Inflammatory Bowel Disease (IBD) affects thousands worldwide, causing chronic inflammation and discomfort in the digestive tract. While its two main forms—Ulcerative Colitis (UC) and Crohn’s Disease (CD)—present different challenges, both can severely impact quality of life. Now, with new insights into the gut microbiome, researchers are exploring how restoring microbial balance might transform the way IBD is treated.
With growing understanding of the gut microbiome, gastroenterologist Dr Ho Gim Him discusses new ways to treat IBD by restoring microbial balance.
IBD isn’t caused by infection but rather by an immune system malfunction that leads to inflammation in the digestive tract.
While Ulcerative Colitis is limited to the colon and rectum, Crohn’s Disease can affect any part of the gastrointestinal tract. Both conditions are marked by unpredictable flare-ups and remission phases, which can cause long-term intestinal damage. As scientists looked deeper into what triggers inflammation in the gut, attention turned to a powerful internal ecosystem—the microbiome.
The gut microbiome is a complex ecosystem of trillions of bacteria which plays a critical role in digestion, immunity, and inflammation regulation. In patients with IBD, this ecosystem becomes disrupted, often showing an overgrowth of harmful bacteria, and a decrease in beneficial microbial diversity. This imbalance, known as dysbiosis, contributes directly to the chronic inflammation seen in IBD. Thus, dietary modifications aimed at restoring a healthy microbial balance are gaining traction in the treatment of IBD.
A range of therapies are administered with the aim of reshaping the microbiome, each with its benefits and limitations:
• Antibiotics reduce harmful bacteria and are particularly effective in managing pouchitis and some Crohn’s flare-ups. However, prolonged use may harm beneficial bacteria and lead to resistance.
• Probiotics add beneficial bacteria (such as Lactobacillus or Bifidobacterium) to reduce inflammation and reinforce the gut lining. They are most effective in mild UC (e.g., VSL#3 and E. coli Nissle 1917), and preventing pouchitis recurrence but not useful for Crohn’s or active pouchitis.
• Prebiotics are dietary fibres (like psyllium and lactulose) that feed healthy bacteria and support microbial diversity.
• Synbiotics combine probiotics and prebiotics, delivering both beneficial microbes and the fuel they need to thrive.
• Fecal Microbiota Transplant (FMT) transfers stool from a healthy donor to reset the microbiome. While promising, it remains experimental and is only recommended in clinical trials.
Pouchitis is a condition where the surgically created pouch inside the body becomes inflamed. It most commonly affects people with Ulcerative Colitis (UC) who have undergone a surgery called IPAA (Ileoanal Pouch-Anal Anastomosis)—also known as a J-pouch surgery.
Medical treatment of pouchitis:
• First-line treatment: Antibiotics (ciprofloxacin, metronidazole) for two weeks
• Recurrent pouchitis: May require longer (approximately four weeks) antibiotic courses or biologic therapy (e.g., vedolizumab) at lowest effective dose
• Prevention of recurrence: Strong evidence supports the use of VSL#3 (a mixture of Lactobacilli, Bifidobacteria, Streptococci) to maintain remission
While probiotics are not advised for treating acute pouchitis, they may be used preventively in chronic cases after initial remission.
Leading medical organisations, including the American Gastroenterological Association (AGA), have issued guidance on the role of microbiome-based therapies, particularly probiotics and faecal microbiota transplant (FMT), in the treatment of Inflammatory Bowel Disease (IBD). However, the current evidence remains limited and often disease-specific.
For Crohn’s Disease, both probiotics and FMT are not recommended for routine use. This is primarily due to a lack of strong clinical evidence demonstrating any consistent benefit. The AGA advises that these interventions should only be considered within the context of clinical trials, where their safety and effectiveness can be more rigorously assessed.
In the case of Ulcerative Colitis, the role of probiotics is slightly more promising, especially in patients with mild disease. Certain strains, such as VSL#3 and Escherichia coli Nissle 1917, have shown potential in helping to induce and maintain remission. FMT, while still not a standard treatment, has demonstrated some positive results in select studies and may be considered for refractory cases (i.e., patients who do not respond to conventional therapy) within research settings.
Pouchitis, a complication that may follow surgical treatment for Ulcerative Colitis, is where probiotics have shown the most clinical benefit. Specifically, the use of high-potency probiotics like VSL#3 has been supported for preventing recurrence in patients who have previously responded to antibiotics.
Despite this, probiotics are not currently recommended for treating acute pouchitis. Likewise, FMT is not advised outside of clinical trials for pouchitis due to insufficient evidence.
The role of the gut microbiome in IBD is a rapidly evolving field. While microbiome-based therapies such as probiotics and FMT offer exciting potential, their application remains limited and highly individualised. In summary:
• Crohn’s Disease responds inconsistently to microbiome interventions
• Ulcerative Colitis may benefit from targeted probiotics
• Pouchitis has the most promising results with preventive probiotic therapy
As research pushes boundaries, the microbiome holds promise not just as a treatment target—but as a key to long-term remission. While we await stronger clinical evidence, patients and physicians alike are already witnessing the first signs of change in how we understand and manage IBD.
