If you've been living with Crohn's disease or ulcerative colitis, you've probably heard about microbiome research. But knowing it exists and actually finding a trial you can join are two very different things. This guide walks you through exactly how to do it.
Why IBD Patients Are a Key Focus of Microbiome Research
Inflammatory bowel disease is one of the most studied conditions in microbiome science — and for good reason. Research consistently shows that IBD patients have a significantly disrupted gut microbiome compared to healthy individuals. Specific bacterial species that protect the gut lining are reduced, while pro-inflammatory microbes increase.
This imbalance — called dysbiosis — isn't just a side effect of IBD. Many researchers now believe it actively drives inflammation and flares. That's why restoring microbial balance has become one of the most promising areas of IBD treatment research.
Types of Microbiome Trials for IBD
Not all microbiome trials work the same way. Here are the main categories you'll encounter:
Fecal Microbiota Transplantation (FMT)
FMT involves introducing stool from a healthy donor into a patient's gut to reset the microbiome. It's already FDA-approved for recurrent C. difficile infections, and researchers are now testing it for Crohn's and UC with promising early results.
Probiotic and Prebiotic Interventions
These trials test whether specific strains of live bacteria (probiotics) or the fibers that feed them (prebiotics) can reduce IBD symptoms, inflammation markers, or flare frequency.
Dietary Interventions
Some trials study specific diets — such as the Specific Carbohydrate Diet or a Mediterranean diet — and measure how they reshape the gut microbiome in IBD patients.
Microbiome-Targeted Drug Therapies
A newer category: drugs specifically designed to shift microbial populations rather than suppress the immune system. Several are currently in Phase 2 trials.
How to Search for IBD Microbiome Trials
The most comprehensive database of clinical trials in the US is ClinicalTrials.gov. MicrobiomeTrials automatically searches and filters this database so you only see trials relevant to the gut microbiome.
To find recruiting IBD trials on MicrobiomeTrials:
- Go to Browse Trials for IBD
- Set the status filter to "Recruiting"
- Browse trial cards — each includes a plain-English summary of what the trial is testing and who it's looking for
How to Read a Trial Listing
When you find a trial that looks interesting, here's what to look at first:
- Status — Only "Recruiting" trials are actively accepting new participants
- Eligibility Criteria — This lists who qualifies (inclusion criteria) and who is excluded. Pay attention to age ranges, disease activity scores (like the Harvey-Bradshaw Index for Crohn's), and medication restrictions
- Phase — Phase 1 trials focus on safety; Phase 2 and 3 focus on effectiveness
- Location — Check whether the trial has a site near you, or whether remote/telehealth participation is allowed
Questions to Ask Your Gastroenterologist
Before contacting a trial coordinator, it's worth discussing the trial with your GI doctor. Good questions to ask:
- "Do my current medications disqualify me from this trial?"
- "Would my disease activity level make me eligible?"
- "Would participating affect my current treatment plan?"
- "Could you refer me to the trial coordinator?"
Your doctor may also know of local trials not yet listed publicly.
What Happens After You Express Interest
When you contact a trial site, you'll typically go through a screening process. This usually involves:
- A phone interview to check basic eligibility
- A medical records review
- Sometimes a screening visit with labs and endoscopy
Even if you don't qualify for one trial, the coordinator may know of others that fit your situation better.
The Bottom Line
Finding a microbiome clinical trial as an IBD patient has never been easier — the science is advancing rapidly and there are more trials than ever. The most important step is just starting the search. Use MicrobiomeTrials to find trials explained in language you can actually understand, and then talk to your doctor about whether any are a fit for you.