Natural Remedies for Bacterial Overgrowth

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Bacterial overgrowth in the small intestine is thought to be a condition that may be present for years without causing obvious symptoms. A condition that is not recognized in conventional medicine, small intestine bacterial overgrowth is associated with chronic digestive problems such as gas, bloating, diarrhea, and/or constipation. People may be told they have irritable bowel syndrome (IBS).

For instance, a study by researchers at Cedars-Sinai Medical Center in California examined 202 people who met the diagnostic criteria for irritable bowel syndrome and gave them a test for bacterial overgrowth called the lactulose hydrogen test.

Researchers found that 157 of the 202 people (78 percent) had bacterial overgrowth. When the unwanted intestinal bacteria were eradicated, symptoms of IBS improved in 48 percent of the subjects, particularly diarrhea and abdominal pain.

It's not just people with IBS-like symptoms that have bacterial overgrowth. Non-digestive symptoms such as a lack of energy may be the primary concern. Some alternative medicine practitioners believe that it can be involved in chronic fatigue syndrome, fibromyalgia, allergies, arthritis, lupus, autoimmune diseases, diabetes, and other chronic conditions.


Bacteria in the small intestine may result in impaired absorption of nutrients. Bacteria may lead to fat malabsorption through a process called bile acid deconjugation. Carbohydrate absorption may be affected and result in carbohydrate fermentation in the intestines and gas, bloating, pain, mucus in stools, foul-smelling stools and gas, and diarrhea. According to alternative medicine practitioners, sweets and starchy foods cause the worst symptoms.

Toxic metabolic substances produced by the bacteria may injure intestinal cells and impair absorption, resulting in nutrient deficiencies, food allergies and intolerances, and impaired digestive enzyme activity.


The small intestine normally contains relatively small numbers of bacteria. However, some alternative medicine practitioners believe that certain factors may promote the growth of excess bacteria.

  • Decreased motility in the small intestine: caused by excess dietary sugar, chronic stress, and conditions such as diabetes, hypothyroidism, and scleroderma.
  • Hypochlorhydria: as people get older, the amount of stomach acid they secrete declines. If there is less stomach acid, bacteria are more likely to proliferate. Overuse of antacids is also thought to lead to bacterial overgrowth.
  • Structural abnormalities in the small intestine: gastric bypass surgery, small intestinal diverticula, blind loop, intestinal obstruction, and Crohn's disease fistula are some of the structural factors that may be involved in bacterial overgrowth.
  • Other possible causes include immune deficiency, stress, certain medications such as steroids, antibiotics, and birth control pills, inadequate dietary fiber, and pancreatic enzyme deficiency.


  • Abdominal bloating and gas after meals
  • Pain
  • Constipation
  • Chronic loose stools or diarrhea: studies have found 48% to 67% of people with chronic diarrhea had bacterial overgrowth.
  • Soft, foul-smelling stools that stick to the bowl
  • Fatigue: megaloblastic anemia due to vitamin B12 malabsorption
  • Depression
  • Nutritional deficiency despite taking supplements
  • Weight loss
  • Abdominal pain
  • Mucous in stools
  • Bloating worse with carbs, fiber, and sugar

Natural Remedies

Due to a lack of research, fairly little is known about this condition. While antimicrobial drugs may be prescribed, the condition isn't always medically recognized.

If you are experiencing symptoms, it's important to talk with your doctor. Self-treating and avoiding or delaying standard care may be harmful to your health.

According to alternative medicine practitioners, there are three parts to the natural treatment of bacterial overgrowth:

  • Diet: Low carbohydrate diet
  • Eradicate unfriendly bacteria in the small intestine using herbs such as enteric-coated peppermint oil.
  • Replace: Bacterial overgrowth impairs friendly bacteria ("probiotics") and digestive enzymes.

Herbal Supplements

Enteric-coated peppermint oil is one of the more common supplements for small intestine bacterial overgrowth. The course of treatment is usually 1 to 6 months. A typical dose of enteric-coated peppermint oil is one to two capsules three times a day, taken in between meals with a glass of water. Side effects can include heartburn, rectal burning, and minty burping.

Other herbal antimicrobials used to treat bacterial overgrowth may include:


During treatment, alternative medicine practitioners usually recommend going on a diet that limits the intake of sweet and starchy foods. One such diet is the specific carbohydrate diet, which restricts grains, starchy vegetables, and some legumes, and was created to address digestive disorders such as bacterial overgrowth, Crohn's disease, and ulcerative colitis.

  • Medium Chain Triglycerides: Unlike regular oils, which a person with bacterial overgrowth may not be able to assimilate, medium chain triglycerides are absorbed directly without the need for digestive enzymes. Medium chain triglycerides, such as coconut oil, are often recommended for people with bacterial overgrowth or any type of malabsorption. 
  • Digestive enzymes: Digestive enzyme supplements can support the body's digestive enzymes until the function is restored. They should be taken before meals. More on digestive enzymes.
  • Vitamins and minerals that may be deficient in people with bacterial overgrowth include vitamin B12, magnesium, calcium, iron, zinc, copper, vitamin A, D, E, K.
  • Probiotics: needed to replace healthy bacteria in the intestines. Lactobacillus Plantarum and Lactobacillus GG are some types that have been used for bacterial overgrowth.


The "gold standard" test is to take bacterial cultures of small intestine fluid.

Lactulose hydrogen breath test: The most common test is the lactulose hydrogen breath test because it is less invasive. Lactulose is a non-absorbable sugar that's fermented if there are intestinal bacteria, resulting in hydrogen production. If there is bacterial overgrowth, fasting hydrogen levels will be high. In addition, after ingesting glucose, there will be a significant rise in hydrogen.

Other tests are the Schilling test (for a vitamin B12 deficiency). A small bowel follow-through may be done to look for structural problems.

One of the underlying issues in bacterial overgrowth may be insufficient stomach acid, called hypochlorhydria. Stomach acid naturally declines with age.

Related Conditions

  • Leaky gut syndrome
  • Vitamin and mineral deficiency
  • Non-alcoholic steatohepatitis (NASH)
  • Chronic fatigue syndrome
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