How to talk to your doctor about fecal transplant: a patient’s perspective

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a patient's perspective

Kathy Lammens is a Ph. D. in Philosophy and mother to a child with Ulcerative Colitis. After much effort, Kathy and her husband succeeded in persuading their doctors to let them try Fecal Microbiota Transplant (FMT), an experimental therapy, to treat their daughter’s UC. In this article she advises how to respectfully negotiate with your doctor to secure their assistance with FMT. Note that in the USA doctors are only permitted to carry out FMT to treat Clostridium difficile that does not respond to antibiotics. This does not stop a doctor testing your donor, should you wish to try FMT at home, to treat another condition. 

When my husband and I first introduced the possibility of doing fecal microbiota transplant (FMT) as a treatment for our daughter’s ulcerative colitis, two different doctors at two different research hospitals shrugged us off, apparently because its effectiveness in treating inflammatory bowel disease was minimally studied and documented, especially at the time.  That was early 2012.  Somehow, after a few months of talking with them, trying several standard of care treatments, doing a lot of our own research and finding a pediatric clinical trial using FMT for UC, we received their support.  A lot has happened in the medical community since then, with the completion of several clinical trials and conferences dedicated to FMT and research on the microbiome.   

Arguably, there is still insufficient data by medical standards of the effectiveness of FMT on conditions other than Clostridium difficile, a bacterial infection in the colon. There appears to be no universally accepted protocol, for example, for the means of delivery of the transplants or for the duration of the treatment for UC, and, more importantly there is not enough data on its safety and effectiveness.  The use of FMT is not part of the standard of care.  In fact, even in cases of Clostridium difficile, for which FMT has a very high success rate, it is not necessarily easy to find someone who will perform or support it (you can find lists of doctors who do perform FMT for C. diff on and  It is up to us, then, as patients, to advocate for ourselves and our loved ones to ensure we get the care and support we need from our medical providers.

Through this article I hope to offer you some helpful suggestions about how to talk with your doctor about FMT, since it will likely be you, and not him or her, who will express an interest in it.  In short, you should remember that you and your doctor have the same goals; you should familiarize yourself with the research on FMT and your condition; and you should have a plan (which includes having a good idea about the type of support you need).

You and your doctor are on the same team

Doctors want to help their patients get well.  Your doctor wants to help you get well and has the education, expertise and experience that you do not have in treating patients with your condition.  And, you have sought this particular individual to guide you. However, most doctors have not learned about FMT in medical school, and even if they have heard of it, they may not have had other patients express an interest in it.  FMT is new to the medical profession in comparison to most other treatment options.  Doctors know what they know, and they know what treatments have been successful for their patients.  There is comfort in knowing the treatments they use work for many of their patients.  New treatments and the unknown are scary, and they may pose unknown risks.  On the other hand, for you, the patient, the known potential side effects and risks of conventional treatments might be scary.

When preparing to talk with your doctor about FMT, remember that your and your doctor’s goals are the same: for you to be as healthy as you can be and have a good quality of life using treatments that are effective.  Take care in how you bring up using alternative treatments such as FMT for your condition.   Be willing to take suggestions, and hear his or her concerns.

If you are reading this, it is likely that you have tried standard of care treatments that either may not have worked well, have given you side effects, or pose risks that you are not interested in continuing to take.  You may have gone along with treatments and testing with which you were uncomfortable.  Have an open conversation about these concerns. 

Know the research

If you want the support of a medical professional in using a treatment with which he or she likely has no experience, you should be educated on your condition, the conventional treatments available for your condition (as well as their potential side effects), and how FMT might help your condition.  You should also be prepared to talk about why you think FMT may be a better alternative to what your doctor may be recommending or how FMT may be able to supplement the recommended treatment.

Whatever you do, don’t simply say, “I read about FMT on the Internet and I want to try it for my condition”.  It’s fine to read from the Internet, on various support groups and information websites, but some medical professionals may not take well to a conversation based solely on Internet-based evidence (or what might be seen as “pop” medicine).  A conversation I had with one medical provider was far more productive when I presented information on a clinical trial, as opposed to my initial plea that I’d read about its success on Internet support groups.  The anecdotal evidence was important to me – i.e., I have communicated with people directly who have had success with FMT for UC – but the clinical trial using FMT to treat children with UC seemed to hold the attention of our doctor much better. While there are excellent resources and support on the Internet, many doctors will turn their heads away in the absence of published research.  The good news is that there are academic articles out there about FMT and ongoing clinical trials.  Read up on them.  Bring them to your doctor. Perhaps consider enrolling in a clinical trial if your provider can’t or won’t give you the support you need.

