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Evidence based

Evidence Based

This article is based on scientific evidence, written by experts and fact checked by experts.

Our team of licensed nutritionists and dietitians strive to be objective, unbiased, honest and to present both sides of the argument.

This article contains scientific references. The numbers in the parentheses (1, 2, 3) are clickable links to peer-reviewed scientific papers.

Revolting or Revolutionary? A Guide to Fecal Transplant Pills

Written by on February 17, 2024

“Microbiome Pills” May Help Solve Some Stubborn Gut Health Issues

Key Takeaways:

  • “Microbiome pills” are the colloquial name for fecal microbiota transplants taken orally.
  • Fecal microbial transplantation, or FMT, is when you take poop from a healthy, screened individual and introduce it into the gut of someone with poor gut health.
  • Most of the research on FMT and microbiome pills centers around helping chronic C. diff diarrhea.
  • Studies show that FMT can help inflammatory bowel disease and possibly many other conditions, too. 
  • For the majority of gut conditions, traditional probiotics are the better option.
  • FMT is normally reserved for more severe conditions that don’t respond to multi-strain probiotics.
  • You must work with a physician to use microbiome pills.

“Microbiome pills,” or supplements that contain fecal matter donated from a healthy individual’s gastrointestinal tract have an indisputable “ick” factor. But before you scroll past this article in disgust, bear with me a minute. The idea might be stomach-turning, but fecal transplants in capsule form can have significant benefits if you have very poor gut health.

In this article I’ll answer the biggest if, when, and why questions around microbiome pills, including how they compare with probiotic supplements. 

Probiotics are more widely available, cheaper, and more acceptable for most people. However, the emerging research on microbiome pills and fecal microbial transplants in general, suggests they have real worth in specific situations.

In particular, microbiome pills are a good fit for helping people recover from the symptoms of recurrent Clostridium difficile (C. diff) infections. Let’s take a closer look.

What Is a Microbiome Pill?

A microbiome pill, or “poop” pill, is the informal name given to a fecal microbial transplant (FMT) that you consume orally, in capsule form.

Fecal microbial transplantation is where the entire gut microbiome, in the form of a fecal sample, is taken from a healthy donor and transplanted into the intestinal tract of a sick recipient [1]. This practice, which is also known as “bacteriotherapy” or “intestinal microbiota transplantation,” has been around since ancient times but is only now getting the scientific attention it deserves.

FMT operates on the premise that the gut microbiota is intimately connected to almost every bodily system. By replacing a “sick” microbiome with the gut microbes from a healthier human gut, you might help repair conditions and symptoms associated with poor gut health.

FMT can be administered in various ways, of which the oral route is just one, albeit the least invasive and most convenient. Other ways that donated fecal material can be transplanted into a sick individual are via an enema or colonoscopy. Healthy fecal material can even be delivered to the gut via a nasogastric tube that goes down into the stomach or duodenum, or the first segment of the small intestine, just beyond the stomach.

How Are Microbiome Pills Made?

A fecal microbial transplant preparation starts with a fecal sample taken from a healthy donor who is free from autoimmune and metabolic diseases, infections, and cancer [1]. The sample is mixed with saline or glycerol and the solution is filtered to remove particulate matter. The FMT preparation can be used in liquid form for administration via an enema or colonoscopy. Or, it may be used to make microbiome pills by freeze-drying it and putting it in capsules. FMT samples can be frozen at -80°C for up to six months without losing their clinical efficacy [2]. 

Benefits of Fecal Microbiota Transplants

Studies of varying quality suggest that FMT may help with these gut conditions:

  • Recurrent C. diff infection [3, 4, 5, 6, 7, 8, 9, 10, 11]
  • Inflammatory bowel disease (IBD) [5, 9, 12, 13, 14, 15, 16, 17, 18]
  • Bloating and abdominal pain [19]
  • Small intestinal bacterial overgrowth (SIBO) [20]
  • Diarrhea and constipation [9, 19, 21, 22, 23]
  • Irritable bowel syndrome (IBS) [21, 22, 23, 24]

It’s possible that FMT may also have benefits beyond the gut, such as helping impaired cognition and easing anxiety and depressive symptoms [8, 22, 25].

