Treatment for Bacterial Overgrowth

Eating a FODMAP diet, controlling antibiotics and regenerating flora are some of the options for treating bacterial overgrowth. What else do you need to know about it? We have all the information you need right here!
Treatment for Bacterial Overgrowth
Marta Guzmán

Written and verified by Nutritionist Marta Guzmán.

Last update: 25 May, 2022

Do you suffer from gastrointestinal symptoms such as abdominal pain or diarrhea? You may be suffering from bacterial overgrowth in your small intestine. This condition isn’t normal, and in this article we’ll explain the treatment and the most typical mistakes people make.

Bacterial overgrowth in the small intestine

Intestinal bacterial overgrowth or small intestinal bacterial overgrowth (SIBO) is a heterogeneous syndrome produced by an excessive number, or an alteration in the type of bacteria present in the small intestine.

The gastrointestinal symptoms it can produce are diverse and nonspecific, such as:

  • Bloating
  • Flatulence
  • Abdominal pain
  • Diarrhea
  • Dyspepsia (discomfort after meals)
  • Weight loss

What makes this syndrome so particular is that, unlike the large intestine, the small intestine shouldn’t have a large number of bacteria. Specialists believe that the few bacteria that are housed there have been there since birth, living in symbiosis with our intestine.

A man with stomach pain.
An overgrowth of bacteria in the small intestine can lead to various gastrointestinal problems.

Little by little, we’re getting a more profound understanding of this relationship and we’re understanding that it’s vital to achieve a normal digestive process, an efficient activity in the immune system, and an optimal development of our intestine.

The problem comes when these bacteria overgrow. For example, one of the reasons for this bacterial overgrowth may be the excessive intake of foods rich in FODMAPs.

To maintain a good ecosystem of microorganisms along the digestive tract, and thus avoid bacterial overgrowth, the human body uses antibiotic mechanisms such as:

  • Hydrochloric acid in the stomach
  • The production of bile and digestive enzymes (which are also highly antibiotic).
  • pH changes
  • Oxygenation of the intestine

How is it diagnosed?

A good complementary diagnostic test is the hydrogen breath test. This test is based on the fact that certain gases, such as hydrogen or human methane, are produced by the fermentation of carbohydrates by intestinal bacteria. So if the exhalation of these gases occurs too quickly, we know we’re dealing with bacterial overgrowth.

Treatment of bacterial overgrowth

Conventional treatment includes identification of the conditions causing the symptomatology and treatment with antibiotics. However, we can’t forget a fundamental part: controlling our diet. To do so, we suggest you:

  • Avoid antinutrients that boycott the digestive function
  • In the first phase, reduce the consumption of foods rich in FODMAP
  • Provide antimicrobial foods: oregano, thyme, Lapacho tea, coconut fat, among others
  • Recover stomach acidity
  • Recover the function of the bile and exocrine pancreas by consuming nutritional supplements based on digestive enzymes, among others

Typical treatment errors

A doctor pressing down on a stomach
One of the errors that interfere in the treatment of bacterial overgrowth in the intestine is misdiagnosis.

1. Making a single diagnosis

If you suffer from bloating and steatorrhea (fat in the stools), doctors often diagnose you as suffering from bacterial overgrowth. But these same symptoms can be due to:

  • Exocrine pancreatic insufficiency
  • A yeast overgrowth
  • A parasite infection
  • Hypochlorhydria

Therefore, it’s crucial to have a proper diagnosis, based not only on the symptoms, but on all the processes that have led you to suffer the medical condition you have.

2. Treating with antibiotics for too long

Although using some antibiotic treatments is natural, using them for too long can affect the symbiotic bacteria. It can damage the diversity of the flora and make it difficult for the person to live without treatment, since it’s the variety of species of our microbiota that regulates the overgrowth.

3. Diets that are too restrictive for too long a period of time

In the first phase, you should follow a FODMAP diet, as it’ll help you control the overgrowth. However, you must remember that fiber is our bacteria’s food, they’re our prebiotics. Restricting them for too long can also affect the diversity of flora.

4. Terminating the treatment when the symptoms disappear

In addition, once the bacterial overgrowth has been resolved, we must focus on recovering the control mechanisms that have led to this overgrowth. The treatment will be finalized when hypochlorhydria, pancreatic insufficiency, or the need for antacids are resolved, and not only when the symptoms have disappeared.

In conclusion

To summarize, to treat bacterial overgrowth, you first of all need to reduce the excessive intake of foods rich in FODMAPs. In addition, treatment may include antibiotics and other therapeutic options. In any case, the success of the treatment depends largely on a good diagnosis by the physician.

All cited sources were thoroughly reviewed by our team to ensure their quality, reliability, currency, and validity. The bibliography of this article was considered reliable and of academic or scientific accuracy.

  • Miazga A, Osiński M, Cichy W, Żaba R. Current views on the etiopathogenesis, clinical manifestation, diagnostics, treatment and correlation with other nosological entities of SIBO. Adv Med Sci. 2015 Mar;60(1):118-24.
  • Chedid V, Dhalla S, Clarke JO, Roland BC, Dunbar KB, Koh J, Justino E, Tomakin E, Mullin GE. “Herbal therapy is equivalent to rifaximin for the treatment of small intestinal bacterial overgrowth.” Glob Adv Health Med. 2014 May;3(3):16-24. doi: 10.7453/gahmj.2014.019.
  • Quigley EM. Small intestinal bacterial overgrowth: what it is and what it is not. Curr Opin Gastroenterol. 2014 Mar;30(2):141-6.
  • Gibson, P. R., & Shepherd, S. J. (2010). Evidence based dietary management of functional gastrointestinal symptoms: The FODMAP approach. Journal of gastroenterology and hepatology, 25(2), 252-258.

This text is provided for informational purposes only and does not replace consultation with a professional. If in doubt, consult your specialist.