FMT, while potentially a very effective treatment, does not appear to be a panacea.  Be realistic about your expectations when talking with your doctor.  Although it is about 90% effective for Clostridium difficile, it may not have such high success rates for other conditions—most would argue that there hasn’t been enough research done to make claims of effectiveness and safety for most conditions.  Know that FMT will likely be only part of your overall plan to achieve health (e.g., you may continue with some or all of your conventional medications, take nutraceuticals, or make dietary changes).  Have some ideas for how you will handle the rest, and ask your doctor for input.  This is something you may be able to work on together.

Accept that you are taking a risk by trying FMT.  Perhaps compare your perceived risks of FMT (there is simply not enough data on the risks of FMT) with the risks of the current medications and treatments offered for your condition.  Many of the conditions patients want to treat with FMT are conventionally treated with medications that are associated with dangerous side effects.  For example, there are medications prescribed for UC that carry Black Box Warnings on them.

Have a plan

Before talking with your doctor, know where you want to administer FMT—at home (where presumably you would do everything from preparing the enema to administering it), in a clinic, or in a hospital.  You should also know how you want it to be administered—via enema, “poop pills”, nasogastric tube or colonoscopy.  If you want FMT administered anywhere other than in your home and by you, your doctor may be prevented from supporting you because of current FDA regulations.

Have a timeline in mind—your doctor likely will be uncomfortable if your symptoms significantly worsen while doing FMT.  Perhaps agree that you won’t try FMT until your symptoms are a bit under control, or that you will stop if you don’t see improvement after a certain period of time.  You do not want to appear reckless in your approach.  Perhaps be open to have extra labs done to monitor your condition or have more frequent office visits for a while.  Remember that your doctor and you are on the same team.  If you want support, both of you should have some sense of comfort in choosing the treatment you choose or at least in the way your progress is being monitored.

If you are on medications and wish to discontinue them, have a timeline and be sure to have a discussion with your doctor about it.  Be open to suggestions.  Perhaps you want to stay on your medication indefinitely as part of your complete plan to maintain your health.  Talk about that, too.  This is another one of those places where you may give a little for the patient-doctor relationship.

Know what support you need

Different patients have different needs and desires for medical support.  Unlike many medical treatments and procedures, there are a few ways that FMT can be administered, as I mentioned above.  Your support needs will be different depending on which route you would like to go.  For example, if you want to do enemas at home, you may just want your doctor to know that you will be doing fecal transplant, or you may want him or her to write labs for donor testing.  You may want extra labs done on yourself as you go through the process.  Alternatively, you may want to consult with a doctor that has some experience with FMT.  In that case, you may want your consultant to have a conversation with your doctor, if that’s a possibility.       

If you want to have FMT done in a clinic or hospital setting, you will need more support, since your doctor will need to play an active role.  You should know what the FDA policy is in terms of the kind of support your doctor can provide.  In the US, for example, the only condition that can be treated with fecal transplant by a physician (where the physician is actually administering the FMT) is refractory C. diff that does not respond to antibiotics, unless you are involved in a clinical trial, your provider has an Investigational New Drug Application (IND), or your provider is attached to an IND.  

How would you go about having an FMT done in a clinical setting for a condition other than C. diff?  Well, it is my understanding that you may have to find a clinical trial in which to enroll, or ask your doctor to attach him or herself to someone’s existing IND.  Know that that may make quite a bit of extra work for your doctor.  In addition, keep in mind that even if your physician wants to help you, he or she may not be able to due to the policy of the institution by which he or she is employed.

In short, it is important that you go into your medical provider’s office having knowledge about your condition, FMT and the support that you would like to have.  Having an understanding of the support your doctor can provide will help you decide what support is reasonable to request.  Remember that nobody knows exactly why FMT works when it does, how long it takes to see results, and for FMTs one needs to achieve and maintain health.  Don’t expect answers to questions to which your doctor simply doesn’t have the answers.  Know that what you are doing is experimental and there are many unknowns.  And, of course, good luck to you in your quest to find better health. 


If you enjoyed this article you may also enjoy:

Kathy’s Story

Emma’s Story (Video by Kathy’s daughter)

How to talk to your doctor about fecal transplant: a doctor’s perspective 


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