In the last few months and years, the term microbiota has been used more and more often. Microbiota includes all microorganisms in and on our body, such as bacteria, viruses or fungi that are not an original part of our organism, and we cannot live without them. Although it is somewhat ironic that we tirelessly fight against these microorganisms so that they do not cause various diseases, there are also those microbes that protect our body from them, help in the development of the human immune system and enable the digestion of food for energy production. We find them in different parts of the body, and the most interesting part is our intestines. In some people, dysbiosis of the intestinal flora can occur, and thus they are deprived of the many benefits that it provides. However, there is a technique that allows such patients to develop a new intestinal microbiota, and the procedure is called fecal transplantation.

Why is gut microbiota important?

In the introduction, we explained what microbiota is, and besides being found in the intestines, we can also find it on the skin, in the mouth and nasal cavity. Intestinal microbiota is the largest and most diverse population of microorganisms in our body, and it can vary between gender, race and age and largely depends on an individual’s diet.

Intestinal bacteria can synthesize various vitamins, essential (those that the human body cannot synthesize) and non-essential amino acids and carry out the biotransformation of bile. Also, they ensure the metabolism of indigestible carbohydrates such as cellulose. In addition to participating in the metabolism of various substances, they play an extremely important role in the fight against other, dangerous for humans, microorganisms by producing numerous antimicrobial compounds that destroy pathogens, and they can also compete for nutrients and binding sites in the intestinal mucosa, thus preventing colonization of such pathogens.

How does intestinal dysbiosis occur?

The gut-brain axis is a communication system that encompasses neural, hormonal, and immune signals between the gut and the brain, offering the gut microbiota and its metabolites access to the brain. As the brain can manage gastrointestinal functions and as this interaction is bidirectional, it has been proven that stress affects the composition of the intestinal microbiota by changing intestinal peristalsis and the secretion and production of mucin. These effects will cause a change in the habitat of the intestinal microbiota as well as its microbial composition and metabolism. In addition to stress itself, which is ubiquitous in modern society, various other diseases can also cause intestinal dysbiosis, whether these diseases are related to the gastrointestinal system (irritable bowel syndrome and inflammatory bowel disease) or systemic metabolic diseases (type 2 diabetes and obesity).

Fecal transplantation

The intestinal microbiota changes over time due to various factors such as the aforementioned stress, diseases, but also frequent use of antibiotics and travelling. Studies have shown that the gut microbiota can recover, but its continued disruption can lead to loss of function and resistance, which has implications for human health. In order to somehow recover that microbiota for health benefits, we can apply fecal transplantation.

Fecal transplantation is a medical procedure of transplanting a small sample of stool from a healthy colon into a diseased colon. Each sample of healthy stool contains thousands of beneficial bacteria and the rest of the microbiota to participate in the fight against pathogenic ones. It is usually prescribed to treat severe bacterial infections, such as Clostridium difficile infection. In addition, it can be given as a treatment for inflammatory bowel disease, irritable bowel syndrome, obesity, liver disease, diabetes and various food allergies.

This method is relatively new and has been tested in the treatment of Clostridium difficile infection. Most doctors prescribe fecal transplantation when other treatments have repeatedly failed.

Incorporation of feces from a healthy to a diseased colon

Intestinal microbiota in the form of feces can be introduced into the gastrointestinal tract in several ways, such as colonoscopy, upper endoscopy, enema and oral capsule. Colonoscopy involves passing a thin tube with a tiny camera into the large intestine through the rectum. Through this tube, it is possible to deliver a fecal sample into the large intestine. An upper endoscopy involves a similar tube passing through the nose or mouth through the esophagus and stomach into the colon. The disadvantage of this method is that the microbiota must travel through the small intestine to reach the large intestine. An enema uses a tube that delivers a sample of microbiota through the rectum, which then spreads to the colon without risk of significant environmental change. Fecal transplant tablets contain live gut microbiota, are administered orally, and are designed to remain intact until they reach the colon.

Symptoms and risks

Symptoms after the procedure can include bloating, gas, nausea, vomiting, abdominal discomfort and fever. Side effects are expected and there is no cause for concern.

There are always certain risks of transferring harmful pathogens into the patient’s intestine, but that is precisely why samples are rigorously checked before implantation in order to minimize the risk.

Will fecal transplantation be more widely used in the future?

The idea of ​​intestinal microbiota transplantation goes back centuries. With the development of modern medicine, the understanding of its functions and roles is growing. As time goes on and knowledge accumulates, in the future this procedure could be offered as a solution not only to bacterial infection, but also to many other difficult-to-treat diseases.

Translated by: Nina Šlopar


1. Microbiome, 2024., , accessed on 15.3.2024.

2. MJ Bull, NT Plummer. Part 1: The Human Gut Microbiome in Health and Disease. Integrative medicine. 2014, 13,6, 17-22.

3. Fecal transplant, 2023., , accessed on 15.3.2024.

Photography source

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