Interview with Dr Mark Davis N.D.

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Mark Davis photoIn November 2011, I ran into a friend of mine, GI Dr, Glenn Eisen.  He asked how my UC was.  I replied that it was under control, but had really not gone into remission for four years, despite Remicade infusions and many other meds. He was not my MD, but was familiar with my case. I had had IBD since 1978.  I asked him “What are the odds that I will need to have my colon removed at some point?” He did not answer directly, saying “there is hope for a new treatment being studied, fecal microbiota transplant.”  I went home and hit google.

My HMO Doc was open minded, but could not directly support me per company protocol.  I knew that I could order screening tests on my own – but didn’t want to.  Like 99% of patients, I wanted a professional to guide me. I was very relieved to find Dr. Mark Davis in my hometown of Portland, Oregon, USA and was among his first FMT patients in January 2012.  The procedure was a great success as I have written in my success story. 

Dr Davis specializes in naturopathic treatment of IBD. Up until the recent FDA suspension of FMT 75% of his practice involved FMT.  I am grateful that I met him and that he has agreed to be interviewed for the launch of PoP.

How did you end up doing FMT for a living? 

As a student at the National College of Naturopathic Medicine, one of my favorite professors was Dr. Seven Sandberg-Lewis, an ND with over thirty years of clinical practice.  I did as many clinical rotations with him as I could, just because I liked his approach to medicine.  For some reason, about a quarter of his practice is people with inflammatory bowel disease, so I got used to working with that patient population.  

He usually saw particularly complex patients who were referred to him by local gastroenterologists or primary care naturopathic doctors, and I saw a lot of them have really improved quality of life under our care. We mostly used dietary interventions, botanicals, supplements, homeopathy and probiotics.  Although we were able to help a lot of them, we certainly weren’t able to help all of them, and so I was always poring through the literature to see if I could find anything else that could help our patients.  

One of the things I happened upon was Thomas Borody’s 2003 paper, “Treatment of Ulcerative Colitis Using Fecal Bacteriotherapy.”  It described six patients with active ulcerative colitis who had “failed maximally tolerated standard UC therapies” but who became asymptomatic and able to withdraw from all meds after five fecal slurry retention enemas preceded by antibiotics and an oral bowel lavage.  After we confirmed with the Oregon Board of Naturopathic Medicine that FMT was in our scope of practice, we tried it with an ulcerative colitis patient who saw a lot of benefit.  When I got my degree and could practice on my own, I realized that (at that time) literally no physician in North America was offering FMT for IBD, so I wanted to fill that niche.

What conditions have you treated with FMT and what were the results?

C diff colitis, post-C diff colitis, UC (including ulcerative proctitis all the way through ulcerative pancolitis), Crohn’s disease, microscopic colitis, IBS-C, IBS-D, IBS-A, chronic constipation, intestinal candidiasis, multiple sclerosis, autoimmune lymphadenopathy, idiopathic abdominal pain following long-term antibiotic use, probably others.  I’ve pretty carefully tallied my results with colonic inflammatory bowel disease (see table) but haven’t carefully recorded results for others.

I’ve used FMT with about twenty-five patients with colonic IBD and about thirty-five patients with other indications.  I used to cite a higher number because I would count people whom I’d just sent my protocol without having met, but since they aren’t my patients and I don’t follow their outcomes very well, I have stopped doing that.  


total #

complete no relapse

complete with relapse

partial no relapse

partial with relapse


no symptoms to start

Ulcerative Colitis








Ulcerative Proctitis








Micro Colitis








Crohns Colitis








Total          #








Table 1: Improvement after FMT in 25 patients with colonic IBD

How do you control the quality of your donors?  What risks do you see with donor banks?

Before I was put on hiatus by the FDA, I was using four active donors (and had screened many more).  I started out screening people according to the Fecal Microbiota Transplantation Workgroup protocol, and after a few months added on a PCR stool test that looks for and measures relative amounts of certain organisms by looking for their DNA.  

I remember when I got the test back for my first set of donors – despite having been screened with a normal parasite test (an O&Px3), one was positive for Enterobius vermicularis, the human pinworm!  I had to call up the three patients I’d used that donor for thus-far and offer to screen them for free.  Pinworm is generally harmless, and none of the three patients turned out to have it, but it highlighted that there is so much going on with the fecal microbiome and we cannot realistically test all of it.  

