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Small Intestinal Bacterial Overgrowth (SIBO) – What You Need to Know

Updated 4/12/2023 by Dan Jackowiak NC, HHP

Small intestinal bacterial overgrowth, abbreviated as SIBO, occurs when the bacteria in your small intestine overgrow, and their balance is disrupted. Normally, the bacteria in your digestive tract act as gut flora, necessary to maintain digestive health. Most of your gut bacteria live in the large intestine and colon. In the large intestine, gut flora helps in food breakdown, synthesizes vitamins, and aids in waste elimination. (1)

Sometimes, a poor diet or certain medications disrupts the balance of your gut flora. As a result, the gut flora typically found in the large intestine overgrow and colonize in the small intestine, which causes SIBO (small intestinal bacterial overgrowth).

The digestive tract is naturally lined with mucus that lubricates and protects it. The overgrowth of bacteria may damage the mucosal lining of the digestive tract, creating additional room for the bacteria to attach and multiply rapidly.

These colonized bacteria feed on the undigested food passing through the small intestine and produce hydrogen or methane in your gastrointestinal tract, leading to excessive bloating. (1)


What Causes SIBO (small intestinal bacterial overgrowth)?

After the breakdown of food by enzymes in the stomach, food particles pass through the digestive tract from the stomach to the intestine. Stomach acidity and intestinal motility are the protective mechanisms in the body to maintain the flow and keep the gut flora in balance. (2)

Stomach acidity kills the harmful bacteria, and intestinal motility moves food along the intestine towards the colon. The presence of bile prevents the overgrowth of gut flora. At the end of the digestive tract, the ileocecal valve prevents the backward movement of stool from the large intestine to the small intestine.

Normally, bacteria and food travel through the gut to the colon – the last part of the digestive tract. Several factors may affect stomach acidity and intestinal motility, disrupting healthy gut flora balance and developing SIBO. (3)

These factors may include:

Physical obstructions in the gut: Damage to the gut from surgeries or Crohn's disease may cause small pouches to develop in the small intestine. These pouches in the intestine walls allow the bacteria to accumulate instead of passing it to the colon, putting you at the risk of SIBO.

Damaged Muscles: Certain health complications, such as diabetes mellitus and scleroderma, may cause damage to gut muscles. If the digestive tract's muscular activity is not regular, your body will not move food and bacteria from the small intestine to the large intestine. Thus, it increases the chances of SIBO.

Foods: Excessive consumption of sugary foods, refined carbohydrates, and alcohol may disrupt intestinal motility or stomach acidity, which may cause SIBO.

Certain Medications: Steroids, antibiotics, and acid-blocking drugs are certain medications that may disrupt the normal gut flora.

What are the Signs and Symptoms of SIBO?

SIBO may produce several gastrointestinal symptoms ranging from digestive imbalance to chronic illness. Common symptoms of SIBO include: (4)

  • Abdominal pain and cramping
  • Bloating and Gas
  • Diarrhea or constipation (less common than diarrhea)
  • Fatigue
  • Loss of appetite
  • Uncomfortable fullness after eating
  • Weakness

If the SIBO persists for longer, the bacterial overgrowth may not allow the intestine to absorb nutrients from the food properly. The insufficient absorption of nutrients may cause protein deficiency, vitamin and electrolyte imbalance in the body.

Complications Associated with Insufficient Nutrient Absorption

  • Inadequate absorption of vital vitamins, especially vitamin B12, can lead to serious complications, including pernicious anemia and peripheral neuropathy.
  • Vitamin A deficiency may cause night blindness.
  • Vitamin A deficiency affects the levels of calcium in the body, resulting in metabolic bone disease. It may also lead to muscle twitching and muscle spasms.
  • In severe cases, your body is unable to absorb fats from food. It leads to the release of excessive fat in feces resulting in the foul-smelling oily stool that may cause anal leakage.

How Can SIBO be Diagnosed?

Small intestinal bacterial growth(SIBO) is a serious infection that damages the small intestine. The increased bacterial population in the small intestine causes diarrhea, bloating, and pain. It can also lead to malnutrition. It affects adults, older people, men and women equally, causing irritable bowel syndrome IBS. The IBS can further cause digestive and intestinal issues. So, the proper diagnosis and treatment of SIBO are very important.

