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Do you want to start feeling better?

Yes, Where Do I Start?

What You Should Know Before Trying FMT for IBD

Why You May Want to Start with Other Natural Therapies Before Pursuing FMT for IBD

Key Takeaways:
  • FMT (fecal microbiota transplantation) involves taking stool from a healthy donor and transplanting a portion of their healthy microbiota into the gut of someone who is ill.
  • FMT is FDA-approved to treat recurrent Clostridium difficile infections.
  • But a significant amount of research suggests FMT is also safe and effective for treating inflammatory bowel disease (IBD), especially ulcerative colitis.
  • There are many other natural, science-backed treatment options (like probiotics, diet, and meditation) to try for IBD before pursuing FMT.
  • If you continue to struggle with IBD symptoms and flares despite trying other natural gut-healing treatments, you may want to speak with your healthcare provider about FMT.

If you’ve been experiencing the symptoms of IBD even after dietary and lifestyle improvements, hearing about a new and novel therapy that promises relief can be extremely exciting. Fecal microbiota transplantation (FMT) is an emerging topic of conversation in the gut health space. Many of my own patients have come in with the belief that it may be (finally) the key to their healing. But for many, there are other avenues that may hold more promise. 

For example, when Kyle first came to the clinic, he’d been struggling with Crohn’s disease (a type of inflammatory bowel disease, or IBD) for years. Despite having had surgery and using IBD medications, he still felt unwell and was having abdominal pain with absolutely everything he ate, even foods most of us would consider healthy. He was also constipated, bloated, and had low energy, headaches, and low-back pain. It was no wonder that FMT seemed like one of the last hopeful avenues.

And unfortunately, Kyle’s experience is pretty common for people with IBD. They may struggle off and on for years with flares and end up on strong medications or even having surgery to try to stay ahead of the inflammation. If you’ve been on a similar treatment merry-go-round without much improvement, I want to reassure you that there is a path to healing—and it may not require FMT.

So let’s get into the other options for IBD, the treatment plan that worked for Kyle, and when FMT may be worth considering. But before I get into the nitty-gritty of FMT for IBD, I want to give you some background on what IBD is and how it’s usually treated.

Inflammatory Bowel Disease 101

Inflammatory bowel disease (IBD) is an umbrella term most often used to describe two gut disorders—ulcerative colitis (UC) and Crohn’s disease. As you can probably tell from the name, IBD involves significant inflammation in the small or large intestine, or both. Depending on the severity, IBD can cause gas, cramping, bloating, diarrhea, urgent or frequent bowel movements, and abdominal pain [1, 2, 3]. IBD patients can also struggle with other symptoms like [1, 2, 3]:

  • Brain fog
  • Fatigue
  • Eye inflammation
  • Arthritis or joint pain
  • Weight loss
  • Skin issues
  • Hemorrhoids

As with other autoimmune conditions, if you have IBD, your symptoms can wax and wane. You may go through periods of feeling pretty good (referred to as remission), only to end up in a flare with symptoms that significantly disrupt your daily life. You may be placed on strong medications called biologics that suppress your immune system to control inflammation, and that can cause frequent infections and undesirable weight gain. In some cases, the damage from IBD could require surgery [1].

While this may all sound pretty terrifying, please know there are many natural, safe, and effective treatment options for managing IBD. In addition to a number of diet and lifestyle tweaks, one emerging area of research is fecal microbiota transplant, so let’s dig into the specifics. 

What is FMT?

A fecal (sometimes spelled faecal) microbiota transplant (FMT), aka bacteriotherapy or intestinal microbiota transplantation, is the process of relocating beneficial gut microbes (bacteria, fungi, protists, and viruses) from a healthy person to someone with an illness like IBD [4]. 

