Introduction

The human gut has a complex and diverse ecosystem known as the gut microbiota, comprising approximately 10¹⁴ microbial cells, outnumbering cells of the human body by more than tenfold.¹ This microbiota, which includes bacteria, viruses, fungi, and protozoa, is unique to each individual and may consist of up to 1,500 different species.¹ Extensive research on gut microbiota has revealed that it is a crucial regulator of overall health.²

Maintaining the right balance of gut bacteria, a state referred to as eubiosis is essential for preserving homeostasis and ensuring the proper functioning of the body.¹ In contrast, an imbalance in the gut bacteria known as dysbiosis can lead to a range of health issues, from gastrointestinal disorders to systemic inflammation and metabolic diseases.¹ One notable example is small intestinal bacterial overgrowth (SIBO), where abnormal microbial colonisation of the small intestine leads to excessive fermentation, gas production, and various digestive symptoms.¹ SIBO is defined as an increase in the bacterial content of the small intestine above normal values (100000 cells per mL).³

Another condition which arises due to gut dysbiosis is Pouchitis. Pouchitis is the inflammation of the ileal pouch created during surgery of the intestine. Ileal pouch-anal anastomosis (IPAA) is advised for those patients with severe and uncontrollable inflammatory bowel disease (IBD), including ulcerative colitis (UC) or sometimes Crohn’s disease. The ileal pouch is created from the limbs of the small intestine after the removal of the colon and rectum (large intestine) in patients with the above-mentioned diseases. The end of the small intestine is connected to the anus through an internal J-shaped pouch.⁴ This is a complicated procedure that involves surgery in two stages and ultimately leads to an ileal pouch being connected to the anus directly for waste removal.⁴

Patients with an ileal pouch, particularly those who develop pouchitis may experience a wide range of gastrointestinal symptoms. These commonly include increased bowel movement frequency, urgency, abdominal cramping, bloating, pelvic pressure (feeling of heaviness or fullness in the pelvic area), and nocturnal incontinence (involuntary passing of stool).⁵ However, these symptoms are not exclusive to pouchitis and may overlap with other conditions affecting the pouch.⁵ One such condition is SIBO. Symptoms of SIBO include bloating, flatulence, and abdominal pain which also coincides with symptoms of pouchitis.⁶

Bloating, diarrhoea, and abdominal discomfort are shared symptoms of pouchitis and SIBO, often leading to diagnostic confusion and underscoring the need for accurate differentiation to guide appropriate treatment. Thus symptoms alone are often insufficient for diagnosis, highlighting the importance of detailed evaluation to distinguish pouchitis from other potential causes of pouch dysfunction such as SIBO.

Causes of Pouchitis

Although the cause of pouchitis is not completely understood, research shows that it can respond or not respond to antibiotic treatment. Some of the causes are:

Altered microbiota

In healthy ileal pouches, the microbiota resembles that of the colon. However, patients with ulcerative colitis who undergo pouch formation show reduced microbial diversity, which declines further with pouchitis. Gene sequencing studies confirm this progressive loss of microbial richness. No specific pathogen has been consistently identified, suggesting that overall microbial imbalance, rather than a single organism, drives pouchitis.⁷

Immune dysregulation

Patients with certain risk factors are believed to have a sensitive immune system, leading to chronic inflammation. Although the exact pathogenesis is not fully understood, it is assumed that over time, the immune system becomes the dominant driver of disease, rather than the microbiota alone. In such cases, immunosuppressive therapy may be required, as antibiotics alone are no longer effective.^8,9

Antibiotic overuse or pouch ischemia

Although antibiotics are the first-line treatment for pouchitis, overuse can disrupt the normal pouch microbiota, promoting dysbiosis and contributing to disease persistence. Repeated antibiotic use also raises the risk of resistance, and reduces effectiveness.^7,10 Ischemia is a common cause of pouchitis, often occurring with inflammation. This happens due to mesenteric tension, which impairs blood flow and causes tissue ischemia or hypoxia (lack of oxygen). The low-oxygen environment may promote the overgrowth of anaerobic bacteria, such as Clostridioides difficile, which further worsens inflammation.^5,8

Symptoms of Pouchitis⁵

• Diarrhea
• Abdominal pain
• Urgency/incontinence
• Fever, malaise

Causes of SIBO

Motility disorders (e.g., IBS, diabetes)

Diabetes (type I, type II, and gestational) and motility disorders like IBD and IBS are significant risk factors for SIBO. In diabetes, factors such as hyperglycemia, delayed gastric emptying, and neuropathy, promote bacterial overgrowth by reducing gut motility. Similarly, conditions like Crohn’s disease, prior bowel surgery, and IBS also reduce motility, increasing the risk of SIBO. Disrupted gut movement allows bacteria to accumulate in the small intestine, leading to symptoms like bloating and nutrient malabsorption.^1,3

