Fecal Transplants for Gut Health & More: What You Need to Know About FMT

Over the last couple of years, I’ve seen fewer and fewer jaws drop when somebody brings up FMT (fecal microbiota transplantation) in conversation.

This once shocking sounding therapy is being talked about more than ever, but you probably still have a lot of questions.

In this article, I’ll tackle the most important things you need to know about FMT for gut health and gastrointestinal conditions.

Your Gut Microbiome: A Quick Overview

Before we get into fecal microbiota transplantation, let’s start with a quick primer on the microbiota and the gut microbiome.

The gut microbiome is the entire ecosystem in your gut which includes various kinds of bacteria, fungi, genes, and other microbes, as well as the environmental factors that influence them. The microbiota refers more specifically to the community of microorganisms within this ecosystem.

We also have other microbiomes throughout the body, including the oral microbiome, the skin microbiome, and (for some) the vaginal microbiome. But for the purposes of this conversation, we’ll stay focused on the gut microbiome.

Microbiome Balance and Dysbiosis

There are trillions of microorganisms found within the gut microbiome, and they all contribute in some way to the ecosystem. While no two people’s microbiomes are exactly the same, we all need our communities of gut bacteria, fungi, and microbes to be balanced and diverse to maintain good health.

When the microbiome is out of balance, this is called dysbiosis.

Dysbiosis is a major underlying cause of and contributing factor to just about every health condition you can imagine, digestive or otherwise, from IBS, IBD, and food intolerances to rheumatoid arthritis and other autoimmune conditions, depression, diabetes, heart disease, chronic fatigue syndrome, and Alzheimer’s.

What is FMT (Fecal Microbiota Transplantation)?

Fecal microbiota transplantation (FMT) is a procedure that involves collecting stool from a healthy donor and introducing it into the digestive tract of a patient with a diseased colon or a gastrointestinal condition.

The idea is that we can take a healthy, balanced, diverse gut microbiota and transfer it, via a stool sample, to the recipient in order to restore the balance, health, and diversity of the recipient’s own microbiome.

FMT is most commonly done for patients with a clostridium difficile (c. difficile) infection that doesn’t respond to antibiotic treatment, for which it’s been shown to be extremely effective.

Research is ongoing looking at the potential benefits of FMT for at least 30 different conditions including IBS, celiac disease, Sjögren’s syndrome, and allergies.

Given that gut dysbiosis can impact virtually every health condition, there are essentially limitless possibilities when it comes to the conditions that could benefit from restoring microbiome balance using FMT. (1)

FMT vs Probiotics

Probiotics (supplemental beneficial bacteria) have long been the go-to way to improve balance and diversity in the gut microbiome. So how do they compare to FMT?

The biggest difference between the two is that probiotic supplements are more limited in terms of total species and strains.

With probiotics, you’re typically introducing a few beneficial species or strains to your existing microbiome. With FMT, you’re bringing in an entire intestinal microbiota filled with a massive variety of bacterial, fungal, and other microbial species that are all interacting with each other.

That’s not to say that FMT is necessarily “better”. It’s a more robust technique, but it’s also less accessible, much more costly, and not necessary for everyone at every stage (more on that below).

And, depending on the current state of your microbiome, even just introducing a few species with probiotics can still lead to widespread changes within the ecosystem.

What Conditions Can Fecal Transplants Help With?

Because of the massive influence the gut microbiome has on all kinds of chronic health conditions, fecal or poop transplants may be able to help with a wide variety of health concerns and diseases.

Here are a few of the most promising uses of FMT based on available research so far:

• Treatment-resistant Clostridium difficile (C diff): Fecal microbiota transplantation has been shown to be about 90% effective for clearing out c. difficile infections. (2) This is currently the only FDA-approved use of FMT, and it’s reserved for cases that have recurred at least twice or that don’t respond to antibiotics.
• Irritable Bowel Syndrome (IBS): FMT has also been found to be about 90% effective in treating IBS. (3) Research shows improved digestive symptoms, improved fatigue and quality of life, and significant changes to intestinal bacterial profiles.
• Inflammatory Bowel Disease (IBD): FMT has been shown to be more effective than placebo, antibiotics, and laxatives at improving symptoms of IBD. (4) Most research so far has focused on ulcerative colitis (UC), but early studies are also showing promise for Crohn’s disease.
• Autoimmune Conditions: IBD is one example of an autoimmune condition that FMT can help with, but researchers are also seeing promising results for other autoimmune diseases including rheumatoid arthritis, lupus, and type 1 diabetes. (5) Even though these aren’t necessarily thought of as digestive conditions, the gut microbiome plays a crucial role in their development and pathology, and in immune system function overall.
• Autism Spectrum Disorder (ASD): Gut dysbiosis has long been implicated in autism spectrum disorder. Clinical trials have shown that FMT can improve both behavioral symptoms and gastrointestinal symptoms, as well as overall wellbeing, for children with autism. (6)

