In Conclusion

Whether fasting is chosen for health, prevention, weight loss, or for religious and cultural reasons, its effects on the gut microbiome and metabolism are not neutral. They depend on duration, frequency, dietary composition, and, most importantly, on each individual’s biological background.

In this way, fasting ceases to be a general practice and becomes a personalized regulatory strategy, based on objective data and the individual health profile. Understanding the underlying mechanisms and conducting targeted laboratory investigation form the foundation for safe and effective choices.

What You Can Do Today:

• Discover what is truly happening in your body through EnteroScan®, a specialized functional analysis of the gut microbiome, so that you can implement dietary practices that are appropriate for your individual physiology.
• See how Functional Medicine can help you in practice, by identifying root causes instead of just masking symptoms.
• Subscribe to our newsletter to be the first to receive updates on new preventive tests, wellness articles, and practical advice from Diagnostiki Athinon.

References

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2. Paukkonen I, Törrönen EN, Lok J, Schwab U, El-Nezami H. The impact of intermittent fasting on gut microbiota: a systematic review of human studies. Front Nutr. 2024;11:1342787.
3. Fazeli PK, Steinhauser ML. A Critical Assessment of Fasting to Promote Metabolic Health and Longevity. Endocr Rev. 2025;46(6):856-876.
4. Maulvi FA, Desai DT, Vyas BA, Shah DO, Willcox MD. Fasting as a Multisystem Health Modulator: A Narrative Review of Metabolic, Cardiovascular, Immune, Neurocognitive, and Psychospiritual Effects. Curr Nutr Rep. 2026;15(1):4.
5. Smith RL, Soeters MR, Wüst RCI, Houtkooper RH. Metabolic Flexibility as an Adaptation to Energy Resources and Requirements in Health and Disease. Endocr Rev. 2018;39(4):489-517.
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7. Fernandes I, Mariana M, Lorigo M, Cairrao E. The Influence of Plant-Based Diets on Metabolic Syndrome. Diabetology. 2024; 5(3):255-270.

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