Gut restoration

What is gut restoration?

The term includes the Latin word “sanare,” which means “to restore” or “to heal.” While restoring the intestinal tract plays only a minor role in conventional medicine, it holds much greater significance in alternative and holistic approaches. In the past, a common saying warned, “Death sits in the gut.” This expression highlights the intestine as a vital organ for the immune system—and rightly so.

A disrupted gut microbiome affects the immune system just as much as an overly permeable intestinal lining. The latter can lead to what is known as “leaky gut” or irritable bowel syndrome. The goal of restoring an unhealthy gut is to address existing issues and reestablish its full functionality. The focus lies on regenerating both the gut microbiome and the intestinal lining.

The intestinal tract is not only immunologically relevant but also responsible for the utilization of food. It ensures the absorption of nutrients and the elimination of indigestible or intolerable substances.

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The difference between intestinal cleansing and gut restoration

During an intestinal cleanse, the bowel is completely emptied. This can be achieved through an enema or colonic irrigation, as well as by drinking a solution containing Epsom salts. Laxatives are not recommended, especially when used frequently and without medical supervision. The purpose of intestinal cleansing is to fully empty and clean the bowel—for example, in preparation for a colonoscopy.

In contrast, gut restoration aims to reestablish the full functionality of the intestinal tract. The goal is to improve the composition of microorganisms within the gut microbiome. The importance of a healthy, balanced microbiome for maintaining overall health is substantial. If harmful gut bacteria proliferate excessively, they can trigger a range of health complaints.

Why is gut restoration beneficial?

Restoring a gut that is no longer fully functional can be beneficial for several reasons. In particular, gut restoration is recommended after any course of antibiotics, as antibiotics can significantly disrupt the gut flora. Without appropriate supportive measures, the microbiome may not regenerate quickly or thoroughly enough. However, the absence of a balanced and healthy gut microbiome can have considerable negative effects on overall health.

A healthy gut microbiome consists of billions of microorganisms—germs, bacteria, and fungi—that live in symbiosis with our body as long as conditions are balanced. When the gut microbiome is optimally composed, it helps protect the body from external pathogens. At the same time, around 70–80 percent of the immune system is located in the gut. The microbiome also plays a key role in energy supply and in the digestion of food.

When disturbances occur at these levels, they can have noticeable effects on overall well-being. Restoring the intestinal lining helps reestablish its barrier function. Rebalancing a disrupted gut microbiome creates a new equilibrium between the “beneficial” and the “harmful” microorganisms in the gut.

Causes of an imbalanced gut flora

The gut is home to around 400 different microorganisms. Beneficial gut bacteria should predominate. The gut microbiome can become imbalanced due to:

Diseases of the intestinal tract
Medications, especially antibiotics or laxatives
An unhealthy diet high in sugar, refined flour, heavily processed foods, and chronically low in fiber
The use of hormonal medications or oral contraceptives
Stress—particularly chronic stress

A balanced diet made up of freshly prepared, minimally processed foods, sufficient fiber and roughage, as well as resistant starch helps maintain a healthy gut microbiome. Effective stress management and adequate hydration also support a balanced and resilient microbial environment in the gut.

Causes of an imbalanced gut flora

The gut is home to around 400 different microorganisms. Beneficial gut bacteria should predominate. The gut microbiome can become imbalanced due to:

Diseases of the intestinal tract
Medications, especially antibiotics or laxatives
An unhealthy diet high in sugar, refined flour, heavily processed foods, and a chronic lack of fiber
The use of hormonal medications or oral contraceptives
Stress—particularly chronic stress

A balanced diet based on freshly prepared, minimally processed foods, sufficient dietary fiber and roughage, as well as resistant starch helps keep the gut microbiome healthy. Effective stress management and adequate hydration also support a balanced and stable microbial environment in the gut.

When is gut restoration recommended?

In any case, restoring the gut microbiome is beneficial after antibiotic treatments, prolonged medication use, or infections. Chronic stress also has a negative impact on the gut microbiome. In addition, unsuitable dietary habits or conditions such as irritable bowel syndrome can alter the balance of microorganisms in the gut. Further reasons for considering gut restoration may include:

The start of a fasting program
Persistent immune weakness or frequent infections
Ongoing digestive issues
Recurrent fungal infections, such as Candida overgrowth or vaginal yeast infections
Lack of energy and chronic fatigue
Joint complaints and rheumatic conditions
Food intolerances
Elevated cholesterol levels or unfavorable blood lipid and blood sugar values

When harmful gut bacteria gain the upper hand and displace beneficial microorganisms, health can be compromised. Beneficial gut bacteria thrive on a healthy diet that is rich in fiber and roughage. Under favorable conditions, these helpful microorganisms can feed on supplied prebiotics, probiotics, and resistant starch, allowing them to multiply.

