Analysis of the intestinal flora: the most important questions and answers

Analyse der Darmflora: Die wichtigsten Fragen und Antworten

The intestinal flora is a complex structure of different microorganisms, which fulfills a large number of important functions for our body. Anyone who has a disturbed intestinal flora usually suffers from various digestive symptoms, which can eventually develop into serious illnesses.

If you suspect that your intestinal flora is not in order, there is the possibility to have the intestinal flora analyzed. But in which cases does the intestinal flora analysis really make sense and how exactly is it carried out? In this article you will find out everything you need to know about the intestinal flora analysis: where you can buy a self-test, what costs you should expect and how meaningful the analysis results are.

the essentials in brief

  • Intestinal flora is the totality of all microorganisms that live in our intestines. It supports digestion, forms important hormones and vitamins and regulates our immune system. If the intestinal flora gets out of balance, this can promote certain diseases.
  • An intestinal flora analysis, which is carried out from a stool sample, enables the detection of an intestinal flora disorder. Thus, a timely therapy can be started and the development of various diseases can be prevented.
  • In order to bring a disturbed intestinal flora back into balance, a change in diet is usually necessary. Lactic acid fermented foods as well as probiotics and prebiotics can help to build up the intestinal flora.

Gut flora analysis: What you should know

We have put together the most important questions and answers on the subject of intestinal flora analysis for you. You will learn which tasks the intestinal flora has, which causes lead to their disturbance and how this can affect our body. We will also advise you whether an intestinal flora analysis makes sense for you and how it is carried out.

What is the intestinal flora?

Up to 99 percent of all microorganisms that live in the human body are located in the large intestine. In total, their weight is estimated at 1-2 kilograms and their number at 100 trillion.

The entirety of all these microorganisms is referred to as the intestinal flora or microbiome. They are primarily made up of different types of intestinal bacteria, but also fungi and viruses. If all the microorganisms living in the gastrointestinal tract are in a balanced ratio to one another, the intestinal flora is said to be healthy.

The gastrointestinal tract of an unborn child is still relatively sterile. The first colonization with microorganisms only begins during birth, when the baby is given the first microorganisms from its mother's intestinal flora. As the child develops, the intestinal flora is increasingly colonized by a wide variety of new microorganisms (1).

The colonization of the gastrointestinal tract with bacteria occurs mainly in the first 3 years. After that, the intestinal flora remains mostly stable. The more diverse the intestinal flora develops in childhood, the less susceptible it will be to various disorders.

What are the tasks of the intestinal flora?

When microorganisms were first discovered in the gut, they were all thought to be pathogens. We now know that there are also "good" bacteria in the intestines that are not only harmless, but even vital.

The following tasks are attributed to the "good" intestinal bacteria:

  • The intestinal bacteria support the digestive work. They form special enzymes that break down food components that could otherwise only be processed incompletely. The resulting degradation products cover a large part of our body's energy requirements.
  • The intestinal flora is extremely important for a functioning immune system. With a surface area of ​​around 400 square meters, the intestinal mucosa represents the first and largest interface of the body. The bacteria that live here produce lactic acid, which lowers the pH value of the intestinal flora. Since this is inhospitable to many pathogenic bacteria, it prevents them from spreading. Researchers also assume that the intestinal bacteria are constantly involved in training the gut-associated immune system (2).
  • The intestinal flora produces important vitamins and hormones. These include vitamins B2 (riboflavin), B12 (cobalamin) and K as well as the hormones serotonin and dopamine.

The "good", health-promoting intestinal bacteria include, for example, the lactic acid-producing lactobacteria, which are also known as probiotics. They prevent pathogens from multiplying by acidifying the intestines.

What causes the intestinal flora to be out of balance?

As long as there is a balance in the intestinal flora, the microorganisms living there are harmless. However, if the composition of the intestinal flora is out of balance, it can also have a harmful effect on our body.

The following factors can unbalance the intestinal flora:

  • high-sugar or high-fat diet
  • antibiotics
  • gastric acid blockers
  • regular use of laxatives
  • alcohol
  • permanent stress

Several studies also point to the harmful effects of medication on the intestinal bacteria. A research group has examined the effect of 41 different drug classes on the human intestinal flora.

In general, a diverse colonization of the intestinal flora is desirable.

The study results suggest that about half of commonly used drugs harm the "good" gut bacteria. These primarily include proton pump inhibitors, metformin, laxatives, and antibiotics (3).

