A fecal transplant – also referred to as bacteriotherapy or fecal microbiota transplantation – has shown promise for GI tract ailments otherwise difficult to treat. What is a fecal transplant? Pretty much what it sounds like. It’s the introduction of beneficial bacteria and other fecal components into the GI tract of an unhealthy person by implanting a stool sample from a healthy donor. It is performed by a medical professional and is typically performed under sedation with a scope, like that used for a colonoscopy. It can also be performed – again by a health professional – by mixing the healthy stool sample with sterile saline and inserting it as a retention enema. Other methods include inserting a nasal tube in the intestine or swallowing a capsule. Because of recent developments (see below), the capsule method might currently be the preferred route of administration. Even though fecal transplants have only been employed in modern medicine for the last few decades, they were reportedly used in Chinese medicine as early as the fourth century A.D.

The donor process

Stool samples from healthy donors are screened to rule out the presence of parasites, yeast overgrowth, etc. The donor provides a health history and is also screened for other diseases that can be spread through bodily fluids – like hepatitis and HIV. Other contraindications for donating include: (1) having taken antibiotics in the previous three weeks, (2) having a history of inflammatory bowel disease or colorectal cancer, (3) having chronic diarrhea, or (4) being on a cancer chemotherapy drug. Although a recipient can utilize a healthy friend or relative as a donor, there are also stool banks for this purpose – similar to a blood bank.

The gut’s microbiome is made up of all the bugs – bacteria, yeast, viruses, etc. – and their respective genetic material and metabolic byproducts. Because of inconsistent fecal transplant results, gastroenterology is now taking a closer look at the gut microbiome of donors. This is not an easy task because no two gut microbiomes are alike – as unique to each individual as a fingerprint. The makeup and diversity of the bugs in the donor’s gut can significantly influence the outcome. Donors who have a diverse assortment of beneficial bugs are identified as Super Donors.1 An imbalanced gut microbial content is called dysbiosis and is usually characterized by low microbial diversity. If a transplant is successful, then a shift in the make-up of the microbial community in the gut toward healthier, more diverse numbers of organisms is seen on stool examination, which is followed by clinical improvement.

In addition to rich diversity, other factors appear to be associated with improved transplant outcomes, including certain species of beneficial bacteria and the ability of these bacteria to increase levels of important short-chain fatty acids (SCFAs; butyrate in particular). Butyrate is important for gut health because it provides the main fuel for the cells that line the colon. For example, bacteria from the genera Roseburia, Oscillibacter, Blautia, and Dorea increase in abundance in a successful transplant.1 

There also might be some degree of need for compatibility between donor and recipient. For example, if a beneficial bacterial strain is present in the stool donation, then it is more likely to increase in abundance if that strain is already present in the recipient’s gut.1 In addition to short-term benefit, it is hoped the transplant will result in long-term remission of the disease it is being used for. Several factors can affect this, including genetic differences between donor and recipient, antibiotic exposure, and diet. Rapid changes in diet can result in large shifts in the make-up of the gut flora in as soon as one day. Dietary fiber is one of the most well-established methods of increasing the beneficial bacteria that make butyrate and other beneficial SCFAs.

And it appears that it might not be just the bacterial strains in the sample that provide benefit. A fecal sample provides other components that some research shows are important – including proteins, viruses, DNA, and metabolites (like SCFAs). This sets a fecal transplant apart from a targeted probiotic approach, which would only include specific beneficial bacteria.

What conditions benefit from fecal transplant?

Although from a regulatory perspective fecal transplants are still considered investigatory, any condition associated with gut dysbiosis might benefit from one – conditions within or outside the gut have been studied. (Read more about the regulatory status in the DIY fecal transplant section.)

Clostridium difficile (C. diff)

C. diff. is one of the really bad guys. Even though strong antibiotics are used to treat it, C. diff. is one of the most frequent causes of antibiotic-associated diarrhea – which creates a viscous cycle. Normally, in a healthy gut, C. diff. behaves itself and is kept in line by an array of beneficial bacteria. Problems begin when an antibiotic kills off the good bacteria but not the C. diff. (which is only killed by very specific and strong antibiotics). A C. diff infection can cause severe diarrhea and a form of colitis (inflammation in the colon). Because of the double-edged sword created by antibiotics, C. diff. infections were among the first in modern times to be treated with fecal transplants, which have been fairly to very effective (67-82 percent) at resolving infections that were either recurring or unresponsive to treatment.2 Some reports suggest a 90-percent or higher success rate.

