FMT Protocol

At this stage, FMT for bipolar disorder—or any mental illness—is entirely experimental. There is no established or standardised protocol; much of the process involves trial, error, and personal experimentation. Researchers and clinicians still don’t know what the most effective method of delivery is (e.g., colonoscopy, enema, capsules), nor what dosage provides optimal results. In my own experience, it took 10 FMTs to reach full remission, with no noticeable improvements until after the sixth treatment—around the three-month mark. In contrast, I know a young woman with bipolar I who achieved remission from both depressive and manic symptoms after taking just 88 FMT capsules. That said, for most people I’ve encountered, it seems to require multiple FMTs over time to experience a significant reduction in depressive symptoms. For instance, the Centre for Digestive Diseases in Sydney has used a protocol involving approximately 29 FMTs administered over the course of a year. Ultimately, discovering the right dosage and frequency for you will likely be a personal and experimental journey.

I believe your FMT protocol will depend heavily on the practical realities of your donor situation. If your donor is your partner and you live together, you’ll have far more flexibility and opportunity to prepare and administer FMT regularly. On the other hand, if your donor lives across town—or further—logistics will limit how frequently you can collect and use their stool. If you’re purchasing FMT from a provider like Microbioma, your protocol will also depend on what you can afford and what they’re able to supply. Microbioma typically ships either six full enemas or 120 capsules per order (they also offer smaller, half-sized enemas). That amount might be enough to reduce symptoms or even achieve remission—but it also might not, depending on your individual response. If you’re fortunate enough to be accepted into a clinic and can afford the treatment, your protocol will be guided by the clinic’s own FMT schedule. Just keep in mind that many of these clinic protocols aren’t yet strongly backed by scientific evidence—they’re often based on experience rather than established research.

If I were starting this process over again and had unlimited access to donor stool (which I now do), I would probably follow a protocol similar to that used by the Centre for Digestive Diseases (CDD) in Sydney. They’ve been offering FMT for decades and have developed one of the more established protocols. I personally know two men with bipolar II who were treated at CDD—both initially experienced improvements. One relapsed after a period of high stress and a COVID infection, but went back into remission after receiving top-up FMTs. Unfortunately, the other didn’t maintain long-term symptom relief and relapsed after about two years.

At the CDD, patients receive an initial FMT via colonoscopy in the clinic, followed by a structured at-home enema program using frozen donor material. The schedule is intense: five FMTs in the first week, four in the second, three in the third, then three per week for one month, followed by weekly, then fortnightly FMTs—totalling 29 FMTs over 26 weeks. That’s a lot, and it’s likely many people won’t need that many to see symptom relief—if FMT is effective for them at all. Still, the logic makes sense to me: frequent FMTs early on may help establish the new microbiome more effectively, with ongoing maintenance doses helping to ensure long-term colonisation and stability.

While I can’t say definitively what the best protocol is, if I were to start again with regular access to donor stool, I’d aim to do multiple FMTs in the first week, tapering down over time—at least for three months or until I noticed a significant reduction in symptoms. Back in 2016, there was no precedent for using FMT to treat mental illness, so we guessed our way through it, doing just one FMT every two weeks. Looking back, I don’t think that was frequent enough, and it may explain why I didn’t notice any changes until three months in—after six FMTs.

When it comes to FMT pills, I’m not aware of anyone who has combined both pills and enemas in the same protocol—but I personally think it could be beneficial. Enemas deliver a large, concentrated dose of donor microbiota directly to the lower colon, while pills could act as a smaller, more continuous “maintenance” dose between enemas. For example, you might do an enema and then take one or two pills per day in the days following, helping to maintain a steady microbial presence. Pills also have the potential to reach further into the gastrointestinal tract—particularly the upper large intestine—which enemas typically don’t reach.

The downside to DIY FMT capsules is that they’re more time-consuming and technically tricky to make compared to enemas. Enemas are quicker to prepare and administer, though I’ve personally done both.

If you decide to use capsules, most anecdotal protocols seem to begin with a large initial dose (a “loading” dose), often 10–20 capsules at once, followed by smaller or spaced-out doses. I can tell you firsthand that 20 capsules in one sitting is a lot! In clinical trials and commercial FMT settings like OpenBiome, patients are sometimes asked to take up to 60 capsules in a single session—which, in my opinion, is likely a cost-saving measure to reduce the number of clinic visits and to avoid at-home handling of the capsules.

