Is Fecal Transplant for You? 


If you do not change direction, you may end up where you are headed.

Lao Tzu

So you’ve tried everything and are desperate?  The best the doctors can offer you is a cocktail of increasingly hazardous drugs or chopping out your colon? Or perhaps you’ve been told that your mysterious digestive illness is all in your head?

You spend your nights trawling the internet in search of options. Instead what you find are many cyber-sufferers like yourself, and a truckload of miracle cures offered if only you will part with money you don’t have.

You’ve reached the last resort: a poop transplant. You’re at the point where you are ready to do the unthinkable and squirt someone’s fecal matter up you if it means you might get well. In fact the more you think about it, the more it makes sense.

Be assured that fecal transplant is not a last resort. A lifetime on drugs is a last resort. Losing your colon is a last resort.  Trying to kick-start digestive recovery by infusing healthy bacteria into your ravaged gut is not a last resort. It’s the Ultimate Pro-biotic.

But where do you start? How do you make this decision? What other factors should you consider? Will you use a clinic or DIY? How do you choose donor? How will you persuade your doctor to help you?

If this sounds like you, then keep reading.

Step 1

Rule out all mainstream medically recognised causes of your condition. 

See a doctor, get a referral to a gastroenterologist and go through their standard screening. Depending on your conditions this is likely to include diet, fecal and breath tests, blood tests, colonoscopy, endoscopy etc. Make sure that you are tested for auto-immune conditions as these often go hand in hand with gut conditions and will need to be addressed as part of a recovery plan.

Step 2

Be sure that your problem is dysbiosis related 

Dysbiosis means imbalance of normal intestinal flora and it may or may not be the contributing to your problem. If you have the money, you can invest in a microbial diversity test to confirm that the problem is dysbiosis. These are available through a complementary medical practitioner. If you respond well to pro-biotics then this is a clear indication that dysbiosis is a contributing factor in your illness. However, if you don’t respond to pro-biotics this doesn’t mean you won’t benefit from FMT as pro-biotics are not as powerful and indeed can make your gut worse in the wrong proportions.  Likewise if your condition improves on anti-biotics or when your gut is empty this also suggests dysbiosis is a problem.  

Step 3

Investigate perpetuating factors that may sabotage a successful fecal transplant.  

How far you investigate such factors before taking on fecal microbiota transplant (FMT) will depend on the nature of your gut condition and the difficulty you’re going to experience accessing FMT.  If you have C Diff which is known to respond brilliantly to FMT, just do it.  Get that FMT into you asap.  FMT works for some cases of Ulcerative Colitis, with success rates as high as 70-80% being reported. Likewise if you have convenient, cost-free access to a screened donor, go for it.

But if you are planning to spend a fortune on an expensive clinic or it is going to be difficult to find a healthy, willing and convenient donor then at least rule out some of the more obvious perpetuating factors before going to all the expense / trouble of FMT.  For example there is not much point doing FMT without investigating diet as a perpetuating factor. You could spend thousands of dollars on a clinic or many painstaking hours driving across town to collect donor samples, only to undo all the good results by not identifying a pre-existing food intolerance.  Low stomach acid is another very common perpetuating factor that affects people with chronic digestive illness. It is easy to treat and no amount of good bacteria will fix your gut if your digestive system is not working properly further up.

We all seek simple solutions but particularly if you have been sick for a while it is likely you have accumulated a number of perpetuating factors that contribute to your dysbiosis. Perpetuating factors can sabotage the success of FMT so addressing them needs to be part of a holistic recovery plan.

Step 4

Find a Clinic / Donor

For a list of Clinics, see here. Many of the clinics listed only treat C Diff but if they are located near you it is still worth contacting them to see if they will consider taking you on. You won’t know if you don’t ask.

Note that in the USA clinic-assisted FMT has been halted for everything but antibiotic-resistant C Diff. This should only be temporary until the FDA completes its investigation. It does not stop your doctor from doing donor screening or advising you how to do FMT at home safely.

If you have decided to go with DIY Donor FMT then don’t jump in too quickly. Take the time to make a list of your requirements.  Finding a suitable donor in a world where people poop daily is not as easy as it may seem. But nor is it as difficult as the screening process coupled with the embarrassment factor might suggest.

Be in no doubt that “all poo is not created equal”. Someone with no history of gut problems can still carry bugs in their gut that create other conditions in their body. Something as seemingly unrelated as acne, thrush, UTIs, fibromyalgia or mood swings can be linked to dysbiosis in the gut. People with heartburn, allergies and autoimmune disorders are definitely out. There are links between all of these and gut dysfunction.