The risks I see are that there could be an organism in the donor feces that we don’t test for or don’t find despite testing, which could be harmful to the patient.  Some people use family members and don’t screen them using labs as long as they have a clean health history and no risk factors, but I had someone screen a healthy young friend who turned out to be positive for C diff despite having no GI symptoms (which occurs in about 3% of young people if I remember correctly).  I tried to control donor quality by not only making sure they had a clean health history and no risk factors, and doing the lab testing, but asking them to let me know if they acquired any risk factors (a new intimate partner, travel abroad) and re-testing relevant factors sooner than I otherwise would have if indicated.

When people around the world have contacted me interested in treatment, I’ve generally encouraged them to seek out a local eligible donor, work with a local provider to provide antimicrobial pretreatment if it’s indicated, and try self-preparing and self-administering at home.  Dozens of people have come to see me largely because they simply do not have a healthy person who is willing and able to be a stool donor for them.  It’s been really rewarding to have maintained a donor bank for the sake of those people.

Prior to the FDA suspension I was administering FMT via enema, so aside from the clinical experience & knowledge I’ve accumulated and the training and scope of practice to prescribe antibiotic pre-treatment, I wasn’t actually doing anything that someone with an eligible donor can’t do at home.  

The only other North American provider I know of who’s used a donor bank system is Alexander Khoruts, who has published about using his system to treat C diff colitis.  Dr. Khoruts has run his as a volunteer donor system, whereas I’ve been compensating my donors.  I figure I’m asking them to eat certain foods, avoid certain foods, get regular testing, keep me in the loop about new intimate relationships, international travel, etc.  I think his system does avoid certain ethical complications, but my system worked well for me before I suspended the program because of the FDA.

Which is better, fresh or frozen?

For most people I think frozen is fine (although I personally have only banked fecal slurries at significantly below -30C, so there isn’t a lot of crystal formation and most home freezers only go to about -20C).  For some people I think fresh may be necessary or better, but I don’t know how to identify those people.

How long is frozen good for?

According to a paper by Alexander Khoruts, fecal slurries that have been centrifuged and reconstituted, frozen at -80C and thawed seem to be just as effective for C diff colitis as fresh ones. I’ve used quite a bit of frozen in my practice (without the centrifuge part, but stored at below -70C) for up to eight weeks, and I’ve seen frozen give UC patients a lot of benefit.

What is your view on anti-biotics prior to FMT?

It’s really hard to know the answer and we simply don’t know without an RCT to tell us.  My clinical feeling is that not everybody needs antibiotic pre-treatment to have a durable good result but some probably do.

Which is better? Colonoscope or enema?

I’ve seen enema-administered FMT be a complete life-changer for some of my IBD and C diff colitis patients, so that method (which is the lowest cost and lowest risk) seems effective for at least some.  I worked with one man with UC who didn’t seem to respond to enema-administered FMT at first, and the fiber foods I was recommending really seemed to flare him up.  I referred him to a gastroenterologist who delivered an initial bolus of fecal slurry via colonoscope, then he followed up with enema-administered infusions, and he had a great outcome.  For him I think the colonoscopic dose was a necessary part. For some of my patients who didn’t respond to enema-administered FMT, I wonder if they would have responded to colonoscopically administered FMT.

Does donor diet matter?

The donor is donating his or her colon flora, so we want him or her to have good quantities of healthy, diverse colon flora.  I encourage donors to eat moderate to high amounts of a diverse range of fiber foods at all or most meals, and to stay well-hydrated.

If a recipient has allergies should the donor change diet?

Any foods that provoke true allergies (an IgE reaction, characterized by hives, swelling, redness, shortness of breath) in the patient should be strictly avoided by the donor for at least five days before the first donation.  Foods that provoke a food hypersensitivity reaction (usually an IgG reaction, characterized by a flare of symptoms in other organ systems) should probably be avoided for five days before starting to donate.  Carb and fiber foods that cause symptoms due to their effect on the patient’s gut flora do not need to be avoided.

How long should a patient continue FMT?  

For IBD I say until symptom free then at least weekly for eight weeks minimum, or until colonoscopy with biopsy shows no macroscopic inflammation and no microscopic inflammation in the unprepared tissues.  My protocol states ten consecutive days with eight subsequent weekly infusions. 

How long should medications be continued once symptoms subside?

Opinions differ and it depends on the condition and the medication.   Although I use some pharmaceuticals in my practice that is not my area of focus and I prefer to let gastroenterologists take the lead on those kinds of issues.

Some doctors say colonic IBD patients should continue with oral mesalamines for life to decrease chance of colon cancer, even when they are asymptomatic and there is no inflammation apparent through endoscopy.  Other docs say that the colon cancer risk comes from inflammation so if there is no inflammation we can decrease the meds.  Patients who seem to be benefitting from regular Infliximab (Remicade) infusions are particularly hard to take off, because if they go off then on again there is less chance of it benefitting them and more chance of them developing an allergic reaction to the drug.