SIBO shows a wide range of nonspecific symptoms of varying severity, making it difficult to diagnose. A doctor will ask about a person's symptoms and medical history to diagnose SIBO. They may probe the abdomen for indications of bloating or extra gas. The symptoms may arise from diseases related to protein, lipid, and vitamin malabsorption. When there is malabsorption, SIBO should be suspected. (5)

Specific tests are also performed to diagnose SIBO. These tests are ordered by the doctor depending upon the symptoms and patient situation. These tests check bacterial growth, body electrolyte level, and poor absorptions of fat and protein. Common tests are:

  • Breathing Test

The breath test is a noninvasive test used frequently to diagnose SIBO. The breathing test detects the presence of hydrogen or methane in the breath at regular intervals after a person consumes a fluid containing a sugar solution, such as lactulose or glucose. If the sample liquid includes glucose, the test should take two hours. If the sample liquid is lactulose, the test should take three hours. (6)

The presence of hydrogen in the breath before the hour suggests the existence of bacteria in the small intestine. These bacteria in the small intestine react with the ingested sugar and produce hydrogen or methane, subsequently expelled through the breath. It confirms the diagnosis of small intestinal bacterial growth SIBO. (7)

You will be asked to clean your mouth with mouthwash to clean out extra bacteria. Next, you have to provide a baseline breath sample in a balloon. Then you are asked to consume a small amount of either glucose or lactulose-containing beverage. You will be prompted to submit another breath sample by blowing up a balloon every 20 minutes.

There are certain concerns about the validity of the breath test for SIBO diagnosis. The test yields false results for some patients depending upon the transit time of food through the digestive system. This is more common in patients with gastroparesis.

Breath tests for SIBO are also not able to distinguish species. However, in a 1999 study, the findings showed the overgrown bacteria to be Streptococcus (71%), Escherichia coli (69%), Staphylococcus (25%), Micrococcus (22%), Klebsiella (20%), Proteus (11%) for microaerophilic bacteria, and Lactobacillus (75%), Bacteroides (29%), Clostridium (25%), Veillonella (25%), Fusobacterium (13%), and Peptostreptococcus (13%) for anaerobic bacteria.

However, according to a study published in May 2012, Escherichia coli, Enterococcus spp and Klebsiella pneumoniae were the most common isolates within patients with SIBO.

You can do this simple test for SIBO to verify that's what you have.

You could also do this stool test to get a better idea what you are infected with, and what would be the best things to take to get it under control.  Or, see your doctor and have them do Jejunal Aspiration test to identify the bacteria that are overgrown. The lab can then test to see what kills these species.

  • Jejunal Aspiration

Jejunal aspiration is considered the more accurate test for the diagnosis of SIBO. It is the standard gold test to study bacterial growth. Its results are considered accurate as it involves endoscopy.

It involves the collection of a fluid sample from the central portion of your small intestine. After that, the sample is cultivated and tested for the presence of bacteria. A long, flexible endoscope tube is sent down your throat and upper digestive system to acquire a fluid sample in your small intestine. The fluid sample is analyzed in a laboratory for bacterial growth. If you feel any difficulty in breathing after the test, you must contact your doctor immediately. (8)

Certain other tests like blood tests are also done to study electrolyte imbalance and nutrient deficiency.

How Can SIBO be Treated?

SIBO can be treated with a combination of antibiotics and essential nutrients. The main purpose of the treatment is to control any associated illness that is promoting the infection. Antibiotics are the best way to treat SIBO. Antibiotics decrease the number of bacteria in the small intestine, which helps to cure the underlying illness. Nutrient uptake helps antibiotics to overcome this illness.

The most common antibiotics for SIBO are: (9)

  • Amoxicillin
  • Metronidazole
  • Rifaxamin
  • Ciprofloxacin

The main purpose of all these antibiotics is to reduce the small intestine bacterial overgrowth. It is important to note that not all bacteria are eradicated with these antibiotics as some of them are important for the body's functioning. While a single round of antibiotics for 1-2 weeks may be adequate, SIBO tends to recur. Thus, additional doses of antibiotics may be necessary. In certain cases, antibiotics are routinely cycled, which means that they alternate 1-2 weeks on the antibiotic with 1-2 weeks off.

Furthermore, underlying vitamin and mineral deficiencies caused by malabsorption should be addressed. Nutritional support is necessary to improve vitamin deficiency. Quiet often, the patient must receive vitamin B12 injections as prescribed by the doctor. One must have a balanced diet to reduce intestinal stress. Avoiding a high sugar diet is also important during SIBO treatment.

Treating SIBO Naturally

A 2014 study that was published in The Global Advancement of Health and Medicine, points out that herbs are just as effective for SIBO as antibiotics with a lot less side effects. But treatment times with natural compounds take twice as long as antibiotics, typically four weeks verses two weeks.

If the antibiotics are the way you decide to go, I would at the very least, take Biofase while on the antibiotics to reduce the chance of yeast over growth and to reduce the bacterial biofilms, which will make the antibiotics more effective.

Looking at this published study from Global Advances in Health & Medicine in 2014,  we find that a 4 consecutive week treatment of herbs had a positive response rate of 46% vs 34% for a 2 week course of the antibiotic Rifaximin. The Rifaximin non-responders who received herbal therapy afterwards, achieved a 57% success rate with no side effects.

Triple antibiotic therapy for these harmful bacteria achieved a 60% success rate but there were side effects in some individuals including, hives, anaphylaxis, diarrhea and Clostridium difficile infection.

