Let's talk about something that’s gotten a lot of attention over the past few years — fecal transplants. Yes, it’s exactly what it sounds like. And while it might seem like a strange or even extreme treatment, it’s also one of the most fascinating examples of how much the medical world is beginning to recognize the importance of the gut microbiome.

But as with most things in medicine, there’s both good and bad news here. So let’s unpack what we actually know about fecal transplants — when they help, when they don’t, and even when they can make things worse.

What Exactly Is a Fecal Transplant?

A fecal transplant, or fecal microbiota transplantation (FMT), is a procedure where stool from a healthy donor is placed into the intestinal tract of someone who’s sick. The idea is to “reset” or “repopulate” the gut microbiome by introducing beneficial bacteria from a healthy person.

FMT can be done in a variety of ways — through colonoscopy, enema, capsules, or even a nasogastric tube. Regardless of how it’s done, the goal is to restore a healthy balance of microbes.

The Good: Where It Truly Works

There’s one condition where fecal transplants are undeniably effective and well-studied — recurrent Clostridium difficile infections, often called C. diff.

C. diff is a type of bacterial infection that usually occurs after antibiotic use. It causes severe diarrhea, inflammation, and can even be life-threatening. In these cases, fecal transplants have shown remarkable success rates — often above 85 to 90 percent — in curing infections that failed to respond to antibiotics and other treatments.

For these patients, it can be life-changing. In this specific scenario, I think can be an excellent tool is sometimes warranted, and one that modern medicine has rightfully embraced.

What About Ulcerative Colitis?

Some patients with Ulcerative Colitis (UC) have also tried fecal transplants. UC is a chronic inflammatory disease of the colon, and because gut bacteria play a role in inflammation, the idea is that introducing a healthier microbiome might help.

The evidence here is mixed:

• Some studies show about 30–40% of patients achieving remission with repeated FMT treatments.

• A positive response is more likely in mild-to-moderate UC than in severe disease.

• It’s still considered experimental.

And for Crohn’s disease, the data are much weaker, and it’s generally not considered an effective treatment at this time.

In either case it’s not the first thing that I would recommend, and we’ve generally been able to help both UC and Crohn’s patients improve without resorting to FMT.

The Bad: When It’s Not Supported by Research

Now let’s talk about where fecal transplants have not been shown to help — and this includes many of the conditions for which people are desperately seeking answers, such as IBS (Irritable Bowel Syndrome), Candida overgrowth, and SIBO (Small Intestinal Bacterial Overgrowth).

It’s understandable that people want to try FMT for these issues. After all, these are all conditions connected in some way to gut bacteria or gut health. And many people who haven’t seen us are not getting help and are desperate for answers. But the problem is that the science just hasn’t supported its use outside of C. diff and a few UC cases.

For IBS specifically, several clinical trials have tested whether fecal transplants help — and the results have been inconsistent, at best. Some studies show mild benefit, others show no improvement at all, and a few have even shown that people got worse.

Part of the issue is that IBS isn’t caused by a single bacterial imbalance. It’s a complex condition with many possible triggers — from immune system reactivity and food sensitivities to stress, inflammation, and even the nervous system. Simply dumping in someone else’s bacteria doesn’t address the root cause of why your gut microbiome is out of balance in the first place.

The Ugly: When It Makes Things Worse

I’ve personally seen patients who have undergone fecal transplants in an attempt to fix IBS, Candida, or SIBO — and ended up feeling much worse afterward.

In some cases, their digestion became more unpredictable, or they developed new symptoms they didn’t have before — things like bloating, pain, or food reactions. I’ve even seen people develop what looked like brand-new infections, or long-term shifts in their microbiome that made it even harder to recover.

This isn’t something you can just undo with a probiotic or a round of antibiotics. Once you’ve altered your microbiome in that way, it can take years — if ever — to rebalance it naturally.

The Better Path Forward

If you’re struggling with IBS, Candida, or chronic digestive problems, the real solution isn’t FMT. It’s understanding why your gut is out of balance — and addressing the underlying issues that are creating the problem.

That’s exactly what we do at the IBS Treatment Center.

We identify and treat the root causes of your imbalance — whether they’re dietary, immune-related, microbial, or otherwise. And when you heal the gut in a way that’s personalized to you, the microbiome naturally shifts toward a healthy balance on its own.

Closing Thoughts

Fecal transplants are an amazing example of how powerful the gut microbiome can be — but they’re not a one-size-fits-all solution.

They can be lifesaving in the right situation, like recurrent C. diff. They show some promise in Ulcerative Colitis, but for IBS, Crohn’s, and most other digestive issues, the benefits are unproven — and in some cases, they can even make things worse.

So before you consider something as invasive as a fecal transplant, make sure you understand why your gut is unhealthy — and choose an approach that helps your body heal safely, naturally, and permanently.

If you found this helpful, don’t forget to share this post with anyone you know who’s been curious about fecal transplants or struggling with digestive issues.

Remember to take good care of your body. It’s the only place that you have to live.

Related Content:

Gut-Sinus Connection: The Surprising Link Between Gut Health and Chronic Sinus Problems

All About Microscopic Colitis

Garlic and the Microbiome: Good Food Reactions vs Bad Food Reactions

Irritable Bowel Syndrome and Chronic Gastritis