Why would this be helpful? Well, FMT is based on the understanding that the gut microbiome is intimately tied to practically every body system. People with certain chronic inflammatory diseases, like autoimmunity, tend to have altered gut microbiota when compared to healthy people. Taking robust, diverse gut microorganisms from a healthy person and transplanting them into someone who’s sick may help heal their gut dysfunction, and by extension, their disease [4]. 

As I discuss in Healthy Gut, Healthy You, you can think of FMT as essentially an extremely powerful probiotic. The difference here is that probiotics don’t colonize, or take up residence in your gut. But stool, with its enormous amount of microbes, can recolonize a sick person’s gut and possibly improve their health outcomes.

Using fecal matter to heal diarrheal and other diseases may have originated in China around 300–400 AD [4]. This concept hit the Western mainstream in the 1950s when doctors used fecal enemas to treat potentially life-threatening Clostridium difficile infections. C. diff is a bacterium that infects the large intestine, often after a round of antibiotics, and causes frequent diarrhea, belly cramps, and possibly many worse symptoms [5].

A huge body of research has confirmed that fecal microbial transplantation is overwhelmingly (about 90%) successful for treating recurrent C. diff. The Food and Drug Administration (FDA) approves FMT for cases of C. diff that don’t respond to antibiotics or have recurred at least twice [4, 6]. 

Outside of recurrent Clostridium difficile infections [7, 8, 9, 10, 11, 12, 13, 14, 15], FMT may be helpful for treating:

  • Bloating [16]
  • Abdominal pain [16]
  • Diarrhea [16, 17, 18]
  • Constipation [13]
  • Irritable bowel syndrome (IBS) [17, 18, 19, 20]
  • IBD [9, 13, 21, 22, 23, 24, 25, 26, 27]
  • Gout [28]
  • Impaired cognition [12, 29]
  • Alcohol use disorder [30]
  • Autism [31]
  • Lupus [32]
  • Organ transplant rejection [33]
  • GI cancer survival [34]
  • Anxiety and depression [18]
  • Metabolic syndrome [35]

As you can see, FMT has the potential to help people with many types of health conditions. 

Now you may be wondering how fecal matter is transferred from one person to another. It’s not as simple as you might think! Here’s how the process works:


Typically, healthy donor or multi-donor stool comes from stool banks. Although there may be exceptions, stool banks should only use fecal samples from healthy donors who have been thoroughly screened for factors like autoimmunity, metabolic diseases, infections, pathogens, and cancer that could place the recipient at risk [4, 36]. When it’s transplant time, the donor stool sample is mixed with saline or water and filtered. The isolated sample (fresh or frozen) is then delivered in one of several ways [4]:

  • Oral capsule to be swallowed
  • Nasogastric or nasoduodenal tube (a feeding tube through the nose into the stomach or small intestine)
  • Colonoscopy (a procedure where a flexible tube is inserted into the colon through the anus)
  • Endoscopy (a procedure where a flexible tube is inserted into the mouth to reach the stomach and small intestine)
  • Enema (injection of liquid into the rectum via the anus)

While others exist, there are only two FDA-approved FMT products for preventing recurrent C. diff infections [37]:

  • VOWST (formerly known as SER-109): an oral pill 
  • Rebyota: administered anally into the rectum (as an enema)

You should know that FMT isn’t currently FDA-approved to treat IBD, but we have strong scientific evidence supporting its use for the condition. Let me share that research with you.

FMT for IBD: The Research

Since FMT is FDA-approved to treat C. diff infections, it’s probably no surprise that it’s helpful for people with IBD who have recurrent bouts of C. diff or who haven’t responded to standard C. diff treatment. For example, a 2022 meta-analysis of IBD patients with C. diff found that 80% of them were cured of C. diff after an initial FMT treatment, and 90% were cured of C. diff after 2 or more treatments [9]. An umbrella analysis (highest quality of evidence) also found that IBD patients who used FMT had 80% higher C. diff cure rates than those who took a placebo or antibiotics [13]. 

