Understanding and Managing Small Intestinal Bacterial Overgrowth (SIBO)

Small Intestinal Bacterial Overgrowth (SIBO) is a condition characterized by the abnormal growth of bacteria in the small intestine. This can lead to a range of uncomfortable symptoms and complications. In this blog post, I will explore the causes, symptoms, diagnostic tests, treatment options (including natural and antibiotic approaches), and preventive measures for SIBO.  


What is SIBO?

SIBO occurs when there is an excessive amount of bacteria in the small intestine. Normally, the small intestine has a relatively low bacterial population, but when the balance is disrupted, it can result in various symptoms and health issues due to the increased production by bacterial fermentation in the gut. The overgrowth of bacteria causes inflammation to the intestinal lining and interferes with the proper absorption of nutrients, leading to digestive symptoms and other systemic effects.  


Symptoms of SIBO

The symptoms of SIBO can vary from person to person, but they commonly include:

  • Abdominal bloating and distention
  • Diarrhoea or constipation (or both, alternating)
  • Abdominal pain or discomfort
  • Excessive gas and belching
  • Reflux/heartburn
  • Fatigue and weakness
  • Joint pain
  • Brain fog
  • Nutritional deficiencies (due to malabsorption)
  • Weight loss (in severe cases)



What causes SIBO?

Here are 12 main causes and contributing factors of Small Intestinal Bacterial Overgrowth (SIBO):  


1. Impaired Motility:

The small intestine relies on proper muscular contractions (peristalsis) to propel food and bacteria through the digestive tract. Any condition or factor that disrupts this motility can lead to bacterial overgrowth. Examples include intestinal adhesions, scar tissue, or conditions like gastroparesis or intestinal dysmotility.  


2. Structural Abnormalities:

Structural abnormalities in the gastrointestinal tract, such as strictures, diverticula, or intestinal obstructions, can create stagnant areas where bacteria can accumulate and multiply. Additionally, surgeries or procedures that alter the structure or function of the digestive system can also contribute to SIBO.  


3. Hypochlorhydria:

Low stomach acid levels (hypochlorhydria) can impair the initial stages of digestion and allow bacteria to survive and thrive in the small intestine.  


4. Medications:

Certain medications, such as proton pump inhibitors (PPIs), which reduce stomach acid production, or long-term use of antibiotics, can disrupt the natural balance of gut bacteria and promote SIBO.  


5. Food Poisoning or Gastrointestinal Infections:

Food poisoning can disrupt the digestive system’s bacterial balance, leading to bacterial overgrowth in the small intestine and potentially causing SIBO. Contaminated food introduces pathogenic microorganisms into the small intestine, disrupting the normal bacterial flora and impairing digestion and nutrient absorption. This imbalance allows bacteria to proliferate, while damage to the small intestine’s lining further promotes the growth of bacteria in inappropriate quantities.  


6. Gallbladder dysfunction:

When the gallbladder is not functioning properly, such as in cases of gallstones, inflammation, or impaired bile flow, it can lead to inadequate bile secretion. This can disrupt the normal digestion and absorption of fats, impairing the balance of bacteria in the small intestine. Bile acids possess antimicrobial properties and help control the growth of bacteria in the small intestine. Therefore, when gallbladder dysfunction disrupts bile flow, it can contribute to the development of SIBO by allowing bacteria to proliferate in the small intestine.  


7. Inflammatory bowel conditions:

Conditions such as Crohn’s disease, ulcerative colitis, and irritable bowel syndrome with diarrhea (IBS-D) are characterized by chronic inflammation and structural changes in the intestinal lining. These alterations can disrupt the normal movement and function of the small intestine, creating an environment favorable for the overgrowth of bacteria. The chronic inflammation and impaired intestinal motility associated with these conditions contribute to a higher risk of SIBO development.  


8. Pancreatic insufficiency:

When pancreatic function is compromised, as is the case with pancreatic insufficiency, there is a deficiency of digestive enzymes such as lipase, amylase and protease. The lack of enzymes can result in impaired digestion and malabsorption. The undigested nutrients provide an abundant food source for bacteria in the small intestine, encouraging their overgrowth. Furthermore, pancreatic insufficiency can alter the pH balance in the small intestine, creating an environment favorable for bacterial overgrowth.  


9. Chronic constipation:

Constipation can lead to the accumulation of fecal matter and a slowing down of intestinal transit time. As a consequence, the bacteria normally present in the colon can migrate upward into the small intestine, where their numbers can multiply and cause SIBO. Constipation can also disrupt the natural movement and motility of the gastrointestinal tract, impairing the clearance of bacteria from the small intestine. This allows for the overgrowth of bacteria and the disruption of the normal balance.  


10. Mold toxicity:

Mold exposure can lead to immune system dysregulation and inflammation in the body, which may affect the gastrointestinal tract. Chronic inflammation and immune dysfunction can disrupt the normal gut barrier function, compromising the integrity of the intestinal lining. This compromised barrier can allow for the translocation of bacteria from the colon to the small intestine, leading to the development of SIBO. Additionally, mold toxicity can cause gastrointestinal symptoms such as diarrhea, bloating, and abdominal pain, which may contribute to gut dysmotility and alterations in the gut microbiota, potentially promoting SIBO.  