If you’re familiar with using probiotics, you’ll know that there’s a lot of overlap between the above FMT benefits and the benefits of probiotics.

I’ll touch on the differences between microbiome pills and probiotics in more detail later. For now, know that probiotics are still the winner in terms of cost, accessibility, and relative effectiveness for most common gut conditions. 

That said, specifically for the first two in the above list—C. diff infection and inflammatory bowel disease—there is a lot of evidence that FMT is highly effective. Especially for severe and stubborn cases of C. diff and IBD, FMT may be a more effective treatment than probiotics. 

Microbiome Pills for C. diff

Clostridium difficile, or C. diff, is a bacterium that usually lives harmlessly in your gut along with all the other gut bacteria and various microorganisms that make up the gut microbiome. Sometimes, however, usually after intensive antibiotic use, C. diff can grow out of control. A C. diff overgrowth can cause chronic, debilitating diarrhea, often accompanied by stomach cramps and colitis (inflammation of the colon) [26].

Standard treatment for C. diff is usually antibiotics, which is problematic because antibiotics probably caused the C. diff infection in the first place. Worse, many C. diff infections are resistant to standard antibiotic medications, which means many doctors may turn to last-resort antibiotics like vancomycin. In comparison, more benign treatments like FMT and probiotics make sense. Not only do they appear to counter the public health problem of antibiotic resistance [27], but probiotics and FMT are both useful for treating C. diff infections [28]. Compared to placebo, Saccharomyces boulardii may be the most effective probiotic against C. diff, but FMT is more effective overall—even better than vancomycin, according to a 2020 systematic review [28].

Revolting or Revolutionary? A Guide to Fecal Transplant Pills - FMT%20Treatment L

Indeed, research shows that FMT is a remarkably effective treatment for recurrent C. difficile infections—on average about 90% of patients get total symptom relief with the treatment according to a meta-analysis of 37 studies [29]. 

That’s impressive! Now, how effective is FMT for IBD? 

FMT Holds Promise for IBD 

There is good evidence that microbiota transplants are effective for treating inflammatory bowel diseases (IBD), including both Crohn’s disease and ulcerative colitis [13, 30] .

A 2022 umbrella analysis found that patients who tried FMT were 70% more likely to experience clinical remission (IBD symptoms go away) than those who took a placebo, antibiotic, or laxatives. An umbrella analysis offers the highest quality of evidence because it combines the results of multiple meta-analyses for better statistical power [9].

Recent individual meta-analyses of FMT delivered to IBD patients in various ways (oral, nasal, colonoscopic, or enema) have also found similarly positive actions. For example: 

  • Compared to a placebo, FMT led to a 44% increased likelihood of IBD patients achieving clinical remission [15]. 
  • Compared to controls, FMT led to higher rates of [31]:
  • Clinical remission of ulcerative colitis symptoms (50% FMT vs 30% controls)
  • Endoscopic remission, or improvements in how cells look under the microscope (27% FMT vs 16% control) 
  • Compared to a placebo, FMT led to a four times greater odds of people with ulcerative colitis reaching clinical and endoscopic remission [16]. 

Though we have less research on FMT for Crohn’s patients, another recent meta-analysis showed that 62% of patients achieved clinical remission after having FMT [32].

Furthermore, in one clinical trial of patients with ulcerative colitis, FMT treatment was about as effective as conventional steroid treatment but with fewer side effects. Ulcerative colitis patients who had their whole microbiome replaced via FMT also had lower levels of inflammatory blood markers, suggesting FMT had a systemic anti-inflammatory effect [14].

However, it’s worth noting that for people with ulcerative colitis in particular, oral microbiome pills may be less effective than other forms of FMT. The best effect appears to come from FMT delivered directly into the lower digestive tract (through an enema or colonoscopy) [13]. Much more limited research suggests that all types of FMT were similarly helpful for Crohn’s patients, but we’ll keep our eyes out for more studies to confirm this [30].