Where FMT doesn’t work in a patient or only works for a while, what factors do you believe perpetuate the dysbiosis?

There are several possibilities: the symptoms aren’t caused by an underlying colon dysbiosis, the donor doesn’t have the necessary microbiome to benefit the patient, there are errors in preparation or administration, or something is preventing the donor microbiome from taking over (large amounts of retained stool in the colon, redundant colon, etc.)

In my experience and in the literature, FMT for a simple infectious C diff colitis is generally long-lasting or permanent.  The fact that the durability of the treatment is much more variable for UC, Crohn’s colitis, and other conditions speaks to the different nature of those conditions.  Infectious colitis is largely about the pathogen and somewhat about the rest of the microbiome.  With UC, Crohn’s disease, certain types of IBS which seem to respond, I think there’s not only a microbiome component but mostly likely a genetic and/or epigenetic component as well, so a variety of external factors could trigger this predisposition to disease.  There are stories about a round of antibiotics or an acute gastroenteritis triggering relapse after successful FMT, and there are stories about it seeming to just… wear off after a while.  In those cases I imagine that there’s a remnant of the sufferer’s native colon microbiome that was originally suppressed, but re-grows and triggers the immune response.

Why is the mainstream medical profession so dismissive of FMT? Given the success with C Diff what’s wrong with trying it for more difficult chronic gut conditions?  Where’s the harm?

In my experience the mainstream medical profession has been quite interested in FMT, particularly gastroenterologists.  The reason to question the use of FMT is that it hasn’t been rigorously studied in large randomized controlled trials (RCTs).  That’s generally the route to getting a therapy accepted for mainstream use.  Remember Rofecoxib (Vioxx)?  It was an NSAID that was pulled from the market for increasing the user’s chance of a heart attack.  There was an increase of three heart attacks per thousand people that were on Rofecoxib for a year.  

What clinician sees enough people and is scrupulous enough about their record-keeping to be able to notice that of the thousand people they’ve put on Rofecoxib in the past year, a few more have had heart attacks than otherwise would have?   That kind of information can only come out through large RCTs.  I’ve used FMT with about 100 people.  Dr. Borody has used FMT with maybe 2,000 people over his career.  Would we as clinicians be able to pull out some tiny increases in a bad outcome?  Doubtful.  

The FDA thinks it’s their job (and I applaud them for this) to ask clinicians to keep information in a very systematic way about who they are treating, how they are performing the procedure, what kinds of benefits they’re seeing, and what kinds of adverse events they’re seeing, so they can tell the American people how effective or dangerous this procedure is.  The FDA regulation of FMT has been crippling to my personal practice (which was about 75% focused on FMT), but I think they’re really just trying to do their job.  

What’s the harm? I can only report one detectable adverse event from my own practice.  A young man with IBS-A (alternating between diarrhea and constipation) came to see me at a time when he was maybe leaning a little bit towards constipation but still having a BM most days.  His chief complaint was constant abdominal pain.  He had five consecutive infusions which did nothing to improve his abdominal pain but sent him into a round of 10-15 urgent, watery BMs per day, which apparently self-resolved over the course of about three months.  That’s the only adverse event I’ve been able to detect in my practice, but are there more subtle adverse effects that I was unable to detect?  Who knows!  

Now, all that being said, if I had my druthers, I’d still be able to perform FMT without FDA oversight, not only because it’s how I make a living but because I personally as a patient am willing to take (apparently) slight risks when there is (quite possibly) a lot to gain.  I know others have the same medical aesthetic and I wish that I could legally work with that group of people, but I can’t because of the type of mandate the American people have given the FDA, or at least the way the FDA interprets that mandate.

What are the potential long term risks of FT?

No one knows.  None have been hypothesized so far as far as I know.

It seems that the only therapies promoted by gastroenterologists for IBD are drug therapies. Are they really that brain-washed by the drug companies?

I don’t think of it as brain washing, it’s just their medical culture.  If you want your bicycle fixed, you go to a bike shop, not an auto mechanic, because that’s what they do.  Gastroenterologists are primarily trained to diagnose disease and heal and/or palliate using drugs and surgery, maybe a few dietary interventions.  So if you want that, you go to them.  

If you want more in-depth nutritional suggestions, try a nutritionist or an ND.  If you want more extensive natural therapies like botanical medicines, supplements, hydrotherapy, etc, go see an ND.  As for FMT, its modern usage has been pioneered by gastroenterologists and other MDs – that minority who prioritize potential benefit over unknown risk.

