It's true Max! The world does revolve around us.

The protocols in this post have been updated and expanded in my e-book, FMT Coach: A Guide to Fecal Microbiota Transplantation.

Still feeling good. I had a scare this week: I began to feel what I thought were UC symptoms recurring, (achy body, gurgly gut) so I took another infusion. No reason not to be safe. Then 24 hours later, I was laid up—body aches, weak, and D. Oh no. Flare up. S**t, I thought. Turns out, it was a real, live stomach flu—my wife had the same thing just a few days ago, and today I am on the mend. Boy, I was scared. Stupid stomach virus mimicking UC symptoms. Thanks for all your comments and questions. I hope to answer most of them in this post; however, this post will be colitis-specific because that’s what I have. That’s what I treated, and that’s what I know best. For those with Crohn’s, I don’t know how this treatment effects your condition. I will say this upfront: Do this in partnership with your doctor. That is, don’t go off and do this without a doctors supervision. This is not medical advice, rather a recounting of my story. I hope that it will help you.


4/1/11 Addition: Slate Magazine did an article on Bacteriotherapy. You can read that article here.

This post is long. You may want to take it in pieces.

P.S.–The amazon links in this post are affiliate links, which means that if you click through my site through one of the below links, I am credited a small percentage of the sale. I use that to buy books that in turn feed the content of this blog. Some day I’d love to generate enough through those links to buy copies of Breaking the Vicious Cycle to give away for free to those starting the SCD.

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The Theory

If changing the bacterial population of the colon decreases inflammation, and improves colitis, then colitis is at least in part pathogenic; an altered bacterial community sets off a cascade reaction which leads to inflammation and damage of the colon. Probiotics, communally oriented bacteria, such as Lactobacillius and certain Bifidio Bacteria have been shown to improve inflammation in the colon; however, those bacteria are transient and are not even in the top 40 most abundant species in the healthy human gut. It follows, then, that the best probiotic would be a complete mix of bacteria from a healthy, gut-normal person.

Antibiotics have also been shown effective in some cases. Therefore, the combination of the two make sense for treatment. Kill the ‘damaged’ flora; replace it with a complete, healthy flora.

Talking with Your Doctor

I wrote a post on talking with your doctor back in July, 2010. I still stand by this post. Two years of meeting with my doctor, using the principles I outlined in July form the foundation, the basis for a good trust relationship; it is this relationship, and the trust I built with my doctor that allowed us to even enter a productive dialogue about a non-conventional therapy like Bacteriotherapy. If you don’t have that kind of relationship with your doctor, then chances are you won’t get far enough in the conversation to need the tools I will outline below. Start by building a trust relationship. It also helps if you have an awesome doctor.

Before I even considered talking with my doctor about bacteriotherapy, I made sure to do credible research. Not research that is credible for the lay person (no blogs, no website language), but peer-review research. I searched the scientific literature for studies, case studies, and articles that are peer-reviewed; articles that he was most likely to take seriously. Next I read them. No really, you’d be surprised at how many people find a study and just read the abstract, or skim the intro and conclusions. I read everything. Then I summarized it in an executive summary 2-page briefing document for him.

This accomplished a few things: (1) it made sure that I remembered what was in the papers. It ensured that I knew more about Bacteriotherapy than he did. It made sure I could answer his questions—on the fly; (2) It gave him something tangible to hold, to read; (3) It showed him that I was serious, and that I had a plan; I knew the risks (this is important). From there it was easy. I entered the conversation with a subordinate posture, with respect: you, my doctor, are the expert. But I was clear what I wanted to do. I asked for him to partner with me. Notice I didn’t ask for permission, but I asked for his partnership. I needed him, and I made him an integral part of the process. This is out of respect (I love my doctor), and out of necessity.

The conversation went something like this:

[Usual small talk and greeting] “Dr [Name], I came in to talk with you about starting a new treatment. It’s a little off the beaten path, but I’d like to run it by you.”

“Ok, Matt, fine. But I thought your diet was doing you pretty well?”

“It is. It is, but it’s only gotten me about 80% of the way. I still have colitis. My goal is to have a clean scope one day.”

[Smiles] “Ok, what do you want to talk about?”

“Have you heard of Bacteriotherapy? I’d like to try it. I’ve outlined the procedure I’d like to use here (hand him the 2-page summary), and I’d like you to partner with me in a 17 day trial. The risks are minimal compared with the drugs we’ve tried.”

[Reads my summary with a concerned look] “I’ve heard of this, but it’s pretty far off the beaten path.”