It’s also important to note that FMT may not be a permanent solution: IBD and C. diff patients often need follow-up FMT treatments to help maintain remission [17].

How to Access FMT

Two FMT-derived treatments have FDA (Food and Drug Administration) approval and are available in the US for human health conditions. A doctor can prescribe an oral microbiome pill, known as SER-109 (or VOWST™), or administer a fecal transplant known as RBL (or Rebyota™) into the rectum. 

There are also reputable non-FDA-approved stool banks, such as the one at the University of Minnesota. To access an FMT sample from one of these stool banks, you need to find and work with a doctor who will source and administer the sample for you, usually via a colonoscopy.

Safety First

A 2021 review analyzing the safety of FMT concluded that approved FMT is safe, even in high-risk patients, and any side effects are mostly mild and resolve without treatment [33]. 

However, it is vital to make sure you only source FMT from reputable sources. Before today’s checks and balances concerning stool donors, two people reportedly died after using fecal samples from donors who were not properly screened for intestinal pathogens. 

This underlines why it’s important to work only with reputable doctors and institutions when it comes to FMT. 

Specifically, please don’t ever follow DIY internet instructions that describe how to take someone else’s poop and introduce it into your own body.

Probiotics Are Still a Good First Choice Overall

Although FMT shines brighter than probiotics for a couple of gut conditions, probiotics are also effective and worth trying first to see if they’re all you need. They’re also more affordable.

Although insurance may cover many FMT treatments (especially for C. diff patients), it can have significant cost and access barriers [34]. In contrast, probiotics are relatively cheap and easy to acquire, which makes them a good first option for problems with your gut health.

Research that directly compares the effects of probiotics and FMT on specific conditions is apparently nonexistent. However, separate clinical trials have shown that several gut conditions respond well to both probiotics and FMT.

This table gives a quick overview of research showing the effects of probiotics versus FMT on some common gut conditions. Please work closely with your doctor if you have any of these conditions, especially C. diff or IBD.

Condition Probiotic Treatment FMT Treatment Which is Best?
C. diff A meta-analysis concluded that probiotics can prevent diarrhea from C. diff [35], but a systematic review said we need better trials to unpack the scale of the benefits and recommended dose [28]  A meta-analysis found that, on average, about 90% of patients got total symptom relief with FMT [29].   FMT is highly effective, but probiotics may be worth trying first.If probiotics haven’t helped, FMT is a good option for chronic or recurrent C. diff.
IBD: Ulcerative Colitis (UC)

Meta-analyses have shown: 

  • Probiotics, especially multiple strains, may silence UC disease activity and even put active UC into remission [36, 37].
  • Probiotics can be as effective as the medication mesalamine for UC relapse [38]. 
 Several meta-analyses suggest significant benefit. One found that, compared to placebo, FMT led to a four-times greater odds of clinical and endoscopic remission for people with ulcerative colitis [16].  Both FMT and probiotics are helpful for UC. Consider starting with multi-strain probiotics and  moving on to FMT if you haven’t improved. 
IBD: Crohn’s Disease A meta-analysis found  no clear evidence that probiotics are better than placebo for inducing remission in Crohn’s patients [39]. Overall, there’s much less research on probiotics for Crohn’s than for UC. A meta-analysis showed that 62% of patients achieved clinical remission after having FMT [32]. Another meta-analysis found that FMT had a medium-large positive impact on disease activity in 57% of patients who tried it [30]. Overall,there’s much less research on Crohn’s and FMT than there is on UC and FMT.   Neither is very well studied for Crohn’s, but FMT is the clear frontrunner until further research shows probiotics can treat Crohn’s. 
SIBO (small intestinal bacterial overgrowth) A meta-analysis found that probiotics alone eradicated SIBO in 53% of patients [40], which rivals the efficacy of antibiotics [41]. Probiotics combined with antibiotics can raise the eradication rate to 85% [40].  Research is minimal, but in one randomized clinical trial, FMT improved gut microbial diversity and GI symptoms in people with SIBO (compared with placebo) [20].  Given the research, probiotics are a better first-line treatment for SIBO.
IBS Several meta-analyses have found that probiotics, particularly multi-strain types, can relieve IBS symptoms, particularly abdominal bloating and pain [42, 43, 44, 45]. Some decent randomized controlled trials  suggest FMT (especially combined with a low-FODMAP diet) can benefit patients with IBS [21, 23], but many meta- analyses have shown FMT led to no improvement in IBS symptoms other than quality of life [9, 46, 47, 48, 49]. Probiotics are the clear best option for IBS.