In addition to C. diff treatment, there’s an overwhelming amount of research showing that FMT is just as effective as conventional IBD treatments—especially for the treatment of ulcerative colitis—and tends to have fewer side effects. For instance, the umbrella analysis I mentioned found that IBD patients who used FMT had a 70% higher clinical (symptomatic) remission rate than those who took a placebo, antibiotic, or laxative [13].Additional meta-analyses have found that, compared to placebo, FMT can significantly increase the likelihood of IBD patients reaching clinical remission [24, 25].  

This table highlights additional strong support for using FMT to treat IBD:

Research Design Study Protocol Findings
2022 Meta-analysis [38] Studies looking at FMT for people with active ulcerative colitis (UC)
  • 3.6x increase in odds of clinical (symptomatic) remission rates compared to the control group
  • 2.6x increase in odds of endoscopic remission (measured during colonoscopy) rates compared to the control group
2023 Meta-analysis [39] Studies looking at FMT for people with active Crohn’s disease
  • FMT had a medium-large positive impact on disease activity in 57% of patients who tried it.
2022 Meta-Analysis [22] Studies looking at FMT vs control for UC patients
  • FMT had higher rates of clinical remission (40% FMT vs 22% control)
  • FMT had higher rates of endoscopic remission (17% FMT vs 9% control)
  • FMT was more effective when delivered directly to the lower GI tract
2023 Meta-Analysis [40] Studies looking at FMT vs control for UC patients 
  • FMT led to higher clinical remission rates (50% FMT vs 30% control)
  • FMT led to higher endoscopic remission rates (27% FMT vs 16% control)
  • All delivery routes were effective for clinical remission, but oral FMT may not be effective for endoscopic remission
2021 Randomized Controlled Trial [27] Patients with active UC  took antibiotics for 2 weeks and then received A) oral FMT, or B) placebo
  • 38% more of the FMT group than placebo group reached clinical and endoscopic remission.
  • Symptoms returned (clinical remission stopped) upon discontinuing FMT. 

Summing this up, numerous placebo-controlled trials and cohort studies have found FMT to be a highly effective treatment option for curing recurrent C. difficile infections, whether in someone with IBD [9, 13] or not [7, 8, 9, 10, 11, 12, 13, 14, 15]. 

FMT may also be a reliable option for helping people with IBD reach remission without the harsh side effects that can accompany traditional IBD medications and surgery [22, 27, 38, 39, 40]. Most studies looking at the efficacy of FMT for IBD involve UC patients, but more research is starting to show its promise for Crohn’s disease as well [39].

FMT Delivery Options

As for the delivery method, if you’re using FMT for C. diff, all options (oral, nasal, or anal) seem to be similarly effective [10]. But oral FMT—which is less invasive and easier to use compared to the other FMT delivery systems—may not work as well for some IBD patients, particularly those with UC. This seems especially true when it comes to reducing inflammation and other disease activity in the intestinal lining. 

For example, according to a 2023 meta-analysis, all FMT delivery routes were effective for improving the clinical response in people with UC. However, oral capsules didn’t improve signs of disease activity, like inflamed colon tissue, when compared to controls [40]. 

Another meta-analysis found that FMT delivered directly into the lower gastrointestinal tract of UC patients (via enema or colonoscopy) was better at treating IBD than when it was delivered orally [22]. 

Relatively limited research on Crohn’s patients suggested that all types of FMT were equally effective, but we need further studies to confirm this [39].

Scientific evidence supports the use of FMT by itself for IBD, but are there any added benefits if we use it in concert with other natural therapies like diet and probiotics? 

Is FMT Best as a Stand-Alone Treatment?

Limited evidence shows that combining a therapeutic diet with FMT could help to increase the effects of FMT in people with irritable bowel syndrome (IBS – a GI condition with some similar symptoms to IBD). For instance, in a non-randomized clinical trial of patients with IBS-D (diarrheal type), FMT plus a low-FODMAP diet led to greater symptom improvements and better quality of life than FMT plus a normal diet [17]. 