“I know, but if you look at the pilot and case studies (hand him the three most important peer-review articles, with important points highlighted for him), almost 100% of people with colitis, idiopathic or otherwise, responded favorably. Some have been in continued remission for 5, 10, and even 13 years. I know they’re just pilot studies and case studies, but that success kind of rate should turn anyone’s head. It turned mine. In the summary I put together for you, I’ve outlined the protocol, and donor screening procedure. I meshed this together from what I thought were the best practices I found in the literature. What do you think? Do we need to change anything? What would you change?”

“These tests are normal stool cultures, and blood tests. Who would you use as a donor? Would they come to me for these tests?…These are serious antibiotics.”

[Snip] (Here we discussed donors, screening, and I brainstormed with him which antibiotics and antifungals we should use. His input here was very helpful.)

“…So basically you just want my blessing and prescriptions for the antibiotics and prep?”

“Yes. That and your partnership; it means the world to me.”

“That’s fine as long as you know the risks. (he explained the risks to me here)…As long as you know the risks…”

As he was writing the scripts, we had a short conversation about how he believes classical medicine doesn’t know everything, and if we can learn something here, then great. He also mused with me about the professional risks to him if something were to go wrong. I sympathized with him in the conversation, and thanked him for being willing to go out on a limb for me—it means a lot. And it does.

“OK, Matt. Good luck.”

I hope I won’t need it. Thanks.”

Finding a Donor

Finding a donor was simple for me. I saw the conversation with my doctor as the biggest hurdle. From there, everything else seemed less stressful. I used a few criteria:

  1. Good health: No acute or chronic diseases, and no family history of them. I wanted someone with a healthy diet, low alcohol consumption, and someone who had not often used antibiotics. It was important that the person had not used antibiotics within the past three months. This ensured that they had a stable flora.
  2. donor screening form: It screened all the variables I felt were important (besides blood and stool bugs): Disease, breast-fed as a child, antibiotic use, family disease history, bowel and health habits, eating habits, alcohol and sugar consumption, and of course the Bristol Stool Chart.
  3. Proximity and reliability: I wanted someone who was close, because you want the sample to be as fresh as possible. I wanted someone who was responsible, and who wouldn’t forget, because I needed one per day for 10 days, and then I would need samples periodically throughout the coming months.

From there, I was actually too embarrassed to ask anyone, so my wife did it for me. She asked a close friend of mine. I’m thankful she did so, because I don’t know if I would have had the guts to ask a friend to poop in a cup for me for two weeks. Thanks my love!

I didn’t ask my wife to be my donor, because she has psoriasis, which may have a link to the gut and gut bacteria. There’s no reason not to be picky here. She also does a lot for me. Since I got really sick almost two years ago, she has had to shoulder a much larger burden than she should have to otherwise. To ask her for yet another thing was too much for me. So it was a marital decision as well as a medical decision.

The literature says that a close family member is the best choice for a donor. I think, Yes and no. On the one hand, a close family member will likely share many bacteria in common with you, and this will decrease the chance of disease, or pathogen transmission. They are also, if they are in your house, awfully convenient. But those are the only two reasons I can think of to make them ideal donors.

On the other hand, a close family member, especially a blood relative like your mother or brother, may share some of the community of pathogenic bacteria that are making you sick. Indeed, I can envision a scenario where someone’s mother has a similar bacterial community to their sick child, but lacks the genetic susceptibility that her child has. In this case, bacteriotherapy may likely fail, and thus, a healthy non-family member, properly screened, would be ideal. So, if there is no reason not to be picky, and if we are avoiding as many risks as possible (because of all the unknowns of colitis), then a healthy non-family member is the best choice. That’s ultimately how I chose.

The Procedure I Used

Antibiotic Therapy (14-28 days) Colloidal Silver 500ppm – 8 oz – Liquid, 4 Tbs./day, for 7 days Klaire Labs – Interfase Enzyme Supplement – 120 Veg Caps, 14 days (8 pills/day in divided doses on an empty stomach). These enzymes, on an empty stomach, help to dissolve bacterial biofilms. Biofilms are a method certain bacteria can use to survive antibiotics. Plaque on your teeth is a biofilm. After those were finished…I began: Vancomycin, 500 mg, Bid (2x/day, 7 days) Flagyl, 500mg, Bid (2x/day, 7 days)

Human Probiotic Therapy (1 infusion/day, until all symptoms subside) (Actually, here, if I had it to do over again, I would do 3-5 infusions beyond the point at which my symptoms disappeared.)

