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How to Do a Fecal Matter Transplant

Updated 1/16/2020

Medically reviewed by Dr. Vibhuti Rana, PhD - Written by Dan Jackowiak Nc, HHP

Dr. Vibhuti Rana, PhD says... The facts and information regarding the fecal matter  transplant process and success rates in this article are medically correct.

Sometimes, the last resort to solve bad bacterial problems is fecal matter transplant. It is also the best way to restore good bacteria to the intestine that have been wiped out by antibiotics or Candida yeast, or to restore or start new good bacterial colonies.

Most people think, and most probiotic manufacturers claim that simply taking probiotics will restore good bacterial levels. This is false. When probiotics are being manufactured, the ability of those bacteria to reproduce is lost, and in about three weeks they will all die. In order to continue getting benefit from the probiotics you must keep taking them. While you take them, their levels will of course rise. Also, they do take a load off your own bacteria so they can reproduce. In time, one of your bacteria can become trillions.

I continued to take probiotics for three years after I treated myself for yeast and bad bacterial problems. Today, 15 years later, I do not have any intestinal problems. Had I known about fecal matter transplant back then, I probably could have cut down my treatment time by two years.


One of the side effects of antibiotics other than Candida yeast overgrowth, is an over growth of bad bacteria due to dysbiosis. Antibiotics, in theory and in practice, target different species of bacteria and are suppose to not affect the rest. But the thing is, they will also kill certain species of good bacteria while leaving some of the other bad guys, depending upon the resistance levels of those bacteria.

In other words, the antibiotic will kill the bacteria it is targeted to, while greatly reducing your good Bacteroidetes and Firmicute bacterial levels, allowing other bad bacteria levels to raise. Clostridium difficile is the most common bad bacterial species that gets out of control from use of antibiotics apart from yeast of course.

When out of control, these bad bacteria can cause inflammation, diarrhea, constipation, bloating, gas, abdominal pain, and sometimes death. I believe they are the primary cause of syndromes such as IBS, IBD, Colitis, Crohn’s, diverticulosis, etc.

Dr. Vibhuti Rana, PhD says...

Fecal matter transplant, or Bacteriotherapy, as it is medically named, is basically a transfer of stool from a healthy individual (with a healthy gut microbiota) to an affected individual lacking the necessary good bacterial balance. The recipients are mostly facing gastrointestinal issues like IBD, Crohn’s, Colitis, etc. A stool DNA test is used to detect C. difficile colitis, a GI complication that is associated with chronic illness. Firstly, there is a targeted antibiotic therapy that kills C. difficile using metronidazole, vancomycin and fidaxomycin. (Source) When recurrent C. difficile infections occur, then fecal transplant is the treatment of choice.

Fecal Matter Transplant Success Rates

Fecal matter transplants have shown tremendous success for combating antibiotic-caused Clostridium difficile infections and Ulcerative Colitis. The US National Library of Medicine is loaded with studies proving the effectiveness of these transplants. The long term success rates run about 90% for C. difficile infections without treating the bacteria first. If the C. difficile is treated first, success rates run as high as 98%.

In the absence of a fecal matter transplant, Vancomycin, and other antibiotics by themselves have a 66% success rate. However, in spite of the 66% success rate, recurrence occurred in 15% to 30% of cases. Patients treated a second time have a 40% chance of recurrence and it gets worse from there.

I am not aware of any studies done on fecal matter transplants and Small intestinal bacterial overgrowth (SIBO) but many people with SIBO have reported a clearing of symptoms. However, if you have predisposing factors  such as bad diet, low stomach acid, motility problems, insufficient bile or enzyme production, it might not help.

Fecal Matter Transplant Preparations

Before doing the actual fecal matter transplant. It is best to knock down the bad pathogen levels if they are present. You do this by either taking antibiotics or natural herbal antibiotics like I outlined on the bad bacteria webpage. The protocol however is slightly different and here it is for you to review.

You will need:

1 - 180 capsule bottle of Biofase

1 - Microfase

1 - Uva Ursi


Take 3 capsules of Biofase one hour before breakfast and at bedtime every day for 30 days. If this seems to be too much for you to handle at first, you have an upset stomach or pain, drop the dose and work up as you are able.

Take 2 capsules of Microfase 30 minutes after Biofase in the morning and 30 minutes before dinner.

Take either 3 capsules of Uva Ursi with meals twice a day, breakfast and dinner would be best, or 2 capsules three times per day with meals for one week then don't take it for a week, then repeat the process.

At the end of this 30 day process you will be ready for the fecal matter transplant.