Structural abnormalities (e.g., adhesions, strictures)

Structural issues with the ileocecal valve are a known risk factor for SIBO. When the valve malfunctions, it can allow the reflux of colonic bacteria into the small intestine, particularly the ileum, promoting bacterial overgrowth. A study found that low ileocecal valve pressures were linked to a higher risk of SIBO. This indicated that compromised valve integrity contributes to microbial imbalance and supports the development of SIBO.^3,6

Reduced stomach acid, prior surgeries

Reduced stomach acid due to the use of PPIs (proton pump inhibitors) can promote the overgrowth of bacteria.¹ Also prior surgery such as bariatric surgery (to reduce obesity) or surgery to treat ulcerative colitis, has been a cause for SIBO.^1,3

Symptoms of SIBO

Symptoms of SIBO include:⁶

• BloatingGas
• Diarrhea or constipation
• Nutritional deficiencies (B12, iron)

Diagnosis

Pouchitis

Endoscopy with biopsy

Endoscopy with biopsy is a central component in assessing pouch inflammation and diagnosing pouchitis. During endoscopy, the mucosal surface of the pouch is evaluated for ulceration, along with erosions and bleeding. Biopsies taken during the procedure allow for the study of cells of the intestinal lining, which plays a critical role in confirming pouchitis.⁸

Pouchitis Disease Activity Index (PDAI)

The Pouchitis Disease Activity Index (PDAI) is the most commonly used tool to assess inflammation in the ileal pouch. It considers symptom severity, endoscopic findings, and histological changes. A PDAI score of ≥7 points is typically considered diagnostic for pouchitis. However, this score is not exclusive to pouchitis, as elevated PDAI values can also be seen in other conditions such as irritable pouch syndrome, cuffitis, or Crohn’s disease of the pouch, which may mimic or overlap with pouchitis.¹¹
SIBO:

Hydrogen/methane breath test

Breath testing is a commonly used, non-invasive method for diagnosing SIBO. The test involves ingesting a carbohydrate substrate(typically 10 g of lactulose or 75 g of glucose) which is fermented by bacterial overgrowth in the small intestine to produce hydrogen (H₂) and/or methane (CH₄) gases. These gases are carried to the lungs via the bloodstream and exhaled. A positive result is indicated by a rise in hydrogen above 20 ppm within 90 minutes or a methane level of ≥10 ppm at any point within 2 hours.¹

Small bowel aspirate (rarely used)

Another method for diagnosing SIBO is jejunal aspirate culture, where an endoscope is used to obtain a fluid sample from the duodenum. The sample is cultured for aerobic and anaerobic bacteria, with a bacterial load >10³ CFU/mL considered diagnostic. Although accurate, this method is invasive, costly, and requires specialised personnel. Furthermore, the lack of a universally accepted bacterial threshold and limitations in detecting the full diversity of the gut microbiome reduce its practicality in routine clinical use.¹

When to screen for both conditions together

Since the symptoms of both pouchitis and SIBO overlap, it is important to keep this in mind while diagnosing the patients who have undergone IPAA. Sometimes, SIBO may be the cause of pouchitis.

Treatment strategies

This delicate balance can be influenced and restored through interventions such as prebiotics, probiotics, and dietary modifications, which have gained significant attention as tools to optimise gut health and prevent or treat disease.^1,6–8 Here is a comparison chart for both conditions:

Prevention and long-term management

Maintaining a balanced gut microbiome is crucial to prevent recurrence and manage the long-term health of patients with both SIBO and pouchitis. Dietary strategies, including individualised meal planning and implementation of a low FODMAP diet when required, can help reduce symptoms and prevent flare-ups.¹ Probiotics and prebiotics play a supportive role in restoring microbial balance, though their use should be tailored based on individual response and condition severity.² Lifestyle adjustments such as stress reduction, regular physical activity, and adequate sleep are advised. Long-term management often requires multidisciplinary care; involving a gastroenterologist to treat symptoms and a dietitian to provide personalised nutritional guidance to support gut healing.

Summary

In conclusion, SIBO and pouchitis are different yet interconnected conditions occurring due to microbial imbalance. Overlapping symptoms often complicate diagnosis, emphasising on thorough evaluation of patients. Personalised treatment approaches—ranging from antibiotics, diets and probiotics —can help restore gut health. Prevention and long-term care depend on maintaining eubiosis through lifestyle and medical support.