Frequently Asked Questions about FMT


What are the FDA requirements to qualify for FMT treatment of antibiotic resistant C. difficile?

You must have a C. difficile infection which is not responding to standard therapies. You can read the entire statement on FDA discretionary enforcement here.

What is C. difficile?  Would I know if I had it?  Should I get tested in case I qualify for FMT?

Clostridium difficile infection (CDI), popularly known as C. difficile or C. diff, is an opportunistic infection that causes inflammation of the colon, or colitis.

It is characterized by frequent watery diarrhea (3 times a day or more for 2 days or more) with abdominal cramping. Severe infection may be accompanied by fever, bloody watery diarrhea and painful abdominal cramping.

CDI sometimes occurs following the use of an antibiotic. The most common antibiotics that can create risk for CDI are broad-spectrum antibiotics, especially ampicillin, amoxicillin, cephalosporins, and clindamycin.

There are asymptomatic carriers of both toxigenic and non-toxigenic Clostridium difficile, asymptomatic means they have these bacteria in their gut flora but do not have symptoms. The prevalence of asymptomatic carriers may be as high as 15%.

You need to have a stool test ordered by your physician to diagnose a case of CDI.

For more information about C. diff infections, the American Gastroenterological Association has an excellent page here.


How likely is my condition (especially C. difficile) to return after FMT treatment?

There is currently very little data from randomized clinical trials, however, the clinical data that exists indicates that FMT has a very low recurrence rate, much lower than any antibiotic, especially in CDI that has already recurred multiple times. 


I am taking antibiotics; can I do FMT?

We begin FMT 24-48 hours after completion of an antibiotics course. We do not recommend doing FMT while taking antibiotics.


Would I be able to acquire OpenBiome donor stool through you?

I do not currently contract with OpenBiome for stool products. For those who qualify for treatment I offer pre-screened, pre-prepared FMT from Microbiomes, LLC.


What is the difference between human sourced probiotics and the FMT by capsules that you offer?

FMT capsules deliver an entire microbiome, including many strains of bacteria that are extremely difficult to culture. Human sourced probiotics are generally strains of bacteria sourced from humans and cultured in a lab. The closest thing to a synthetic FMT was developed by Elain Petrof’s lab in her RePOOPulate project, which uses an artificial colon to grow out 33 bacteria from the human colon.


I follow a very specific diet to avoid symptom flares; what about diet changes before/during FMT?

For treatment of C. diff, there is no special diet you need to follow, other than restricting yourself to clear liquids for 24 hours prior to the procedure.

If you are planning a home treatment for a condition other than CDI, and you need tailored dietary guidance and support, I can answer your questions via remote educational consultation or an in-person appointment.


Where can I find a donor?  Can you put me in contact with your donors?  Can you recommend a donor?

According to current FDA guidelines, I am unable to give you access to pre-screened donors or to recommend/connect you with a donor who is unknown to you. If you qualify (LINK TO FDA GUIDELINES PAGE) for treatment in-office, I can treat you using a prescreened donor. Otherwise, the most I can do is to help screen your donor if they can come to the clinic in person to establish a doctor-patient relationship.


What methods of administration do you use for FMT?

I offer FMT via capsules delivered orally or via retention enema delivered rectally at home. I am not able to offer in-office treament with FMT enemas at this time.


How much does FMT cost? Is it covered by insurance?

Unfortunately, FMT is not covered by insurance. If you have a HSA/FSA you may be able to use these funds to cover the cost of your treatment. Contact your HSA/FSA administrator to ask about this possibility. For current pricing structure please see the FEE SCHEDULE page.


How long does the FMT treatment take?

FMT CAPSULES: For treatment with FMT capsules, you can expect to be in the clinic for a minimum of 1 hour, which includes a brief follow-up interview, and between 15 and 30 minutes during which capsules will be dispensed and taken orally in-office with water. Each round of FMT is 35 triple-encapsulated, frozen capsules provided by Microbiomes, LLC.

FMT ENEMA: At this time, I am not able to provide in-office administration of FMT treatment via enema. However, FMT enemas can be dispensed frozen for thawing, instillation, and retention at home. Feel free to ask about this option during your initial consult.


Is your donor material prepared in an anaerobic environment or with minimal oxygen exposure?

The lab where our FMT material is processed takes precautions to minimize oxygen exposure during storage and processing, however, their process is not anaerobic. Strictly anaerobic conditions are not necessary to provide a high enough viability for effective fecal transplant product.


I had C. diff and have not been completely healthy since, but I don’t test positive now; what can I do?

As a licensed naturopathic physician, I have a great number of tools at my disposal to help resolve post-infectious IBS or other lingering symptoms. I use botanicals, supplements, diet and pharmaceuticals to address these symptoms. I may also suggest testing for food allergy and sensitivity, or other diagnostic tests to determine underlying causes of your symptoms.


I am opposed to antibiotic treatment; can I just start with FMT to treat my C. difficile?

The FDA discretionary enforcement policy  for FMT only allows FMT for Clostridium difficile infection that is not responding to standard therapies.


I have a J pouch, can I do FMT?

There is one reported case of the use of FMT for a case of pouchitis caused by C. difficile infection. It was successful.


I no longer have a rectum, can I do FMT?

You may be a candidate for a fecal transplant using capsules.


Can I do FMT during a flare of my symptoms?

Yes. However, if you are using FMT via enema, may have difficulty retaining the enema.


Can you recommend a provider of FMT in my area? 

A good place to start is the Providers & Trials page on the Fecal Transplant Foundation website or the Find a Practitioner page on the American Gastroenterological Association FMT website. Please note that these lists are not at all exhaustive and you may have find a provider closer to you by calling gastroenterologists or infectious disease doctors and asking their offices.


Do you know of a provider who offers FMT for conditions other than C. difficile?

The FDA only allows FMT to be used for treating conditions other than C. difficile in the setting of a clinical trial. To see what clinical trials are currently enrolling, search ‘fecal transplant‘ on

Overseas, both Taymount Clinic (UK, Bahamas) and Newbery Clinic (Argentina) are offering FMT services for diagnoses other than C. difficile colitis.

Can I do FMT at home via enema?  Do you offer guidance?

Many people perform FMT at home via enema. I offer remote educational consultations by Skype or telephone, or you can come in for an appointment. Please call Portland Natural Medicine at 503.239.1022 to schedule.


For patients with C. diff, who are not responding to standard treatment, I can provide pre-screened FMT enemas to be administered at home.

Do the medications taken and/or the food eaten by the donor matter during FMT?

Yes, in some instances. If you have specific concerns, I recommend that you schedule an appointment or an educational remote consultation.


Does age of my donor matter?

The standard recommendation is that donors should be older than 3 and younger than 60 because this is the age range with the greatest diversity of colon flora.


Does the blood type of my donor matter?

Blood type does not appear to be important in having successful FMT.