But an incorrect diet, especially one that is high in sugar, also has a major impact on the balance of our intestines. This is confirmed by another study, the results of which show that six commonly used artificial sweeteners are toxic to gut bacteria (4).

Unhealthy food

Unhealthy eating habits can also have a negative impact on the intestinal bacteria. A diet high in fat and sugar in particular can throw the intestinal flora off balance. (Image source: unsplash / Sander Dalhuisen)

Stress can also negatively affect the proper functioning of our intestinal flora. A study shows that the diversity of gut bacteria can decrease as a result of prolonged stress. This in turn can promote the development of autoimmune diseases (5).

How can a disturbed intestinal flora affect the body?

The intestinal flora plays an extremely important role in the proper functioning of our body. If it is disturbed, which is also known as dysbiosis, it can promote various gastrointestinal, but also metabolic, psychological and even malignant diseases.

The following diseases are associated with the dysbiosis of the intestinal microflora:

illness Description
Chronic inflammatory bowel diseases (especially ulcerative colitis and Crohn's disease) and irritable bowel syndrome Patients with IBD and irritable bowel syndrome have a reduced variety and altered composition of the intestinal bacteria. As a result, inflammatory pathogenic processes in the intestinal mucosa are amplified.
Type 2 diabetes mellitus, obesity It still remains unclear whether dysbiosis is the cause or consequence of metabolic diseases. However, studies show that the composition of the intestinal flora in overweight people and type 2 diabetes patients differs from the intestinal flora in healthy people.
Multiple Sclerosis, Arthritis, Lupus Erythematosus In autoimmune diseases, the immune system not only attacks pathogens, but also endogenous tissue. Since the intestine is the seat of the immune system, a disturbed intestinal flora can promote the development of autoimmune diseases.
allergies If the composition of the intestinal flora changes, the pathology in food allergies and allergic respiratory allergies can intensify. This often happens as a result of treatment with antibiotics.
depression, schizophrenia Several studies indicate that gut bacteria can contribute to the development of mental illness. A healthy gut flora ensures the production of various neurotransmitters, such as serotonin, whose dysfunction is associated with depression.
colon cancer Researchers suspect that certain intestinal bacteria prevent the development of colon cancer. If their number decreases, effective control of tumor growth is not possible.


In order for the microbiome to perform all its vital tasks, the microenvironment in the gut must cooperate. It is therefore important to ensure a healthy and balanced composition of the intestinal flora.

For whom is an intestinal flora analysis useful?

If the intestinal flora is out of balance, the intestine sends us different warning signals. Although occasional digestive problems can be perfectly normal, there are certain symptoms that could be related to dysbiosis, especially if they are long-term.

The following symptoms can be a sign that your intestinal flora is calling for help:

  • intestinal cramps
  • Diarrhea
  • stomach pain
  • gas
  • increased susceptibility to infection
  • constipation
  • recurring skin and fungal infections
  • nausea

The digestive problems mentioned above are often related to food intolerance. However, if these occur regularly and regardless of what you have eaten, then an intestinal flora analysis could be useful for you.

Rapid weight gain can also be a sign of a disturbed intestinal flora.

Since the correct composition of our microbiome plays an important role in the functioning of the immune system, a disturbed intestinal flora can also manifest itself as an increased susceptibility to diseases. So if you also have frequent colds, an intestinal flora analysis could be informative for you.

How can I have my intestinal flora analyzed?

A self-test is used to analyze the intestinal flora, which you can order online from a large number of different providers or buy in pharmacies. At home, you then use an analysis kit to take a stool sample, which you send back to the provider. This will be evaluated for you in a partner laboratory of the provider.

You can order an intestinal flora self-test from these providers, for example:


Your report contains detailed information about the parameters you have selected. You can discuss the analysis results with your doctor or alternative practitioner, who may be able to advise you on possible therapy options.

Intestinal flora analysis

With an intestinal flora analysis, you will receive your personal microbiome profile, which can help you or your doctor to clarify the causes of your symptoms. (Image source: Fernando Zhiminaicela / pixabay)

Note that the intestinal flora test is not suitable for certain groups of people. This includes people with infectious diseases such as HIV and hepatitis, people under the age of 18, but also pregnant and breastfeeding women.

How meaningful are the results of an intestinal flora analysis?

