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Treatment > Surgeries

Stool Transplants: Therapy of the Future for Crohn's, Ulcerative Colitis and IBS?

Dr. med. André Sommer

Dr. med. André Sommer

The concept of stool transplantation initially sounds outlandish: Components of a donor's feces are administered to another recipient. To do this, processed stool components are transplanted into the recipient's intestine. The aim is to improve the colonization of the intestine with microorganisms such as bacteria and viruses (intestinal flora).

Why are stool transplants performed?

In a stool transplant, the intestinal contents of a donor are first processed in a laboratory. Only then is it inserted into the gut of a recipient. The most important part of the transplant is the intestinal flora, also called the microbiome. The intestinal flora is made up of many different bacteria and other microorganisms and their metabolic products.

A healthy composition of the intestinal flora is important because the bacteria take over functions in the body. For example, some bacteria produce nutrients such as vitamin K. Other organisms help fight off diseases. By transplanting a healthy intestinal flora, the intestinal colonization of the recipient can adjust to the donated flora. This helps alleviate bowel problems.

How does disturbed intestinal flora lead to symptoms?

The microbiome in each person has a slightly different composition - it is unique, comparable to a fingerprint. Infections, changes in diet, inflammation and medication can permanently change the microbiome. It is possible that some types of bacteria are too strong, while others are underrepresented. This can result in indigestion, diarrhea and a lack of nutrients. A classic example of this is post-infectious irritable bowel syndrome.

Research into intestinal flora is still relatively new. Additional information is always coming out about the role of the intestinal flora in health. For example, there appears to be a connection between being overweight and certain properties of the intestinal flora.

How does a stool transplant help against clostridium difficile?

Stool transplants are already successfully used for a severe form of intestinal inflammation: the therapy-resistant pseudomembranous colitis triggered by the bacterium clostridium difficile. The disease often arises after multiple antibiotics. This kills beneficial bacteria, and the bacterium clostridium difficile can overgrow the intestine. The bacterium can cause colon inflammation (colitis).

Those affected with this disease suffer from severe, bloody diarrhea. Especially in the elderly, this can result in a life-threatening lack of fluids. To make matters worse, only a few antibiotics are effective against clostridium difficile.

The following risk factors exist for this special form of diarrhea:

  • Long hospital stays
  • Feeding via gastric tubes
  • Severe underlying diseases

Stool transplants should be viewed with caution. Such a transplant could also pose health risks. In addition, the long-term side effects are not yet known. So far, knowledge of the intestinal flora has been too limited to be able to estimate the effect of intestinal flora transmission on the recipient.

Can a stool transplant help in other cases?

Some researchers believe stool transplants could also treat IBD and IBS. Other diseases associated with an imbalance in the intestinal flora could also respond well to a stool transplant, because a stool transplant can restore the normal intestinal flora.

After stool transplantation showed good results with clostridial colitis, therapy attempts were extended to other clinical diagnoses. So far, there are only a few patients with ulcerative colitis or IBS who have benefited from a stool transplant.

In addition, study results suggest that a stool transplant could also help with weight loss. So far, however, researchers have only been able to show that obese mice lost weight through stool transplantation from slim mice. Various studies are currently underway to investigate stool transplantation for obesity (metabolic syndrome) in humans.

Can a stool transplant help with IBS?

A few studies looked at whether stool transplantation could also improve symptoms in irritable bowel syndrome. The idea behind this is that IBS, similar to clostridial colitis, often begins with a gastrointestinal infection (post-infectious IBS) before developing into a chronic imbalance of the intestinal bacteria.

In patients with IBS, stool transplantation could alleviate the symptoms in individual sufferers. Patients whose IBS manifested itself mainly through diarrhea responded minimally better to treatment than those with constipation. Long-term results of stool transplants for IBS are not yet available.

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Who is used as a donor for a stool transplant?

There are still discussions about who the ideal donor for a stool transplant might be. Some experts prefer donors who share a living space with the recipient and are therefore exposed to the same environmental influences. This can be a family member or a partner, for example.

Others hope for better effects from selected foreign donors. The reasoning is that here the probability is higher of finding an “ideal” intestinal flora for the recipient. Frozen foreign donations can be used for this purpose, which are preserved in so-called stool banks.

How is a stool transplant performed?

Donated stool can be used either fresh or frozen. It is usually diluted with liquid, for example with 0.9 percent sodium chloride solution. The stool dissolved in saline is then processed into a uniform mixture and then coarse components are removed using a filter. The mixture is usually introduced into the colon as part of a colonoscopy. A gastric tube, a tube that is inserted into the stomach through the nose, is used less often. There are also now capsule-shaped preparations that can be swallowed.

