Natural (Herbal) Ways To Treat Bacterial Overgrowth

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

Instead, people with chronic digestive problems such as gas, bloating, diarrhea, and/or constipation are often 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 greatly under diagnosed.



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.


When the unwanted intestinal bacteria were eradicated, symptoms of IBS (particularly diarrhea and abdominal pain) improved in 48% of the subjects.

It’s not just people with IBS-like symptoms that have bacterial overgrowth. Bacterial overgrowth can also present with non-digestive symptoms such as fatigue.


It’s believed to be involved in:

  • Chronic fatigue syndrome
  • Fibromyalgia
  • Allergies
  • Arthritis
  • Lupus
  • Autoimmune diseases
  • Diabetes
  • Many other chronic conditions.

What Is Bacterial Overgrowth?

It’s not an overstatement to say that the small intestine is the most important segment of the entire digestive tract, which starts at the mouth and ends at the rectum. Nutrients from the food we eat — carbohydrates, proteins, fats, vitamins, and minerals — are absorbed in the small intestine. If anything interferes with the absorption here, nutrient deficiencies can result.


The small intestine normally contains relatively small numbers of bacteria. However, certain factors can cause the growth of excess bacteria.

Through a process called bile acid deconjugation, the unwanted bacteria causes’ fat malabsorption. It also blocks carbohydrates from being absorbed. Sweets and starchy foods cause the worst symptoms. When they’re left to ferment in the intestines, it results in:

  • Gas
  • Bloating
  • Pain
  • Mucus in stools
  • Foul-smelling gas and stools
  • Diarrhea.

A toxic metabolic substance produced by the bacteria injures intestinal cells and impairs absorption, resulting in nutrient deficiencies, food allergies and intolerances, and poorly functioning digestive enzymes.

What Causes 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 declines. 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 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 48-67% 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

Getting A Diagnosis

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 b12 deficiency). A small bowel follow through may be done to look for structural problems.
  • One of the underlying causes of bacterial overgrowth is insufficient stomach acid, called hypochlorhydria. Stomach acid naturally declines with age. Take the hypochlorhydria screening test.

What Conditions Can Bacterial Overgrowth Lead To?

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


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


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 doesn’t open until it is in the small intestine. It kills bacteria in the small intestine.


Other Herbal Treatment Options

  • Grapefruit seed extract – for people who don’t 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


During treatment, it is necessary to limit intake of sweet and starchy foods. People usually experience a noticeable decline in bloating, gas, indigestion, diarrhea, and other digestive symptoms.

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 are often recommended for people with bacterial overgrowth or any type of malabsorption. Coconut oil is a medium chain triglyceride.

Digestive Enzymes

Digestive enzyme supplements can support the body’s digestive enzymes until function is restored. They should be taken before meals. A typical dose is one capsule before each meal.
Vitamins and minerals that may be deficient in people with bacterial overgrowth include vitamin B12, magnesium, calcium, iron, zinc, copper, vitamin A, D, E, and 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.