Although the specific readings that are examined may vary slightly from provider to provider, a gut flora analysis can provide you with results from the following areas, for example:

  • Structure of the intestinal flora: What is the variety of bacteria in my intestine?
  • Balance of the intestinal flora: is there a balance between "good" and "bad" types of bacteria?
  • Ratio of the different bacteria: Is my microbiome possibly contributing to my not being able to lose weight?
  • Food intolerance: Do I have a tendency towards lactose or fructose intolerance, for example?
  • Inflammatory factors: Are there inflammatory disease factors in my intestines that can cause intestinal inflammation?
  • Disorders of the intestinal immune system: Is my immune system weakened as a result of dysbiosis?

In addition to the analysis results, with some intestinal flora tests you will also receive individual recommendations for improving your intestinal flora or a nutrition plan.

Although the results of the intestinal flora analysis can be very useful for creating a nutrition plan, you should always keep in mind that the composition of the intestinal bacteria is subject to short-term fluctuations. These happen, for example, as a result of taking medication or traveling.

How much does an intestinal flora analysis cost?

The price of an intestinal flora test differs depending on the provider and the parameters to be examined. In the following table you will find an overview of the average costs of different variants of the intestinal flora analysis.

Scope of the intestinal flora analysis Costs
Complete gut flora analysis about 70-200 €
Analysis of individual values ​​(e.g. mushrooms, food intolerance) from €30

In principle, the costs of an intestinal flora analysis are not covered by statutory health insurance companies. Special regulations only apply in acute cases of illness and possibly after a stay in the tropics. Patients over the age of 50 are also entitled to annual stool examinations as part of colon cancer screening.

The relatively high costs are one reason why the intestinal flora analysis is only rarely offered by doctors.

When does it make sense to have my pet's intestinal flora analyzed?

Similar to humans, a disturbed intestinal flora in your pet can manifest itself through various defense mechanisms. Gut flora screening may be useful if your pet consistently suffers from the following symptoms:

  • Diarrhea
  • fecal water
  • colic
  • recurring allergies and skin problems
  • stomach problems
  • recurrent parasite infestation

Gut flora screening is performed from a stool sample just like humans, with the difference that this is usually done after consultation with your veterinarian. It is best to find out from your alternative animal practitioner whether they offer an intestinal flora analysis.

The average cost of gut flora screening in animals ranges from €35 to €65, depending on the parameters to be examined. In addition, there are the costs of evaluating the results and creating a therapy plan, which you should calculate with around €70 to €100.

What can I do if the result of the intestinal flora analysis is not good?

The causes of a disturbed intestinal flora can range from an unhealthy lifestyle to taking antibiotics. In this part we have prepared a few tips for you on how to bring your intestinal flora back into balance.

Build up the intestinal flora with a balanced diet

One of the most common causes that throw our intestinal flora off balance is unhealthy eating habits. In order to rebuild a disturbed microbiome, it is first and foremost necessary to avoid the disruptive factors. Ideally, you should limit high-fat, high-sugar, and highly processed foods.

In addition, there are two strategies to positively influence your microbiome through nutrition. On the one hand, you can directly absorb the bacteria that are useful for the intestines. These primarily include bifidobacteria and lactic acid bacteria, which are found in lactic acid foods (15).

They occur naturally in the following foods, for example:

  • yogurt
  • kefir
  • sauerkraut
  • Cheese
  • kombucha

In addition to the above foods, there are microbiological preparations - the so-called probiotics, which contain a high number of appropriate bacteria. You can get these in the form of powder or capsules in pharmacies, for example.


Yogurt is one of the best probiotic foods. The fresher it is, the more lactic acid bacteria it contains. (Image source: unsplash / Joanna Kosinska)

In addition, it is necessary to provide the desired intestinal bacteria with sufficient food. For this we need indigestible food components (prebiotics) that promote the growth of intestinal bacteria. The intestinal dwellers especially love fiber, which includes, for example, inulin, pectin and oligofructose. These are found in the following foods:

  • fruit bowls
  • linseed
  • Jerusalem Artichoke
  • Garlic
  • Chicory
  • artichokes
  • whole grain products

perform intestinal cleansing

Intestinal cleansing is a concept from alternative medicine that is used primarily in cases of susceptibility to infections and chronic complaints such as allergies. In addition, intestinal cleansing is also useful after prolonged antibiotic use.

Intestinal rehabilitation is about rebuilding a healthy intestinal flora.

In the first step it is necessary to clean the gastrointestinal tract. The intestine is usually emptied with the help of a laxative such as Epsom salt and thus freed from "bad" bacteria.

Once the intestines have been cleaned, the next step is to actually build up the intestinal flora. This usually requires a permanent change in diet and the use of probiotics and prebiotics. Sugar, alcohol, white flour, animal proteins and products with many additives should be avoided as completely as possible or at least limited.