Here’s an example protocol from someone I know who used capsules from Microbioma to treat bipolar II:

“My protocol was 15 pills on day 1 and 15 on day 2. Then I waited 7–8 days and repeated the 15/15 combo. I did this for 4 weeks total (I had 120 capsules). I’ve also heard of people doing 10/10/10 or even 30 in a single day. Personally, I believe less is more, and I’ve read similar suggestions. I’d recommend sticking with 15/15 or 10/10/10, and definitely waiting at least a week between doses of 30 capsules—there’s some research backing this.”

(Note: I’m not sure which study he’s referring to.)

Ultimately, whether you use enemas, capsules, or a combination of both, the process remains highly experimental. The best approach is to choose a protocol that aligns with your lifestyle and the availability of donor stool.

FMT pre-treatment with Antibiotics:

Some FMT clinics routinely prescribe antibiotics prior to treatment. Of the people I know who have done FMT for mental illness, only two—both treated at the Centre for Digestive Diseases in Sydney—took antibiotics beforehand. Dr Paul Froomes also occasionally prescribes antibiotics or antifungals prior to FMT, typically based on microbiome analysis. However, most individuals I know who have experienced success with FMT for mental illness did not take antibiotics beforehand. At present, there is limited evidence that pre-treatment with antibiotics significantly improves FMT outcomes in cases of mental illness.

This article published in 2022 "Effect of antibiotic pretreatment on bacterial engraftment after Fecal Microbiota Transplant (FMT) in IBS-D” showed that taking antibiotics pre FMT decreased engraftment of the FMT.

Here is another article from 2019 "Minor Effect of Antibiotic Pre-treatment on the Engraftment of Donor Microbiota in Fecal Transplantation in Mice”. If you scroll down to the discussion part of the article you will read that the results showed that antibiotic pre-treatment provided no significant benefit.

How long will it take to notice an improvement in my symptoms?

The timeline for seeing results from FMT is highly individual and still largely unknown. In my own experience, it took around six FMTs over the course of three months before I noticed any reduction in my depression. In contrast, Alex recently became a donor to a family member with severe depression (MDD), and that person experienced a dramatic improvement within just one week of starting FMT pills—though this appears to be an uncommon outcome. Reports vary widely, with some individuals noticing changes within 1–3 weeks, others in 1–2 months, and some not until after three months or more. Research supports this variability: a study published in Nature Medicine found that while donor strain engraftment can occur quickly, full stabilisation of the gut microbiome may take several months to over a year, depending on individual factors and the condition being treated. See also: Dynamic changes in short- and long-term bacterial composition following fecal microbiota transplantation for recurrent Clostridium difficile infection.

Symptom improvement will vary among individuals but anecdotally I have heard cases of FMT improving:

Depression (MDD & Bipolar)
Generalised Anxiety Disorder (GAD) (*Note: FMT will not help with anxiety related to C/PTSD/trauma).
Hypomania/mania/psychosis
Anhedonia
Insomnia
Libido issues
Some ADHD symptoms
Sensitivities relating to ASD (eg light, sound)
Improved stress tolerance
GI issues
Asthma

Anecdotally I personally know of ~23 people who have experimented with FMT for a variety of mental illnesses with around ~75% success rate. 3 people with BP I, 13 with BP II, 1 OCD, 1 GAD and 3 MDD experienced significant symptom reduction. There are a number of people who have purchased FMT from Microbioma donor 2 and have not experienced any improvement in their symptoms whatsoever yet this same donor has resulted in significant symptom reduction in others. This illustrates the complexity of donor matching (something that is still a medical mystery).

Though the number of people who try FMT for mental illness is growing, it is still a highly experimental therapy.

The first year after undergoing FMT for mental illness appears to be a particularly vulnerable period. Many people who initially experience improvements find that environmental stressors within that first year (or even later) can trigger relapse. In my case, I had to take amoxicillin for a staph infection just a few months after FMT. By the end of the antibiotic course, I began to feel mentally unwell again. Interestingly, after doing another FMT, those symptoms resolved completely within a day. More than a year later, I had to take the same antibiotic again, but this time it didn’t affect my mood—suggesting that my gut microbiome had become more stable and resilient. (I still followed up with another FMT to support recovery.)