Are stool transplants carried out regularly today?

Except for complicated intestinal infections with clostridia, there is too little reliable data to recommend stool transplants. With other diseases, the acute risks are too great and the long-term consequences are unknown.

However, in addition to instructions on stool transplantation, you can also find offers from doctors online. Enormous prices are sometimes charged for such procedures. Most of the cost must be borne by the patient. But great caution and skepticism is advised with such offers. Some doctors make false promises and use the patient’s despair to persuade them to pay large sums.

Beware! There are numerous testimonials, instructions and paid offers from doctors who offer stool transplants on the internet. These offers are not always serious. It is absolutely not advisable to perform a stool transplant yourself. These measures can be harmful to health and even life threatening.

Will stool transplants soon be used more?

The transfer of stool between two people involves many risks, since stool is a mixture of innumerable substances and organisms that has so far been only partially understood. Probably, stool transplants will only serve experimental purposes and will be replaced by more controllable procedures.

Biotechnology and pharmaceutical companies have recently started researching which components of a stool transplant are beneficial for which diseases. The aim is to produce these substances synthetically and to administer them as medication. Stool transplants and donations would then no longer be necessary if this approach were successful. These drugs are also called microbiome modulators. Studies are currently testing their use for inflammatory bowel diseases.

Should you be disgusted by stool transplants?

The subject of bowel movements is private and hardly anyone likes to talk about it. Understandably, a stool transplant sounds strange or disgusting to many. And there are also skeptics among doctors. Stool transplants are currently only used in exceptional cases in which many other therapy attempts have not helped. It is therefore worth trying to put any feelings of disgust behind and instead focus on the possible chances of success of the method, since it may still be able to help in otherwise almost hopeless cases. Concerns should be discussed openly with the treating doctor.

In addition, neither donors nor recipients are aware of the actual transplantation process in detail. For the donor, the procedure is as straightforward as giving a stool sample. During the transplant, the recipient usually receives a sedative during a colonoscopy and does not remember the procedure.

Do stool transplants have side effects?

Since the effects of the intestinal flora are only partially understood, the side effects of stool transplants are difficult to estimate. So far, such transplants are only conceivable as a therapeutic option if all other options have been exhausted (Ultima Ratio).

Typical short-term symptoms after a transplant are diarrhea, abdominal cramps and nausea. Some recipients also suffer from constipation or flatulence. After a stool transplant, there can be very violent, sometimes life-threatening reactions. If, for example, the intestinal wall and thus the intestinal barrier are severely injured (leaky gut syndrome), the bacteria from the transplanted stool can enter the recipient's blood through the intestinal wall in large quantities. A dangerous consequence of this is blood poisoning.

Even if donors are thoroughly questioned and examined before stool is removed, potentially dangerous bacteria can be transmitted to the recipient. Bacteria with multiple antibiotic resistance do not cause symptoms in healthy people. However, when transferring the bacteria to patients with a weakened immune system, stool transplants can even be fatal.

The long-term consequences and side effects of stool transplantation are so far unknown. It is quite possible that with the transfer of stool certain properties and risk factors can also be transferred from the donor to the recipient. In the case of an overweight stool dispenser, the risk of being overweight can also increase for the recipient of the stool. It is also conceivable that the risk of cardiovascular diseases, metabolic diseases, colon cancer, autoimmune diseases and other diseases is increased by stool transplantation.

What happens after a stool transplant?

After a stool transplant, the transplanted bacteria should ideally settle permanently in the intestine and the symptoms slowly subside. Since it has not yet been finally clarified what influence the intestinal flora has on different areas of the body, not all consequences of a stool transplant can be predicted.

What are the requirements for a stool donor?

Donors make their bowel movements available to a facility that stores the material in optimal conditions - much like a blood bank stores blood donations. Before that, the potential donors have to go through extensive tests. This is to prevent diseases from being transmitted through the stool. If you want to donate regularly, the tests have to be repeated every three to four months. The tests (screenings) give rise considerable costs, since some of them are laborious laboratory tests.

The following diseases are an absolute exclusion criteria for stool donors:

  • Irritable bowel syndrome or similar illnesses in the past (e.g. recurrent abdominal cramps, flatulence, increased urge, diarrhea or constipation)
  • inflammatory diseases in the past (e.g. Crohn's disease or ulcerative colitis)
  • Chronic diarrhea
  • Chronic constipation or regular use of laxatives (laxatives)
  • Colon cancer, colon polyps, or other cancers in the digestive system in the past
  • History of abdominal surgery
  • Taking prebiotics (substances that feed bacteria) or other means of regulating digestion
  • Taking antibiotics in the past six months

In addition to diseases of the donor, other factors such as weight, body mass index, blood pressure and age are now also considered. Experts suspect that stool from all-round healthy donors has the best characteristics.