What research are you following right now and when will results be known?

I periodically go to and search for “fecal microbiota transplantation” and “fecal transplant.”  As of this interview there are over a dozen studies the FDA has approved using fecal slurries or standardized fecal microbe culture slurries to treat UC, relapsing C diff, Crohn’s disease, and Type II Diabetes.  

Christine Lee is an infectious disease MD in Toronto who is asking really interesting questions–one trial she’s doing is comparing fresh to frozen fecal slurries for C diff colitis, which I’m particularly interested in because her freezing technique is almost identical to mine.  She’s also comparing fecal slurry enema vs. placebo enema for UC, with a well thought out double blinding technique.  

There’s a Dutch group looking at inserting fecal slurry into the small intestine of people with UC, prepared either from a donor or from the patient’s own stool.  If I had been on their institutional review board I might have questioned the safety of placing bacteria from the large intestine of others (or one’s self, since they are hypothesizing that there may be a problem with the patient’s large-bowel flora) into the small intestine, which has a totally different bacterial community. 

What research is on your wish list?

Antibiotic pre-treatment vs. placebo pre-treatment for UC, FMT for metabolic syndrome, studies for IBD with long-term follow-up, FMT for C diff colitis as a first-line intervention.

Are you collaborating with other FT providers, if so, how?

I had talked with Christine Lee in Toronto about some collaboration, but since I’m not affiliated with a large teaching hospital I didn’t have the resources to be a site in her multi-site trial.  I’ve corresponded with Thomas Borody, Lawrence Brandt and Alexander Khoruts about their techniques, but haven’t done any collaborating with them.

As a practitioner working in a fringe area of medicine, how do you manage liability in your practice?

I have (very expensive) malpractice insurance that specifically states I am covered to perform FMT via enema and colonoscope. 

What do you enjoy about your work? What are the frustrations? 

The thing I enjoy about my work is the extent to which people get better.  I love it when people go from intense symptomology to feeling great as a result of my interventions.  The converse it true, too – it can feel really frustrating when I’m doing my utmost to help someone get better and they just don’t improve at all.

What do you tell people you do when they ask you at a dinner party? What do your kids tell their friends Dad does for a living?

At dinner parties I say I’m a naturopathic physician, and if they ask for more detail I tell them we should talk about it after dinner.  All kidding aside, although I try not to talk about my work over meals I’m usually quite eager to talk about what I do for a living.

I just went and asked my eight year old son and my six year old daughter what I do for a living.  They both said “you’re a doctor!”  I said “what kind of doctor?” and my son said “a poop doctor!” and my daughter said “I don’t think he’s a poop doctor anymore.”  In reality they both know that I’m a naturopathic doctor who uses (or used to use) a lot of fecal slurry enemas as part of my practice.

Dr Mark Davis offers consulting in naturopathic treatment of digestive health issues and specialises in IBD. For further information and pricing contact The Bright Medicine Clinic.  


Other Articles / Interviews with FMT Practitioners

Interview with Dr David Shepard MD  (USA)

Interview with Taymount Clinic’s Glenn Taylor  (UK)

Dr Arnab Ray MD on How to Talk to Your Doctor about FMT  (USA)

Dr Gary H. Hoffman on FMT for C. diff (USA)

Interview with Dr Silvo Najt (Argentina)


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8 replies »

  1. Your graphic is cut off Table 1: Improvement after FMT in 25 patients with colonic IBD. I’d really like to be able to see the entire table.

    Would mixing fecal slurry from different donors make any difference?

    Has baby poo been used as the donor material? It seems like it would be easy to harvest.

    Do you know of any more references of Crohn’s patients getting FMT?

  2. Hi Ken,
    The whole table comes through in my browser, although I noticed that there’s a typo in this version: it should show 4 patients with complete improvement, no relapse. No data that I know of published yet about mixing fecal slurry from different donors. Generally we recommend at least 3yo for donors, since that’s the time that the colon flora starts to become indistinguishable from adult colon flora, but I’ve heard anecdotes of baby poo being used effectively. Besides my 10yo F with Crohn’s colitis (who actually has had a partial relapse since I put this chart together), I treated one adult male with Crohn’s ileitis (who did not benefit) and an adult with UC with some Crohn’s-like elements who benefitted a lot.
    Best regards,

  3. If possible, can you state the results for the patients with ulcerative proctitis? I can not see anything written on this line. The table is cut off on the screen. Is it fair to say NO results?


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