11. Stress & Trauma:

Chronic stress can affect the normal functioning of the digestive system. It can disrupt the balance of beneficial bacteria in the gut, known as the gut microbiota, and impair the movement of the gastrointestinal tract. This altered gut microbiota and impaired motility can create an environment that favours the overgrowth of bacteria in the small intestine, contributing to SIBO development.  


12. Viral/Fungal/Parasite Infection:

Viral, fungal, or parasitic infections can potentially increase the risk of small intestinal bacterial overgrowth (SIBO) through several mechanisms. When the body is affected by an infection, it can lead to various disruptions in the gastrointestinal tract, including changes in gut motility, immune responses, and the gut microbiota.  


How is SIBO diagnosed?

To diagnose SIBO, healthcare professionals may recommend the following tests:  


Hydrogen Breath Test:

This test measures the levels of hydrogen and methane gas in the breath after ingesting a specific carbohydrate solution, typically lactulose. Methane-dominant SIBO is typically associated with constipation and an overgrowth of methanobrevibacter smithii. Hydrogen-dominant SIBO is associated with diarrhoea and an overgrowth of hydrogen-producing bacteria such as escherichia coli, streptococcus, staphylococcus and klebsiella pneumoniae.  

Small Intestine Aspiration:

A sample of fluid is aspirated from the small intestine and analyzed for bacterial overgrowth.  

Stool Testing:

In addition to a SIBO test, a comprehensive stool analysis can help identify imbalances in gut flora and assess the overall health of the digestive system for a more personalized gut protocol.  



SIBO Treatment Options:


Natural Approaches:

Dietary Modifications: Following a low fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (FODMAP) diet can help reduce symptoms whilst treating SIBO by limiting the intake of foods that fuel bacterial growth. A low carbohydrate diet can help in cases where carbohydrate malabsorption has developed due to intestinal inflammation. A long-term anti-inflammatory diet is helpful in preventing relapse.


Probiotics: Certain strains of probiotics can aid in rebalancing the gut microbiota and suppressing the overgrowth of harmful bacteria. Saccharomyces boulardii, a probiotic yeast has been studied for its antimicrobial properties and ability to help restore healthy gut flora. Lactobacillus rhamnosus, a probiotic bacteria, has been studied for its potential to inhibit the growth of pathogenic bacteria and promote a healthy gut environment. Lactobacillus reuteri a probiotic bacteria known for its ability to produce antimicrobial substances, promote gut barrier function, and increase gut motility.


Herbal Supplements: Oregano, berberine, allicin and neem are common herbal remedies that have been studied for their potential effectiveness in treating small intestinal bacterial overgrowth (SIBO). Oregano oil contains compounds such as carvacrol and thymol, which possess antimicrobial properties that may help reduce the overgrowth of bacteria in the small intestine. Berberine, derived from various plants, including barberry and goldenseal, has shown antimicrobial activity against a wide range of pathogens, including bacteria associated with SIBO. Neem, a tree native to India, has been traditionally used for its antibacterial and antifungal properties. Allicin, a compound found in garlic, is known for its strong antibacterial, antifungal, and antiparasitic effects, which may help in reducing the overgrowth of bacteria in the small intestine. Allicin exhibits broad-spectrum antimicrobial properties, including against methanogenic bacteria. Other helpful natural antimicrobial agents used for SIBO include grapeseed extract, caprylic acid, artemisia, thyme, olive leaf and clove.  


Antibiotic Treatment:

Rifaximin: This is a non-absorbable antibiotic specifically targeting the small intestine. It spares healthy gut bacteria. It is commonly prescribed for SIBO and has shown effectiveness in reducing symptoms and treating hydrogen-dominant SIBO. It is used in conjunction with metronidazole or neomycin to treat methane-dominant SIBO.  


Preventing SIBO Relapse:

To minimize the risk of SIBO recurrence, consider the following strategies:  

Address Underlying Causes: Treat any underlying conditions that contribute to SIBO, such as hypochlorhydria (low stomach acid) or structural abnormalities in the digestive tract.

Prokinetics: Medications that enhance gastrointestinal motility can help prevent bacterial stagnation and overgrowth in the small intestine.

Maintain a Healthy Diet: Consume a well-balanced diet rich in fiber, lean proteins, and fresh vegetables and low in refined sugars and processed foods to support gut health and prevent dysbiosis.

Stress Management: Chronic stress can disrupt gut function. Engage in stress-reducing activities like exercise, meditation, or therapy to support overall well-being.  



Small Intestinal Bacterial Overgrowth (SIBO) is a complex condition that can significantly impact an individual’s quality of life. Recognizing the symptoms, undergoing appropriate diagnostic tests, and implementing an effective treatment plan are crucial steps towards managing SIBO. Whether implementing a natural approach or medical approach, it’s important to work with a trained practitioner who specializes in SIBO