Managing SIBO and SIFO
If you’ve been struggling with chronic bloating, digestive discomfort, fatigue, and brain fog despite numerous diet changes and treatments, you may be dealing with Small Intestinal Bacterial Overgrowth (SIBO) or Small Intestinal Fungal Overgrowth (SIFO).
Understanding the root causes, symptoms, and key treatment strategies, including diet, lifestyle changes, and medical interventions, can help you take control of your gut health and achieve long-term relief.
What Are SIBO and SIFO?
SIBO and SIFO occur when bacterial or fungal overgrowth disrupts the delicate balance of the small intestine, leading to chronic digestive issues.
SIBO (Small Intestinal Bacterial Overgrowth): Occurs when bacteria that normally reside in the colon migrate to the small intestine, leading to excessive fermentation of carbohydrates and gas production (Pimentel, 2021).
SIFO (Small Intestinal Fungal Overgrowth): Involves an overgrowth of fungi, particularly Candida, in the small intestine, causing bloating, digestive discomfort, and sugar cravings (Jacobs & Rao, 2015).
Symptoms of SIBO and SIFO
Common Symptoms of SIBO (Small Intestinal Bacterial Overgrowth)
Bloating and excessive gas due to bacterial fermentation of food.
Abdominal pain and cramping caused by inflammation and gut irritation.
Diarrhoea, constipation, or alternating bowel movements, depending on gas types produced by bacteria.
Nutrient deficiencies, including low levels of vitamin B12, iron, and fat-soluble vitamins.
Unexplained weight loss or gain due to malabsorption and metabolic changes.
Food intolerances, especially to high-FODMAP foods.
Acid reflux and belching, often misdiagnosed as GERD.
Chronic fatigue and brain fog, linked to systemic inflammation and gut-brain axis disruption.
Common Symptoms of SIFO (Small Intestinal Fungal Overgrowth):
Persistent bloating that does not improve with bacterial treatments.
Sugar cravings, as fungi like Candida thrive on glucose and refined carbohydrates.
White coating on the tongue (oral thrush), indicating systemic fungal overgrowth.
Skin issues, including eczema, psoriasis, and fungal infections like athlete’s foot.
Fatigue and brain fog, due to fungal toxins affecting cognitive function.
Chronic sinus congestion, often associated with fungal overgrowth in the gut.
Recurrent yeast infections, including vaginal or urinary tract infections.
Joint pain and muscle aches, potentially linked to systemic fungal toxins.
Since SIBO and SIFO often occur together, symptoms can overlap, making proper testing crucial for accurate diagnosis and treatment.
Causes of SIBO and SIFO
Identifying the underlying causes of SIBO and SIFO is crucial for effective treatment and preventing recurrence.
Primary Causes of SIBO
Impaired Gut Motility – Slow digestion allows bacteria to accumulate in the small intestine. Linked to IBS, diabetes, hypothyroidism, and chronic stress.
Low Stomach Acid (Hypochlorhydria) – Stomach acid is crucial for killing bacteria before they reach the small intestine. Chronic stress, aging, H. pylori infections, and frequent use of antacids reduce stomach acid levels.
Structural Abnormalities & Surgeries – Surgeries like C-sections, gallbladder removal, and appendectomies can lead to adhesions and bacterial stagnation. Diverticula (small pouches in the intestine) can trap bacteria, causing chronic overgrowth.
Chronic Stress and Hormonal Imbalances – High cortisol levels impair digestion and immune function, increasing bacterial overgrowth.
Dysfunction of the Migrating Motor Complex (MMC) – The MMC is responsible for sweeping bacteria out of the small intestine between meals. Poor sleep, infections, and chronic gut inflammation disrupt this function.
Frequent Antibiotic Use – Repeated antibiotic courses kill beneficial bacteria, allowing harmful strains to thrive in the small intestine.
Primary Causes of SIFO
Chronic Antibiotic & Steroid Use – These medications suppress beneficial bacteria, allowing fungi to multiply unchecked.
High Sugar & Refined Carbohydrate Diet – Fungi thrive on sugar, making high-carbohydrate diets a major risk factor.
Weakened Immune System – Autoimmune diseases, chronic stress, and nutrient deficiencies impair the body’s ability to keep fungi in check.
Poor Digestive Enzyme Production – Insufficient enzymes lead to undigested food, which feeds fungal overgrowth.
Mold & Mycotoxin Exposure – Mold exposure in the home or workplace can contribute to systemic fungal infections.
Long-Term Proton Pump Inhibitor (PPI) Use – Acid-blocking medications create an alkaline environment that supports fungal growth.