Others I know have relapsed after contracting COVID, and chronic stress has been another common trigger. Pathogens, poor diet, high alcohol consumption, antibiotics and stress seem to be the main culprits for relapse. For women, perimenopause/menopause could be a time where the chance of relapse may significantly increase.

Rapid withdrawal from psychiatric medication can also lead to instability—in my case (and the case of another person with BPI), it caused a manic episode. Even years after initial recovery, major physiological stressors can still have an impact. In late 2020, I contracted Ross River virus, which led to severe post-viral fatigue. Alongside this, I experienced a mild depression that took weeks to even recognise. I had been depression-free for almost four years, so this was a clear sign that my microbiome had been disrupted. Once again, a single FMT resolved the depression within two days. These experiences have led me to believe that I (and those who try FMT for any mental illness) may always be somewhat vulnerable to relapse under certain conditions.

It seems likely that some people may require FMT “top-ups” every few months or years, even after a strong initial response. Encouragingly, many people do find that these top-ups are effective in restoring remission.

Diet during and post FMT

In my view, it’s highly unlikely that someone will maintain long-term improvements from FMT—no matter how successful the initial results—unless they also focus on supporting their gut microbiome through diet. Diet is one of the most powerful and consistent influences on microbiome health. I believe the effectiveness of FMT could be significantly enhanced if both the donor and recipient follow a diet rich in plant diversity, fibre, prebiotics, and fermented foods. Experts like Professor Felice Jacka suggest that my own sustained remission from bipolar I disorder may be largely due to how seriously I’ve taken my diet post-FMT. I follow the recommendations of the Food and Mood Centre and Professor Tim Spector who founded the excellent podcast Zoe Science & Nutrition.

I would recommend perusing the discussion section of this study: Dietary Management for Faecal Microbiota Transplant: An International Survey of Clinical and Research Practice, Knowledge and Attitudes, and the Zoe Blog: Why should you eat 30 plants a week?

I also highly recommend this Zoe Nutrition interview with Professor Felice Jacka from The Food & Mood Centre: How food can improve your mood.

Medications

Please please PLEASE stay on your medications!

An acquaintance used my husband as a donor for FMT. Despite my strong warnings, he decided to stop taking his psychiatric medications—without consulting his psychiatrist—and very quickly ended up in a psychiatric ward.

Personally, I didn’t even consider tapering my medication until I had been completely symptom-free for at least six months. Even then, my psychiatrist was understandably cautious. I was on lithium, Seroquel, and lamotrigine, and although we attempted a gradual withdrawal, it turned out to be too fast. In September 2017, I experienced the worst manic episode—and most intense psychosis—of my life. That was the last time I had a manic episode, but it was also the most frightening. Interestingly, during that episode, my husband came across a case study about a woman who developed mania after GI surgery. Antipsychotics weren’t working for her, so the doctors tried activated charcoal, and remarkably, it helped. Because I wasn’t responding well to antipsychotics either, my husband discussed the case with my psychiatrist. We decided to try activated charcoal as an adjunct treatment. I took 2 grams a day, spaced well away from my medications to avoid interference—and within two days, the mania subsided.

Resolution of a manic episode treated with activated charcoal: Evidence for a brain-gut axis in bipolar disorder.

Another friend of mine with bipolar I disorder received FMT through a clinic and initially experienced a significant reduction in symptoms. Despite my warnings—they decided to stop taking their medications. Not long after, they experienced a manic episode and were also admitted to a psychiatric ward.

It’s a common and understandable hope among people with bipolar disorder to one day live well without medication. I’m incredibly fortunate that this has become my reality, but I know that may not be the case for everyone. FMT may dramatically reduce the severity or frequency of symptoms for some individuals, but many will still require medication to maintain stability.I know several people who have been able to completely stop taking psychiatric medications, while others have successfully reduced either the number of medications and/or their dosages.

In my view, since the gut microbiome can take up to a year to fully stabilise after FMT, it is highly inadvisable to begin tapering psychiatric medications before that point. Even after a year, any changes should always be made under the close supervision of a qualified psychiatrist.

I CANNOT STRESS THIS ENOUGH: DO NOT CEASE YOUR MEDICATIONS