As you can see in the table, two common conditions for which probiotics clearly trump FMT are irritable bowel syndrome (IBS) and SIBO. These are two of the most common conditions we see in patients, and they can be fairly straightforward to treat. 

For my patients with IBS, I recommend probiotics first because of their strong track record for improving symptoms [42, 43, 44, 45] 

When it comes to C. diff and ulcerative colitis, probiotics can be quite effective. Given their lower cost and easier accessibility, it makes sense to try probiotics first (with your doctor’s support) and see if they’re all you need. If not, or if you have Crohn’s disease, it’s a good idea to consider FMT.

Combining probiotics with a low-FODMAP diet can have even greater benefits for gut health and may help you avoid the FMT route. Whatever path you take, I strongly recommend working with a knowledgeable and supportive healthcare provider who can help you zero in on what works best for you. 

Triple Probiotic Therapy 

If you’re considering FMT because probiotics haven’t been a success for you, changing up your probiotic protocol is worth trying first. 

At the clinic, we’ve found that many patients have better success rates when they combine probiotics from the three most effective probiotic categories. These are:

  • Lactobacillus with Bifidobacterium 
  • Saccharomyces boulardii (a beneficial yeast)
  • Soil-based probiotics

High-quality research, including several meta-analyses, supports taking more than just one category of probiotics for a variety of conditions [37, 50, 51, 52]. For example, multi-strain probiotics have demonstrated greater efficacy than single strains for treating IBS [53, 54]. Multi-strain probiotics also performed better than single strains in a meta-analysis of studies using probiotics to treat constipation [55]. 

I’m not saying that triple probiotic therapy will work for everyone. But, given the relatively higher cost and effort of FMT, it makes sense to give multispecies probiotics a try for your gut issues first.

Remember that setting a foundation of good gut health and immune system health with a healthy diet and lifestyle should also come before either probiotics or microbiome pills.

Keep Your Eye on Microbiome Pills for Gut Health 

For now, it’s clear that microbiome pills and other FMT treatments have a solid amount of research backing their benefits for some gut conditions, especially recurrent C. diff infections and inflammatory bowel disease.

That said, FMT doesn’t appear to be better than probiotics for IBS or SIBO, which are two of the most common gut conditions. FMT is also significantly more expensive and difficult to access than probiotics.

Nonetheless, FMT is worth keeping an eye on for future developments. And if you think you’d like to try FMT, always do so with the help of a qualified healthcare provider with access to an approved supplier.

No matter what kind of gut or even non-digestive symptoms may be ailing you, working on your underlying gut health fundamentals can go a long way toward your feeling better. If you need a guide for how to do that, check out my 8-step plan for healing your gut. You can also get it in full detail in Healthy Gut, Healthy You.

Another option reach out for an online appointment with us at the Ruscio Institute for Functional Health, where we specialize in health problems that stem from gut imbalances.

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.

Dr. Michael Ruscio is a DC, Naturopathic Practitioner, researcher, and clinician. He serves as an Adjunct Professor at the University of Bridgeport and has published numerous papers in scientific journals as well as the book Healthy Gut, Healthy You. He also founded the Ruscio Institute of Functional Health, where he helps patients with a wide range of GI conditions and serves as the Head of Research.
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