Diagnosing SIBO and SIFO
Accurate diagnosis is crucial for effective treatment. While symptoms provide clues, laboratory tests confirm whether you have SIBO, SIFO, or both.
Testing for SIBO
The most common and reliable test for SIBO is the SIBO Breath Test, which measures hydrogen and methane gas levels produced by bacteria in the small intestine.
Hydrogen-Dominant SIBO: Usually associated with diarrhoea-predominant SIBO (SIBO-D). Hydrogen-producing bacteria ferment carbohydrates rapidly, leading to excess gas and bloating.
Methane-Dominant SIBO: Often linked to constipation-predominant SIBO (SIBO-C). Methanogenic archaea produce methane gas, slowing gut motility and causing bloating, cramping, and hard stools.
Hydrogen Sulfide SIBO: A less common but increasingly recognised form of SIBO. Patients often experience alternating diarrhea and constipation, extreme bloating, and a distinctive sulfur or rotten egg-smelling gas.
Comprehensive Stool Analysis (GI-MAP or GI Effects): Identifies bacterial strains and measures overall gut dysbiosis.
To perform the SIBO Breath Test, patients drink a sugar solution (glucose or lactulose), and exhaled breath samples are collected at intervals to measure gas production.
Testing for SIFO
SIFO is harder to diagnose because fungi do not produce measurable gases like bacteria. The best diagnostic options include:
Organic Acids Test (OAT): Measures fungal metabolites (e.g., arabinose) in urine, indicating fungal overgrowth.
Comprehensive Stool Analysis (GI-MAP or GI Effects): Identifies fungal strains like Candida albicans and measures overall gut dysbiosis.
Endoscopic or Duodenal Aspirate Test: A more invasive but definitive way to confirm SIFO by taking a small intestine sample.
Managing Diet for SIBO and SIFO
A well-structured diet is critical for treating and preventing SIBO and SIFO.
Best Diets for SIBO and SIFO
Low-FODMAP Diet – Reduces fermentable carbohydrates that feed bacteria.
Anti-Candida Diet – Eliminates sugar, alcohol, and refined carbs to starve fungi.
Elemental Diet – A short-term liquid diet that starves bacteria and fungi while providing essential nutrients.
Additional Dietary Considerations
Incorporate Gut-Healing Foods – Bone broth, non-starchy vegetables, and fibre (if tolerated).
Consume Healthy Fats and Proteins – Supports energy and gut repair without fueling microbial overgrowth.
Avoid Processed and Sugary Foods – Prevents feeding harmful bacteria and fungi.
Comprehensive SIBO & SIFO Treatment Protocol
Diet Adjustments (Low-FODMAP, Anti-Candida, Elemental Diet)
Gut & Immune Support (Digestive enzymes, probiotics, L-glutamine, Zinc Carnosine, stress reduction)
Antimicrobial & Antifungal Therapy (Biocidin, Berberine, Caprylic Acid, Oregano oil)
Detoxification Support (Activated charcoal, zeolite, G.I. Detox+, liver support)
Microbiome Restoration (Spore-based probiotics, prebiotics post-treatment)
Managing SIBO and SIFO requires a comprehensive, multi-faceted approach that addresses the root causes of bacterial and fungal overgrowth. Accurate diagnosis through breath tests, stool analysis, and organic acids testing is essential for distinguishing between these conditions and implementing the right treatment plan.
Dietary modifications, such as a Low-FODMAP or Anti-Candida diet, play a crucial role in controlling symptoms, while targeted antimicrobial and antifungal therapies help eradicate overgrowth. Additionally, supporting digestion, immune function, and gut microbiome balance through digestive enzymes, probiotics, and stress management ensures long-term recovery.
By taking a structured approach to treatment and focusing on long-term gut health, individuals can effectively manage SIBO and SIFO, prevent recurrence, and restore optimal digestive function.
References
Pimentel, M. (2021) Small Intestinal Bacterial Overgrowth (SIBO): Pathophysiology and Treatment Options. Journal of Clinical Gastroenterology, 55(7), pp. 542-550.
Jacobs, C. & Rao, S. (2015) 'Small intestinal fungal overgrowth (SIFO): A common yet overlooked gastrointestinal condition', Current Gastroenterology Reports, 23(9), pp. 1-10.
Quigley, E. M. & Rao, S. S. (2020) 'Small intestinal bacterial overgrowth: Clinical features and therapeutic management', Alimentary Pharmacology & Therapeutics, 51(12), pp. 1303-1321.
Rao, S.S., Rehman, A., Yu, S. & de La Serre, C. (2021) 'Fungal dysbiosis in gastrointestinal health and disease', Frontiers in Microbiology, 12, Article 566230.