In addition, a questionnaire on current diseases, travel to certain countries, and other risk factors must be completed before each donation. In addition, donors should avoid certain foods that contain allergens for about five to seven days before stool donation. This primarily includes nuts, peanuts, eggs and crustaceans.

Possible questions before donating stool for stool transplantation:

  • Known HIV or hepatitis B or C infections or contact with sources of infection
  • Risky sexual behavior
  • Tattoo or piercing in the past twelve months
  • Current infections, for example of the upper respiratory tract
  • Travel to countries with an increased risk of travel diarrhea
  • Body mass index
  • Taking medication regularly
  • Previous diseases such as:

    • Autoimmune diseases (including neurodermatitis and asthma)
    • Chronic pain, chronic fatigue or skin diseases (including fibromyalgia, chronic fatigue syndrome)
    • Nervous or muscle diseases (e.g. autism or Parkinson's).

What is the stool examined for before a transplant?

The fresh stool samples have to go to the laboratory without any great delay because they change quickly if they are not cooled. The stool is then examined for the following pathogens:

Enteropathogenic bacteria

  • C. difficile (Toxin B PCR), H. pylori (antibody)
  • Stool culture for Salmonella, Shigella, Yersinia, Campylobacter, E. Coli O157: H7
  • Treponema pallidum
  • Vibrio
  • Listeria

parasites (including parasite eggs)

  • Blastocystis hominis
  • Dientamoeba fragilis
  • Cryptosporidium
  • Giardia lamblia
  • Microsporidium
  • Taenia
  • Entamoeba histolytica
  • Strongyloides stercoralis


  • Rotavirus
  • Norovirus
  • Adenovirus

The following blood tests are carried out on stool donors:


  • HAV
  • HCV (antibody)
  • HBV (Surface and core antibody)
  • HIV 1/2 (antibody)
  • Human T-lymphotropic virus
  • CMV
  • EBV
  • Strongyloides stercoralis
  • Entamoeba histolytica

Health status

  • Liver function tests: AP, AST, ALT
  • Serum-Triglyceride
  • HDL-Cholesterin
  • High sensitivity CRP
  • Fasting blood sugar

In summary, one can say that stool transplants have so far only been used for intestinal clostridial infections, and only as a last resort if all other therapies have been unsuccessful. Although there is a presumption that stool transplants could also help with other clinical diagnoses such as inflammatory bowel diseases and irritable bowel syndrome, there is as yet no scientific evidence of this.

Since intestinal flora is currently still incompletely understood, it is impossible to predict the long-term consequences of stool transplants. Research is being carried out to reproduce certain components of stool transplants in the laboratory in order to enable more targeted use. Because the effects of stool transplantation on the recipient have not yet been fully clarified, the selection of suitable donors is currently very restrictive. This means that certain previous illnesses result in exclusion from donation and donors have to undergo regular and extensive examinations.

Tojo R, Suárez A, Clemente MG, et al. Intestinal microbiota in health and disease: Role of bifidobacteria in gut homeostasis. World J Gastroenterol. 2014;20(41):15163-15176. doi:10.3748/wjg.v20.i41.15163

van Nood E, Speelman P, Nieuwdorp M, Keller J. Fecal microbiota transplantation: facts and controversies. Curr Opin Gastroenterol. 2014;30(1):34-39. doi:10.1097/MOG.0000000000000024

Bäckhed F, et al. The gut microbiota as an environmental factor that regulates fat storage. Proc. Natl Acad. Sci. USA. 2004;101:15718–15723. doi:10.1038/ng.335

Borody TJ, Paramsothy S, Agrawal G. Fecal Microbiota Transplantation: Indications, Methods, Evidence, and Future Directions. Curr Gastroenterol Rep. 2013;15(8):337. doi:10.1007/s11894-013-0337-1

Cully M. Microbiome therapeutics go small molecule. Nature Reviews Drug Discovery. 2019;18:569-572. doi:10.1038/d41573-019-00122-8

Dr. med. André Sommer

Dr. med. André Sommer

I’m André, a medical doctor from Berlin. Together with a team of medical doctors, nutritionists and data scientists we empower people to understand digestive issues with our app Cara Care.

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