The Gut Microbiome and IBD: Chicken or the Egg?

Which Comes First: Changes in the Microbiome or IBD? 

Is an imbalance in the gut microbiome a cause of inflammatory bowel disease (IBD), or does inflammation change the microbiome?  

It’s a question that researchers are working to answer. 

IBD, which includes Crohn’s disease and ulcerative colitis, is a complex condition shaped by multiple factors including genetics, the immune system, environmental elements, and the trillions of microorganisms living in the digestive tract. Understanding how these factors interact could help researchers uncover why IBD develops and how to treat it more effectively. 

What Is the Gut Microbiome? 

The gut microbiome is the community of bacteria, fungi, viruses, and other microorganisms that live inside the digestive tract. These organisms do much more than simply live alongside us. They help break down food, produce important nutrients, protect against harmful organisms, and support the immune system. 

A healthy gut microbiome isn’t defined by a single ideal combination of microorganisms. Each person’s microbiome is unique, shaped by factors such as genetics, diet, environment, medications, and age. It also changes throughout life. 

Researchers are studying how these communities function and how changes in their composition may affect health, including the development and progression of Crohn’s disease and ulcerative colitis. 

What Does the Microbiome Have to Do With IBD? 

People with Crohn’s disease and ulcerative colitis often have different gut microbial patterns than people without IBD. Researchers call some of these changes dysbiosis, a term used to describe an imbalance in the microbial community.  

Dysbiosis may involve: 

• Lower microbial diversity: Fewer types of microorganisms are present in the gut.
• Changes in beneficial bacteria: Microorganisms that support digestion and gut health may become less abundant.
• How gut microbes may affect inflammation: Changes in gut microbes may affect immune function. 

These patterns are important clues, but they don’t tell the whole story. Researchers are still investigating whether microbial changes contribute to the development of IBD, occur because of intestinal inflammation, or reflect both processes. However, it is known that IBD is not caused by one “bad” bacterium. 

So… Chicken or Egg? Why the Answer May Be Both 

The current scientific understanding suggests that the relationship between the gut microbiome and IBD may work in both directions. 

For example, a person’s genetics may make them more susceptible to IBD. Environmental exposures and diet can influence the gut microbiome, potentially changing how microorganisms interact with the immune system. In some people, these changes may contribute to an immune response. Once intestinal inflammation develops, it can further alter the gut environment and the microorganisms living there. 

This creates a feedback loop: microbiome changes may influence inflammation, and inflammation may reshape the microbiome. 

The Crohn’s & Colitis Foundation is helping advance research into these interconnected factors. Understanding how they influence one another could eventually help researchers identify people at risk earlier, predict disease progression, personalize treatment, and prevent complications. 

Can We Change the Microbiome to Treat IBD? 

Researchers are exploring several approaches to understand whether altering the gut microbiome can improve outcomes for people with IBD. 

• Diet and nutrition: Researchers are studying how different dietary approaches affect the gut microbiome and inflammation. The Foundation’s diet and nutrition research includes studies exploring how diet may influence gut bacteria and their activity.
• Probiotics and live biotherapeutics: These approaches use beneficial microorganisms or carefully selected microbial communities to influence gut health. Learn more about probiotics and microorganisms and the evidence for their use in IBD.
• Microbiome-targeted therapies: Researchers are investigating ways to alter microbial communities, or their activities, to support a healthier gut environment. Through the Foundation’s Microbiome Initiative, researchers are working to better understand how gut microbes contribute to IBD and how that knowledge could inform future treatments.
• Fecal microbiota transplantation (FMT): This approach transfers microorganisms from a donor’s stool into another person’s digestive tract. Researchers continue to investigate its potential role in IBD. Learn more about FMT. 

These approaches show promise, but more research is needed to determine who may benefit, which methods work best, and how to use them safely.  

People living with IBD should talk with their healthcare team before starting supplements or making major dietary changes. A treatment that affects the microbiome does not necessarily control the inflammation associated with IBD. 

Looking Ahead: The Future of Microbiome Research in Crohn’s Disease and Ulcerative Colitis 

After years of studying ways to manipulate the microbiome, researchers have learned that making lasting changes is challenging. Diet, lifestyle, medications, inflammation, and many other factors can influence the microbiome’s composition and function. 

Rather than searching for one perfect microbiome, researchers are exploring how to support a diverse microbial community while effectively managing inflammation.  

The answer to the chicken-or-egg question may not be simple. But every discovery brings us closer to understanding IBD and developing more precise, effective care for the people living with it.  

Learn More About the Gut Microbiome and IBD 

Explore these Foundation resources to learn more: 

• Microbiome: Explore the Foundation’s microbiome resources
• The Microbiome and IBD: Watch the Foundation’s educational webinar
• Probiotics and Microorganisms: Learn more about probiotics and their potential role in gut health