More to our point, a 2022 randomized controlled trial found that treating ulcerative colitis with FMT plus an anti-inflammatory diet led to higher clinical and endoscopic remission rates after 2 months than standard IBD therapy. What’s more, when patients continued with the anti-inflammatory diet for a year, their remission rates were better when compared to those who didn’t follow the diet [21].

When it comes to using FMT plus dietary supplements, like probiotics, there’s very little available research. For now, it’s probably best to discontinue supplements (especially antimicrobials) while undergoing FMT so as to not interfere with the treatment. But again, we need more evidence to know for sure, and your healthcare provider should specify what you can and can’t take during treatment.

Now that you know what FMT is and how it works for IBD, let’s talk about whether or not it’s safe.

Is FMT Safe?

In general, the risks of FMT seem to be very low. Any side effects are often mild, GI-related (like bloating, abdominal pain, diarrhea, and constipation), and self-limiting (meaning they resolve without treatment) [4]. 

For example, two meta-analyses have shown that people with UC who used FMT were no more likely to have negative side effects than those who didn’t [38, 40]. Other research shows that FMT is probably safe for the pediatric population [11], people with Crohn’s [39], and high-risk patients [36]. 

Overall, serious adverse events in FMT studies have been rare and generally not related to the FMT itself [4]. Even long-term, follow-up studies haven’t shown any significant risk of negative outcomes [4]. And to top it off, one small clinical trial found that FMT treatment caused fewer side effects than steroid medications [23]. 

Whew! It looks like we can relax. At this point, it’s fair to say that FMT administered by a qualified professional is generally safe. 

Now you might be thinking, if FMT is safe and effective, why not just give it a try? In my clinical experience, there are many other natural therapies (like probiotics, stress management, and diet) for IBD that can soothe your symptoms and help you reach remission. It makes good sense to start with these effective, low-cost, easy-to-implement options first, and if you don’t achieve your desired results, then consider FMT.

To demonstrate why FMT probably isn’t the best first choice for treatment, let’s get back to Kyle’s story. He didn’t have to go the FMT route, so I want to share what we did to get him into remission.

Healing IBD Symptoms With Other Natural Therapies

While FMT seems promising for IBD, and many consider it a natural approach [4], you probably don’t need to start there. 

Basically, we know of other natural therapies that are safe, effective, cheaper, and often less invasive than FMT, so it just makes sense to try them first. Maybe you have tried some of these, like probiotics or diet changes, but still struggle with IBD symptoms. Sometimes it’s just a matter of trying the right combination of science-based approaches, ideally with knowledgeable guidance.

Read on to see which natural treatments worked for Kyle and allowed him to skip FMT. I’ll walk you through what he did step-by-step to give you a better idea of how powerful these less invasive, natural therapies can be.

Step One: Probiotics

To start, simply adding our triple therapy probiotic protocol led to huge improvements in Kyle’s symptoms—he immediately noticed better digestion, stool consistency, and much less abdominal pain with meals. 

Kyle’s experience with probiotics mirrors what probiotics researchers have found. The results of the following meta-analyses support the use of multi-strain probiotics for maintaining good gut health and decreasing the symptoms of IBD, particularly ulcerative colitis:

  • Probiotics, especially multiple strains combined, can put active UC into remission [41]. 
  • Probiotics were as effective as the medication mesalamine for preventing UC relapse [42].
  • Probiotics can improve small intestinal bacterial overgrowth (SIBO, or dysbiosis), which is often associated with IBD [43].
  • Multi-strain probiotics likely had more benefit than single strains on IBD remission and UC disease activity [44].

Step Two: Stress Management

Kyle felt significant improvements with probiotics, but when he next added the Gupta program (a limbic retraining and holistic health program for chronic conditions) to calm his nervous and immune systems, he described the result as “life-changing.” 

