How does the gut bacteria diversity in ulcerative colitis compare to healthy controls?

Ulcerative colitis (UC) is a chronic inflammatory bowel disease that affects the colon. Research shows that the community of bacteria living in the gut — the gut microbiome — is different in people with UC compared to healthy people. In general, UC patients have less bacterial diversity and an imbalance in the types of bacteria present. This is called dysbiosis. The exact role of these changes in causing or worsening UC is still being studied, but the differences are consistent across many studies.

What the research says

Multiple studies using 16S rRNA gene sequencing of fecal samples have found that UC patients have significantly lower alpha diversity — a measure of how many different bacterial species are present — compared to healthy controls. A 2025 pilot study in Lebanon reported reduced Shannon diversity and Faith's Phylogenetic Diversity in UC patients ⁹. A 2025 study of 71 UC patients and 72 controls confirmed lower Shannon index in the UC group ¹⁰. A systematic review of 83 observational studies also found reduced alpha and beta diversity in IBD, more pronounced in Crohn's disease than UC ¹¹.

Beyond diversity, the types of bacteria differ. The systematic review noted depletion of butyrate-producing Firmicutes bacteria, including Faecalibacterium, Eubacteria, Roseburia, and Ruminococcaceae, in IBD patients ¹¹. The Lebanese study found that genera such as Ruminococcus, Bacteroides, and Coprococcus were depleted in UC ⁹. The 2025 study reported decreased Treponema, UCG-002, and Fusicatenibacter, and increased Sellimonas, Fournierella, and Oscillospira in UC patients ¹⁰. At the phylum level, UC patients showed elevated Bacteroidota and reduced Bacillota and Actinomycetota ⁹. The systematic review also found increased Proteobacteria and Enterobacteriaceae in IBD ¹¹.

These microbial changes are linked to inflammation. The NF-κB pathway, a key driver of inflammation, is activated by bacterial toxins and dysbiosis, contributing to a 'leaky gut' and systemic inflammation ³. Additionally, UC patients have lower fecal levels of nicotinamide (a form of vitamin B3), which is associated with increased bacterial nicotinamidase gene expression and may worsen inflammation ¹⁰.

What to ask your doctor

• Could a stool test to analyze my gut microbiome help guide my treatment?
• Are there specific probiotics or dietary changes that might help restore beneficial bacteria in UC?
• How do my current medications (e.g., anti-inflammatory drugs, biologics) affect my gut microbiome?
• Should I consider a fecal microbiota transplant (FMT) as a potential therapy for my UC?
• What is the role of butyrate-producing foods (like fiber) in managing my condition?