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.

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

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, and 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 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. Intead, they’re left to ferment in the intestines, resulting in gas, bloating, pain, mucus in stools, foul-smelling gas and stools, and diarrhea. Sweets and starchy foods cause the worst symptoms.

Toxic metabolic substances 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 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, 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

Natural Remedies for Bacterial Overgrowth

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.

There are three parts to the natural treatment of bacterial overgrowth:

Diet – low carbohydrate diet

Eradicate unfriendly bacteria in the small intestine using herbs and natural anti-microbial angents

Replace – Bacterial overgrowth impairs friendly bacteria (“probiotics”) and digestive enzymes