Write a ‘must have’ and ‘wish list’ to screen your donors. Remember to be practical. Fresh is best so ideally your donor will need to live nearby. They must also be predictable in their bowel movements and willing to help. You need a donor who will not add to your stress by being unreliable. a minimum your donor must have:

  • regular bowel movements that are firm and formed but not hard
  • good general health
  • good digestive health
  • not prone to gastric upsets
  • no history of anti-biotic use
  • no regular use of anti-inflammatories or painkillers (occasional is ok)
  • no sign of a mood disorder

Male donors are preferable as women have more gut problems.  Children under 16 are not recommended by some practitioners as their fecal matter has not yet matured.  However others have used them without problem. A person who was breast fed and vaginally delivered will have a lower risk of dysbiosis as these are a key to healthy colonisation of intestinal flora in newborns.

Families share more of the same intestinal flora. This could make them better or worse donors depending on their health. Health problems run in families and shared intestinal flora may be the cause. Clearly it depends on the health of your family and this is where you must be the judge.

Some say that multiple donors are better as this injects hybrid vigour into your gut.  Others disagree.   Scientist have discovered that three distinct types of bacterial ecosystems characterise human guts, suggesting that there is merit in trying more than one donor, particularly if the first one doesn’t work.  Some say that relatives are better, others disagree as families can share dysfunctional microbiota. Let common sense prevail.

For tips on how to find and approach a donor see here. For a donor screening questionnaire see here. For the minimum testing of a donor see the list of  Consensus Guidance Tests issued jointly by the US AGA and other organisations.

Some clinics recommend additional testing. Here are some examples. 

OpenBiome (USA)

Bradstreet protocol (USA).

Taymount Clinic brochure (UK)

CDD Home Infusion Protocol for Recipient and Donor (Australia)

Some patients also obtain fecal diversity tests through naturopathic practitioners.  

Step 5

Test your Donor

It is tempting to skip the testing as it takes time, is expensive, will inconvenience your donor and involve your doctor. It is also easy to assume that because someone is healthy they will make a good donor. Think again.  In the Facebook group you will meet many people who have tested potential donors only to find they were carrying asymptomatic parasites. While a parasite might be benign in a healthy person’s gut you don’t want to risk the havoc it might wreak in your fragile gut.  Test your donor.

Step 6

DIY – Fecal Transplant at Home

DIY is not difficult once you know how.  See these DIY  Instructions and the FAQs

The FMT sample should be used within 2 hours of leaving the human body and kept at room temperature until you are ready to use it. Frozen FMT also works but may take longer to colonize.

Step 7

Talk to Your Doctor

stool sampleBe aware that FMT is not yet a widely used procedure and is most commonly used to treat Clostridium Difficile.  While the research on C Diff is conclusive, there still needs to be more research on other conditions. So if you have a condition other than C Diff your doctor will not necessarily feel comfortable referring you to a FMT clinic or testing your donor. You may be made to feel like a ‘bad patient’ who should ‘just learn to live with’ your illness.

It is up to you to make your case in a way that gives the doctor comfort you have thought through the issues and will not hold him/her accountable if FMT doesn’t work.

Before you see your doctor, do your research and prepare your case. If you’re a good talker, talk it through. If you’re a good writer, write it down. If necessary recruit a friend or family member to be your advocate. Be prepared.

It’s important to stress that lack of research doesn’t mean FMT won’t work – or that it will harm.  It just means the science hasn’t caught up with the treatment.   Ultimately it is your decision if you want to take a chance on a treatment that may not work.  Let’s face it you have tried many treatments that haven’t worked which is why you are now having this conversation with your doctor. A reasonable doctor will recognise this.  If they won’t, then listen to their reasons and if they are not convincing find another doctor. You are the person who has to live with this condition, not them.

Read these interviews with a medical doctor and a naturopathic doctor, both who practise FMT.

Step 8

Research & Talk to Others

Before you make your decision read the FAQs, explore this site and join our Facebook group to chat with others on a digestive illness journey, some of whom have FMT success stories to tell. It’s a secret group so only your friendship with Sally will show on your Facebook profile. The Bacteriotherapy Facebook group is not affiliated with PoP but is also a good resource on all things microbiota. It is a closed group so your posts are private but your membership is public.

If your question isn’t answered please feel free to contact us. Together we will change the image of poop.


The first step toward getting somewhere is to decide that you are not going to stay where you are.

John Pierpoint Morgan


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