We recommend that you discuss the individually appropriate diet after the intestinal cleansing with your doctor or naturopath.


The intestinal flora is a complex organ that performs a number of different tasks. If the intestinal flora gets out of balance, this can manifest itself through various symptoms and possibly also diseases. It is therefore important to pay attention to a balanced and diverse composition of our microbiome.

If you have doubts about the health of your intestinal flora, an intestinal flora analysis can be useful for you. You can do this very easily with a home test. This will tell you whether your symptoms are caused by a disruption in the microbiome. With a healthy diet, you can bring the "good" intestinal bacteria back into balance and prevent any serious illnesses.


    Palmer C, Bik EM, DiGiulio DB, Relman DA, Brown PO. Development of the human infant intestinal microbiota. PLoS Biol. 2007;5(7):e177. doi:10.1371/journal.pbio.0050177 Source Hebbandi Nanjundappa R, Ronchi F, Wang J, et al. A gut microbial mimic that hijacks diabetogenic autoreactivity to suppress colitis. Cell. 2017; 171(3):655-67. doi: 10.1016/j.cell.2017.09.022. Source Vich Vila A, Collij V, Sanna S, et al. Impact of commonly used drugs on the composition and metabolic function of the gut microbiota. Nat Commun. 2020;11(1):362. Published 2020 Jan 17. doi:10.1038/s41467-019-14177-z Source Chi, L.; Bian, X.; Gao, B.; Tu, P.; Lai, Y.; Ru, H.; Lu, K. Effects of the Artificial Sweetener Neotame on the Gut Microbiome and Fecal Metabolites in Mice. Molecules 2018, 23, 367. Source Michal Werbner, Yiftah Barsheshet, Nir Werbner, Mor Zigdon, Itamar Averbuch, Oren Ziv, Boris Brant, Evan Elliott, Shachaf Gelberg, Moran Titelbaum, Omry Koren, Orly Avni. Social-Stress-Responsive Microbiota Induces Stimulation of Self-Reactive Effector T Helper Cells. mSystems May 2019, 4(4)e00292-18; DOI: 10.1128/mSystems.00292-18 Source Takaishi H, Matsuki T, Nakazawa A, et al. Imbalance in intestinal microflora constitution could be involved in the pathogenesis of inflammatory bowel disease. Int J Med Microbiol. 2008;298(5-6):463-472. doi:10.1016/j.ijmm.2007.07.016 Source Raskov H, Burcharth J, Pommergaard HC, Rosenberg J. Irritable bowel syndrome, the microbiota and the gut-brain axis. Good Microbes. 2016;7(5):365-383. doi:10.1080/ 19490976.2016.1218585Source Valles-Colomer, M., Falony, G., Darzi, Y. et al. The neuroactive potential of the human gut microbiota in quality of life and depression. Nat Microbiol 4, 623-632 (2019). Source Stefka AT, Feehley T, Tripathi P, et al. Commensal bacteria protect against food allergen sensitization. Proc Natl Acad Sci US A. 2014;111(36):13145-13150. doi:10.1073/ pnas.1412008111Source Russell SL, Gold MJ, Hartmann M, et al. Early life antibiotic-driven changes in microbiota enhance susceptibility to allergic asthma. EMBO Rep. 2012;13(5):440-447. Published 2012 May 1. doi:10.1038/embor.2012.32 Source Davis CD. The Gut Microbiome and Its Role in Obesity. Nutr Today. 2016;51(4):167-174. doi:10.1097/ NT.0000000000000167Source Gurung M, Li Z, You H, et al. Role of gut microbiota in type 2 diabetes pathophysiology. EBioMedicine. 2020;51:102590. doi:10.1016/j.ebiom.2019.11.051 Source Kirby TO, Ochoa-Repáraz J. The Gut Microbiome in Multiple Sclerosis: A Potential Therapeutic Avenue. Med Sci (Basel). 2018;6(3):69. Published 2018 Aug 24. doi:10.3390/medsci6030069 Source Zhang H, Liao X, Sparks JB, Luo XM. Dynamics of gut microbiota in autoimmune lupus. Appl Environ Microbiol. 2014;80(24):7551-7560. doi:10.1128/ AEM.02676-14Source Gareau MG, Sherman PM, Walker WA. Probiotics and the gut microbiota in intestinal health and disease. Nat Rev Gastroenterol Hepatol. 2010;7(9):503-514. doi:10.1038/nrgastro.2010.117 Source
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