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Herbal remedies for bacterial overgrowth

A woman suffering from bacterial overgrowth
A woman suffering from bacterial overgrowth

Bacterial overgrowth in the small intestine is a relatively common condition that can be present for years before detected. That is because despite overuse of antibiotics, antacids, and other medications that wipe out friendly intestinal bacteria, many physicians do not test their patients for it.

Instead, people with chronic digestive problems such as gas, bloating, diarrhea, and/or constipation often are told they have irritable bowel syndrome (IBS) when the underlying problem is actually small intestine bacterial overgrowth. Given that IBS is the number one gastrointestinal diagnosis, bacterial overgrowth could be significantly under diagnosed.

Research studies:

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%) had bacterial overgrowth

What are the causes of bacterial overgrowth?

  • Decreased motility in the small intestine: caused by excess Dietary sugar, chronic stress, and conditions such as diabetes, hypothyroidism, and scleroderma. In the United States, up to 40% of chronic diarrhea in people with diabetes is associated with bacterial overgrowth.
  • Hypochlorhydria: as people get older, the amount of stomach acid they secrete decline. Because stomach acid is acidic and helps to kill bacteria in the small intestine, if there is less stomach acid, bacteria are more likely to proliferate. Another very common cause of hypochlorhydria is due to excessive use of antacids.
  • 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 causes of bacterial overgrowth.
  • Other causes include: immune deficiency, stress, and 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
  • Mucus in stools
  • Bloating worse with carbs, fiber, and sugar

Herbal Remedies that help bacterial overgrowth

It can be difficult to get proper testing and treatment for bacterial overgrowth, because some doctors do not understand this condition. The conventional treatment for bacterial overgrowth is antimicrobial drugs.

Herbs: The most studied natural treatment for bacterial overgrowth is enteric-coated peppermint oil, which is peppermint oil that has an edible, hard shell around it so that the capsule does not open until it is in the small intestine. It kills bacteria in the small intestine.

Other herbals used to treat bacterial overgrowth are:

  • Grapefruit seed extract - for people who do not like taking capsules, grapefruit seed extract can be found in liquid form. Add a few drops to a glass of water and drink in between meals.
  • Oregano oil capsules
  • Garlic
  • Berberine - goldenseal, Oregon grape
  • Olive leaf extract
  • Pau d'arco

Get a diagnosis from your doctor

Before you start taking herbal supplements because you think you have bacterial overgrowth, be smart and get a diagnosis from your doctor. Tell your doctor you think you may have it and request to be tested.

Tests that diagnose bacterial overgrowth

  • The "gold standard" test is to take bacterial cultures of small intestine fluid.
  • Lactulose hydrogen breath test is the most common test because it is less invasive. Lactulose is a non-absorbable sugar that is 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 b12 deficiency). A small bowel follow through may be done to look for structural problems.


If you are taking other medications, refrain from taking herbal supplements without first checking with your doctor. Herbal supplements and over-the-counter medications or prescription drugs can combine to cause adverse side effects. Just because an herbal supplement is extracted from, a “natural” source does not render it any less potent than any other chemicals you may ingest.

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