My supplies:

  1. Disposable Enema Bag
  2. Fleet Adult Enema, Ready To Use, Twin Pack, 9 Oz
  3. Metal Kitchen Strainer
  4. Two plastic food containers (air tight) for collecting samples
  5. Hamilton Beach 51101B Single-Serve Blender with Travel Lid, Black
  6. Small glass bowl
  7. ½ cup measuring cup
  8. Funnel
  9. Metal serving spoon, or soup spoon
  10. 1-2 gallons of Distilled Water
  11. Gloves
  12. Several plastic grocery bags


  1. Natren Bifido Factor, 2.5-Ounce
  2. Natren Life Start Infantis, 2.5-Ounce

Here’s the procedure I used to do the infusions.

  1. Gather sample from donor in a plastic, air tight container. Be sure to use the sample as soon as possible. I tried to use it within an hour, but it should be used within 4-6 hours. Donor can store the sample in the refrigerator.
  2. Rinse glass bowl, funnel, blender, spoon, enema bag hose, and Fleet’s bottle with distilled water. This removes disinfection residuals from tap water.
  3. Assemble the enema device:
    1. Empty the Fleet’s enema bottle, rinse with tap water, wipe lube from the tip.
    2. Cut a 12-14” length of hose from the end of a disposable enema bag, keeping the lubed end for use. Discard the rest.
    3. Attach the newly cut length of hose to the Fleet’s enema cap. Be sure you have wiped the lube from the Fleet’s cap. Push it on firmly; you don’t want it to come off!
  4. Add 2-300g of the sample (about 1-1.25 cups) with probiotics and ½ cup water to the blender. Blend until smooth.
  5. Add distilled water until the sample is the consistency of thick paint. About 2/3 cups total distilled water. Use too much water, and you may not be able to hold the infusion for the desired 6-8 hours.
  6. Pour sample into the strainer and use the spoon to push the sample through the strainer into the glass bowl.
  7. Using the funnel, pour strained sample into the Fleet’s enema bottle.
  8. Secure the cap and hose (now one piece, since you’ve already assembled it) to the bottle.
  9. Rinse the equipment thoroughly with hot tap water. Boil to sanitize for next use. Do not use bleach. Do not boil the Fleet’s Bottle and Enema Hose; instead, rinse thoroughly. I can get about 3-4 uses out of one fleet’s bottle and cut piece of hose.
  10. Take the infusion as an enema as soon as possible from preparation.
  11. After the infusion, lie prone with your hips elevated for 30-90 minutes (or until you are sure you can hold the enema for 6-8 hours; you will need time for your intestines to absorb the water.)
  12. Hold the infusion for minimum 6-8 hours.
  13. Repeat daily until your symptoms are gone.

Maintenance Therapy: Some people may not need maintenance therapy; however, my gut feeling is that most people will need at least some maintenance. Whether that be 1x/month, or more, consider doing maintenance infusions—JIK. My (ideal) maintenance schedule: 1 infusion/week for 1 month. 2 infusions the following month. 1 infusion/month for 9-12 months. This schedule is ideal, and maintenance may be needed more often in the beginning. For example, I felt as though symptoms were returning four days after the end of my ten infusions, so I took another. I think this therapy favors the prudent.

Onward to Health.

Some References to Get You Started:

I found the Perfect Health Diet Series on Bowel Disease helpful. There are lots more references there too. Here is their post on fecal transplants.

  • Borody, Thomas J, et al. 2004. Bacteriotherapy Using Fecal Flora: Toying With Human Motions. J Clin Gastroenterol • Volume 38, Number 6.
  • Rohlke, Faith, et al. 2010. Fecal Flora Reconstitution for Recurrent Clostridium difficile Infection: Results and Methodology. J Clin Gastroenterol., Volume 44, Number 8, September.
  • Grehan, Martin J. et al. 2010. Durable Alteration of the Colonic Microbiota by the Administration of Donor Fecal Flora. J Clin Gastroenterol.  Volume 44, Number 8, September.
  • Floch, Martin H. 2010. Fecal Bacteriotherapy, Fecal Transplant, and the Microbiome. J Clin Gastroenterol  Volume 44, Number 8, September.
  • Dethlefsen, Les & David A. Relman. Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. PNAS Early Addition.
  • Borody, Thomas J. et al. 2003. Treatment of Ulcerative Colitis Using Fecal Bacteriotherapy. J. Clin. Gastroenterol. Volume 37, Number 1, pg. 42-47.

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