Other conditions FMT may be able to help with include (but are not limited to): 

• Other gastrointestinal infections
• Metabolic syndrome (7)
• Food allergies (8)
• Alcohol use disorder (9)
• Chronic constipation, diarrhea, and/or bloating
• Fibromyalgia
• Chronic Fatigue Syndrome (CFS)
• Parkinson’s disease (10)
• Anxiety and depression (11)

Who is FMT Right For?

While FMT may be able to help with all kinds of different conditions and symptoms, it’s not right for everyone.

The biggest consideration I would look at clinically is not necessarily the condition or diagnosis you have, but where you’re at in your healing journey. FMT is definitely not a first step.

I would always recommend starting with the foundations— adopting a personalized, anti-inflammatory diet; cultivating better sleep, stress management, and fitness routines; and often supplementing with probiotics and/or prebiotics.

All of these strategies will help to support a healthy gut microbiome, and they’re much less expensive and often less invasive than FMT. And in many cases, these healthy inputs are enough to restore microbial balance.

But if you already have these foundations in place and you’re not feeling better, still have an imbalanced gut microbiome, and/or are not responding to treatment, FMT may be right for you.

And while it can be difficult to access depending on your diagnosis, your budget, and where you live, if it’s possible for you, it’s often more effective and causes fewer side effects than prescription drugs or other treatments.

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How FMT Works

There are a few different possible methods for doing an FMT procedure, but they should always be done through a reputable medical institution.

These institutions use fecal samples from stool donors who have been shown to be healthy and have been screened for different diseases, pathogens, and risk factors. The donor stool is mixed with saline solution, filtered, and prepared for transplantation.

Fecal samples are then transferred to the recipient in one of the following ways: (12)

• In an oral capsule
• Through colonoscopy
• Using an enema
• Through a nasogastric tube

The delivery method may depend on your specific condition and your health profile. The oral capsule method is the least invasive and therefore preferable for many people, and most research has found that it’s actually just as effective as the more targeted colonoscopy method.

However, there may still be some cases where other methods are more likely to work better. Your healthcare provider will help you identify the best method for your case.

FMT treatment is generally very costly (several thousand dollars) and, if it’s for a condition besides recurrent c. diff, may require travel outside of the country. In most cases, only one treatment is necessary.

LISTEN: Dr. Steven Gundry: The New Microbiome Science (Bacterial Diversity, Pre Vs. Pro Vs. Postbiotics, Fermented Foods, Fecal Transplants, Saturated Fats, & More) 

What To Do Afterwards

The benefits of FMT are generally long lasting. (13) But this does depend on how you care for your new gut microbiome! I like to think of FMT as providing a bit of a clean slate. But from there, if you return to habits and triggers that contributed to your dysbiosis in the first place, you might see symptoms return. Remember that the gut microbiome is always evolving in response to stimuli.

That’s why it’s important to follow up your treatment with healthy lifestyle practices, an anti-inflammatory diet, and good quality sleep. You may also want to continue or add a probiotic and/or prebiotic supplement to keep your gut health and microbiome in tip top shape.

Is FMT Safe?

When performed by a trained health professional, FMT is thought to be very safe, with few reported side effects. If side effects do occur, they’re typically minor and may include bloating, gas, or other short-term digestive symptoms as your system adjusts. (1)

However, FMT should never be done outside of a healthcare setting. The safety of FMT is dependent on thorough screening of stool samples and administration by trained clinicians. DIY fecal transplants may pose several health risks.

READ NEXT: Types Of Gut Microbiome Testing + How It Works | Dr. Will Cole 

Get Support For Your Gut Microbiome

While FMT can be very helpful in some cases, there are many other things that can be done first to restore the balance in your gut microbiome holistically. In our telehealth functional medicine clinic, we work with patients every day on individualized, root-cause focused treatment plans and support.

As one of the first functional medicine telehealth clinics in the world, we provide webcam health consultations for people around the globe.