Harmful gut bacteria, on the other hand, prefer sugar, refined flour, and heavily processed foods high in starch. They feed on these substances and multiply, disrupting the balance of the gut microbiome. This imbalance can be restored through gut restoration measures and the intake of probiotics, prebiotics, and resistant starch. A long-term adjustment of dietary habits is strongly recommended.

Fasting and intestinal cleansing

At the beginning of a fasting period, a preliminary intestinal cleanse is recommended. This can be carried out independently using Epsom salts (a bitter salt used as a laxative), through colon hydrotherapy performed by a qualified practitioner, or by administering an enema at home. During the fasting period itself, all elimination pathways should be supported. The goal is to help eliminate remaining digestive toxins.

Be sure to also check out our article on the topic: Energy through fasting.

Fasting—whether practiced regularly as intermittent fasting or as longer fasting programs—can be beneficial for both body and mind. As a spiritual tradition, it is deeply rooted in cultures around the world and can still offer profound experiences and insights today.

To support detoxification, morning dry brushing and sauna sessions (from the sixth day of fasting onward) can help stimulate detoxification through the skin. A generous fluid intake of up to three liters of drinking water supports kidney function. Walks in the fresh air improve circulation and oxygen supply. Kneipp water treatments, liver wraps, and abdominal massages may also provide additional support.

Gut restoration – step-by-step guidance

To restore the gut, an initial intestinal cleanse is usually carried out, either through colonic irrigation or the use of laxatives. After this first step, it is important to bring the disrupted gut environment back into a healthy balance. Dietary plans, over-the-counter remedies, and herbal teas can support this process. Supplying the body with live gut bacteria through probiotics is just as beneficial as the intake of so-called prebiotics and resistant starch.

Prebiotics and resistant starch are indigestible food components that serve as the primary nourishment for beneficial gut bacteria. Probiotics are commonly taken as powders or capsules and contain dried yet still viable microorganisms. They support the gut microbiome directly and also help strengthen the barrier function of the intestinal lining. With regular intake, harmful microorganisms can gradually be displaced. While their presence in the gut is natural, they should not become dominant.

Since a long-term change in dietary habits is recommended after every gut restoration, nutritional counseling can be very helpful. Going forward, priority should be given to wholesome, nutrient-dense, and fiber-rich foods—especially those that support the gut microbiome. At the same time, heavily processed and industrially manufactured convenience foods should be removed from the diet.

Sugars found in cookies, cakes, or soft drinks, as well as starchy foods and refined white flour products, serve as preferred fuel for disease-promoting microorganisms. Their consumption therefore inevitably encourages the proliferation of these harmful microbes.

Nutrition during gut restoration

During gut restoration, the diet should primarily consist of freshly prepared foods such as fruits, vegetables, herbs, sprouts, nuts, and unrefined cooking oils. It is important to ensure a balanced ratio of proteins, healthy fats, and carbohydrates, as well as vitamins and minerals. Eggs, fish, and meat should be consumed in moderation. A predominantly plant-based diet is alkaline, rich in fiber and micronutrients, and supportive of overall health.

Known allergens and foods that cause intolerance should be avoided. After restoration, probiotics can be supplied through yogurt or the consumption of fermented foods containing lactic acid bacteria, such as fresh sauerkraut, kefir, or kombucha. All legumes and whole grains are considered sources of prebiotics.

Resistant starch can be obtained from bananas, cashew nuts, oatmeal porridge, as well as homemade whole-grain rice or potato salad.

What does an effective intestinal cleanse consist of?

Simply taking a laxative is not the same as performing an intestinal cleanse. Laxatives are, at best, useful for relieving acute constipation. However, they do not remove residual stool or other burdens from the intestines. From a naturopathic perspective, an intestinal cleanse should consist of three components: the intake of psyllium powder, the use of bentonite or zeolite, and the supplementation of a probiotic containing lactobacilli and bifidobacteria.

Psyllium powder swells in the intestines and forms mucilaginous substances—similar to soaked flaxseed—which nourish the intestinal lining. At the same time, psyllium husks and flaxseed are indigestible fibers that gently cleanse the intestines of residues and deposits. Bentonite or zeolite are used as detox-supporting agents. They bind toxic substances and unwanted compounds in the digestive tract and help remove them from the body.

Finally, probiotics serve to enrich the gut flora and support the recolonization of the intestinal tract with beneficial microorganisms. This process can be further supported by the intake of prebiotics and resistant starch.