Research has found that meditation and stress management practices can reduce IBD inflammation, anxiety, and stress, all of which can reduce GI symptoms and improve quality of life [45]. Incredibly, relaxation-based mind-body techniques may also change the expression of genes that appear to contribute to the pathogenesis (development) of IBD [46].  

Step Three: Diet and Abdominal Massage

Kyle made a lot of progress with steps one and two, but he still felt there was room for improvement, especially with regard to his bowel movements and abdominal pain. So, he added a low-FODMAP diet to improve his food tolerance and constipation, and abdominal massage to help with his post-surgical adhesions.

For some people with IBD, high-FODMAP foods can trigger symptoms. For example, a meta-analysis found significant symptom improvement in patients with Crohn’s disease who followed a low-FODMAP diet [47]. A low-FODMAP diet works by limiting certain fermentable starches and sugars that feed gut bacteria. Removing these foods for a trial period can help improve digestive symptoms. 

Because Kyle had once had intestinal surgery for his Crohn’s disease, he also added abdominal massage. A common side effect of abdominal surgery is post-surgical adhesions (abnormally attached tissues), which can cause abdominal pain. The great news here is that a systematic review concluded that soft tissue mobilization (abdominal massage) can improve adhesion symptoms [48].

Kyle said the low-FODMAP diet and abdominal massage dramatically improved his bowel movements and abdominal pain. In the end, incorporating these steps with help from our clinic helped him feel well enough that he didn’t need to look into FMT for his IBD. Ideally, you can try a similar approach and guide your own gut flares into remission.

When working with Kyle and every patient in our clinical practice, we personalize a sequence of treatments to help minimize unneeded interventions and get them healthy as quickly as possible. We prioritize the most impactful science-based treatments first, and add on more specialized interventions only if they’re not improving in meaningful ways. 

So, When Is FMT the Way to Go?

There are no official guidelines for how or when to use FMT for IBD, but I would place it in the ‘less commonly needed’ category

That said, if you’ve used natural therapies to create a healthy foundation, but your IBD symptoms are refractory (not responding to treatment), FMT is definitely something to consider. If you choose to try it, you should only do so under the guidance of a trusted, skilled gastroenterology or other healthcare provider.

Consider Natural Therapies Before FMT for IBD

Inflammatory bowel disease is a relapsing-remitting (repeatedly flaring and receding) autoimmune disorder characterized by high amounts of mucosal (intestinal) inflammation. It can cause you to struggle with bloody diarrhea, abdominal pain, nutrient malabsorption, and fistulas that significantly disrupt your quality of life. Traditional treatment of inflammatory bowel disease often includes strong medications (like corticosteroids and biologics) and surgery, both of which can have undesirable side effects.

Faecal microbiota transplantation is emerging as a viable IBD treatment option. FMT is only FDA-approved to treat resistant C. diff infections, but an overwhelming amount of research shows its effectiveness in inducing IBD remission, especially for people with ulcerative colitis. If carried out appropriately, FMT appears to be safe and may have fewer side effects than IBD medications. 

Before trying FMT, you may want to consider more accessible and inexpensive science-based gut therapies like multistrain probiotics, meditation, an anti-inflammatory diet, and abdominal massage. For more guidance on effective, natural ways to heal your gut, you can check out my book, Healthy Gut, Healthy You. In it, I walk you through the step-by-step process we use in the clinic to help our patients reclaim their gut health. 

However you go about creating a healthy foundation, if you still struggle with IBD flares, you may want to consider discussing FMT with your healthcare provider. And at any point in your gut-healing journey, feel free to contact us at the Ruscio Institute for Functional Health for help creating a personalized plan.

The Ruscio Institute has developed a range of high-quality formulations to help our patients and audience. If you’re interested in learning more about these products, please click here. Note that there are many other options available, and we encourage you to research which products may be right for you.

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