Good Fecal Matter Transplant Donors & Directions

Siblings and intimate partners tend to make the best donors if they do not have any intestinal problems. However, there is still always the risk of introducing something you don't want, such as amoebas, bad bacteria, or different yeast species.

Many times people adapt to these types of pathogens and do not develop any problems because of them, but that does not mean the same won't cause problems for you. So it is really best to get a stool test of your donor. This test would be more than sufficient.

Once you have established who is going to be your donor you need an enema bag and some distilled water. Heat the water so it feels warm and comfortable to the touch of your skin, do not use a microwave. Rather, use a pot on the stove.

Take your donor stool, fresh as possible is best, and place it in a plastic container, add enough warm water to fill the enema bag. Mix it up thoroughly with a wire whisk; some people actually throw everything in a blender.
You don't want the mixture to be as thin as water or it will be hard to hold in, or if it is too thick it won't flow through the bags nozzle. Once the sample and water are mixed, pour into the bag.

Prepare your location and spread a towel or two to lie on in case of leakage; close to, or in your bathroom. On the floor, would be a good choice with a place to hang the enema bag. Lubricate your anus and the enema bag tip with Vaseline or K-Y jelly. Lie down on your left side, insert tip and open the nozzle.

Once the contents of the bag are finished or you feel like you have taken all you can, turn off the flow and remove the nozzle. Now, every 5 to 10 minutes, roll over so you spend time on your back, your right and left side, and your stomach.
By moving to different positions you are helping the mixture to flow up into your colon. Putting a pillow or something under your hips to raise them, will also help the process. Once you have completed this process you can get up on the toilet and release the mixture.

Sometimes some people only have to do one transplant; other times it can take several transplants once every couple weeks to achieve success.

After You've Done the Transplant

It is important afterwards to eat plenty of fresh vegetables lightly steamed to feed those bacteria; fill up to half your plate at meals.

On this webpage I talk about feeding your good bacteria and I would incorporate at least one of those resistant starches. It would be best to follow this for 3 to 6 months. It would also be best to follow the Candida diet as well or at least avoid the sugar, fructose, trans-fats, wheat, corn, and soy. Eat Omega 3-rich meats and fish.

Hopefully these directions on how to do a fecal matter transplant are clear. If not, feel free to contact us from the contact page of this website.

Medical Review by Dr. Vibhuti Rana, PhD

The Human Microbiome Project revealed that at a time, 160 different bacterial species exist in an individual, and they vary depending upon the sex, race, geographical location, diet, etc. (1) The selection of donor is quite critical in this fecal transplant therapy. The first report regarding the use of feces as therapy was published by Ge Hong in fourth-century China for the treatment of a variety of conditions including diarrhea. In a multicenter study conducted by Brandt et al, in the United States, among 73 patients enrolled in the treatment, diarrhea resolved in 82% and improved in 17% of patients within an average of 5 days after FMT. (2) 

To confer a direct microbiota benefit, the donor must not have consumed antibiotics at least in past 6 months and must not be immunocompromised. The New England Journal of Medicine, in 2013, discussed a randomized control trial showing that duodenal infusion of donor feces for recurrent C. difficile infection had a cure rate of 81% versus a cure rate of 31% for patients treated with the standard course of oral vancomycin. (3)

As it can be noted, the FMT is the upcoming and most successful treatment in case of recurrent failures using multiple antimicrobial compounds or drugs.

Have Any Questions About Fecal Matter Transplants?

Do you have any questions about fecal matter transplants or yeast infections in general? Ask your question here or contact us using the contact page of this website. It is also always a good idea to talk to your doctor as well.

Back to Harmful Bacteria Page

Dr. Rana's References

1. Hollister EB, Gao C, Versalovic J. Compositional and functional features of the gastrointestinal microbiome and their effects on human health. Gastroenterology. 2014;146(6):1449–1458. doi:10.1053/j.gastro.2014.01.052.
2. Brandt LJ, Aroniadis OC, Mellow M, Kanatzar A, Kelly C, Park T, Stollman N, Rohlke F, Surawicz C. Long-term follow-up of colonoscopic fecal microbiota transplant for recurrent Clostridium difficile infection. Am J Gastroenterol. 2012 Jul;107(7):1079-87. doi: 10.1038/ajg.2012.60. Epub 2012 Mar 27.
3. Van Nood E., Vrieze A., Nieuwdorp M., Fuentes S., Zoetendal E., De Vos W., et al. (2013) Duodenal infusion of donor feces for recurrent Clostridium difficile. N Engl J Med 368: 407–415.

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