Inflammatory bowel disease

Fecal transplants have also been used to treat chronic inflammation in the colon – inflammatory bowel disease (IBD) – which can manifest as ulcerative colitis or Crohn’s disease. Although dysbiosis is associated with these conditions, there are multiple other factors, like genetics and immune system dysfunction, that can contribute. Because of the chronic nature of IBD and its multiple causes, fecal transplants have not been as consistently effective as those for C. diff. However, in cases not responsive to other therapies, they have shown some significant benefit compared to placebo studies. For example, in one study, 41 percent of fecal transplant patients achieved disease remission at eight weeks, compared to only eight percent in the placebo group.3  Because IBD is a chronic condition, a fecal transplant often needs to be repeated.

Other conditions

Although fecal transplants are not commonly used for non-GI tract conditions, they have been studied for metabolic conditions associated with a disruption in the microbiome – metabolic syndrome, obesity, and type 2 diabetes. For example, in one report fecal transplants from lean individuals into men with metabolic syndrome resulted in significantly improved insulin sensitivity measured six weeks later, which is a step toward improving glucose metabolism and body weight. It also increased butyric acid-producing bacteria.4

DIY fecal transplants. Are they a good idea?

Because fecal transplants are not FDA-approved, many doctors are hesitant to use them. Several years ago, the FDA announced they would exercise “enforcement discretion” regarding their use for treatment-resistant C. diff.5 In other words, the FDA would look the other way, but advised doctors to inform their patients the process is still investigational. For all other conditions, fecal transplants are only permitted if an individual is enrolled in a clinical trial.

Because of the lack of clinical availability, do-it-yourself home fecal transplants have become widely used. But is this safe? Although you can read numerous anecdotal reports of miraculous results, using transplant samples that have not been adequately screened is a bit of a “crap shoot” (pun intended). Because some bad bugs can go unnoticed in a seemingly healthy person, there are reports of viruses, like rotavirus, and bacteria like pathogenic E. coli, causing new infections in the recipient – some of them life-threatening. Also, because the microbiome has numerous effects outside the GI tract, transplantation can have far-reaching effects. For example, one woman who received a sample from her overweight daughter quickly gained 30 pounds.

Several companies are working on making the process easier by providing thoroughly screened, freeze-dried samples to be taken orally – in addition to products provided by other routes, including enemas.7 These are available only in clinical settings.

What else can benefit the makeup of the gut microbiome?

You probably know one or two things you can do from the safety of your home to benefit your gut. If a large part of what makes a fecal transplant successful is the presence of good bacteria (feces is 50-percent bacteria), then a nutritional supplement made up of only beneficial bacteria – a probiotic – should be supportive. And plenty of evidence points to the benefit of probiotics for supporting various aspects of gut health.*

Then there are prebiotics – food for the good bugs. These can be in the form of fiber or as a non-fiber prebiotic. One thing a prebiotic can do to improve the gut microbiome, in addition to supporting growth of good bacteria, is to increase SCFAs like butyrate.*

Are you wondering about the diversity of your own gut – or that of your patients? Wonder no more. You can find this out and much more with Thorne’s at-home Gut Health Test.

If you are interested in diving more deeply into the research on fecal transplantation, then I highly recommend this great review article, which I found invaluable as I was preparing this blog. It’s also listed below as Reference #1.


  1. Wilson BC, Vatanen T, Cutfield WS, O'Sullivan JM. The super-donor phenomenon in fecal microbiota transplantation. Front Cell Infect Microbiol 2019;9:2. doi:10.3389/fcimb.2019.00002
  2. Tariq R, Pardi DS, Bartlett MG, Khanna S. Low cure rates in controlled trials of fecal microbiota transplantation for recurrent Clostridium difficile infection: a systematic review and meta-analysis. Clin Infect Dis 2019;68(8):1351-1358. doi: 10.1093/cid/ciy721.
  3. Paramsothy S, Kamm MA, Kaakoush NO, et al. Multidonor intensive faecal microbiota transplantation for active ulcerative colitis: a randomised placebo-controlled trial. Lancet 2017;389(10075):1218-1228. doi: 10.1016/S0140-6736(17)30182-4. 
  4. Vrieze A, Van Nood E, Holleman F, et al. Transfer of intestinal microbiota from lean donors increases insulin sensitivity in individuals with metabolic syndrome. Gastroenterology 2012;143(4):913-6.e7. doi: 10.1053/j.gastro.2012.06.031. 
  5. Enforcement policy regarding investigational new drug requirements for use of fecal microbiota for transplantation to treat Clostridium difficile Infection not responsive to standard therapies  https://www.fda.gov/regulatory-information/search-fda-guidance-documents/enforcement-policy-regarding-investigational-new-drug-requirements-use-fecal-microbiota [Accessed 4.18.22]
  6. The rise of the do-it-yourself fecal transplant   https://www.webmd.com/digestive-disorders/news/20151209/diy-fecal-transplant [Accessed 4.18.22]
  7.  Fecal microbiota transplantation is poised for a makeover. https://www.the-scientist.com/bio-business/fecal-microbiota-transplantation-is-poised-for-a-makeover. [Accessed 4.18.22]