Furthermore, a month's supply of Rifaximin retails for $1247.39, and according to Medicare part D, a patient's copay in 2014 will be $638.09 for preferred ($703.70, non-preferred) at your local pharmacy or mail order. If you have to use triple antibiotic therapy because the Rifaximin didn't work, your costs are going to increase substantially.

In the above clinical study, patients were given either;

Biotics Research Dysbiocide and Biotics Research FC-Cidal


Candibactin AR and Candibactin BR

Unfortunately, the clinical study itself did not determine which line of products worked better than the other. Reading the customer reviews on Amazon, the Candibactin products seem to work a little better. Looking at the ingredients, I would go with the Candibactin products as well, but it is your choice.

You can also increase your chances of clearing these infections by using the motility agent Iberogast. Clinical studies performed by the Life Sciences Consultancy in Germany, show that without a motility agent, 60% of people treated for sibo tend to relapse.  Follow the dosage directions on the label and take either right before or with meals.

Biofase  is also recommended to reduce the biofilms, which helps the herbs be more effective. Take 2 or 3 capsules of Biofase 1 hour before breakfast and at bedtime. Follow the dosing directions on the Iberogast label.

I would not take a probiotic until after the treatment was completed.

Suggested Directions

First Week

Biofase Take 2 capsules 1 hour before breakfast and 1 capsule 30 minutes before bedtime.
Candibactin AR Take 1 capsule twice a day right before or with breakfast and dinner.
Candibactin BR Take 2 capsules twice a day 30 minutes before breakfast and dinner.
Iberogast Take the recommended dose with meals 3 times per day.

Week Two and Until Products are Gone

Biofase Take 3 capsules 1 hour before breakfast and 3 capsules 30 minutes before bedtime.
Candibactin AR Take 1 capsule three time a day right before or with meals.
Candibactin BR Take 2 capsules three time a day 30 minutes before meals.
Iberogast Take the recommended dose with meals 3 times per day.

If you decide to use the Biotics Research products instead of the Candibactins, just follow the directions on the label in place of the Candibactin products.


If the above protocol initially causes a cleansing reaction that you can't handle due to the severity of your infection, you can always reduce doses and work up as you are able.

Alternative Natural Therapy

An alternative therapy that uses many more herbs with antimicrobial effects, would be to use Biofase for the biofilms, with Microfase for direct killing of the bacteria. Because the bacteriophages in Floraphage eat E. coli it would also be helpful. Floraphage has also been found to reduce Clostridium levels.

Take 2 capsules Biofase with one Floraphage one hour or more before breakfast and at bedtime. Take 2 capsules Microfase 30 minutes before breakfast. Take 2 Microfase 30 minutes before dinner. You can increase from two times a day to three if needed or if you want to be more aggressive.

How Can SIBO be Prevented?

SIBO is generally caused by an underlying medical problem or a physical deficiency in the small intestine. Addressing and treating the underlying cause of SIBO reduces the likelihood of its return. SIBO symptoms are frequently reported months after antibiotic medication has been completed. SIBO management relies mostly on prevention. Changes in lifestyle and diet also help to keep SIBO away. Eating various plant-based foods and avoiding highly processed and sugary foods will allow good bacteria to thrive while preventing unhealthful bacteria from proliferating. (10)

Back to Common Harmful Bacteria Species & Infections

Medical References

1. Dukowicz AC, Lacy BE, Levine GM. Small intestinal bacterial overgrowth: a comprehensive review. Gastroenterol Hepatol (N Y) [Internet]. 2007 Feb;3(2):112–22.
2. Bures J, Cyrany J, Kohoutova D, Förstl M, Rejchrt S, Kvetina J, et al. Small intestinal bacterial overgrowth syndrome. World J Gastroenterol [Internet]. 2010 Jun 28;16(24):2978–90.
3. Chander Roland B, Mullin GE, Passi M, Zheng X, Salem A, Yolken R, et al. A Prospective Evaluation of Ileocecal Valve Dysfunction and Intestinal Motility Derangements in Small Intestinal Bacterial Overgrowth. Dig Dis Sci [Internet]. 2017;62(12):3525–35.
4. Mouillot T, Rhyman N, Gauthier C, Paris J, Lang A-S, Lepers-Tassy S, et al. Study of Small Intestinal Bacterial Overgrowth in a Cohort of Patients with Abdominal Symptoms Who Underwent Bariatric Surgery. Obes Surg [Internet]. 2020;30(6):2331–7.
5. Rao SSC, Bhagatwala J. Small Intestinal Bacterial Overgrowth: Clinical Features and Therapeutic Management. Clin Transl Gastroenterol [Internet]. 2019 Oct;10(10):e00078–e00078.  
6. Rezaie A, Buresi M, Lembo A, Lin H, McCallum R, Rao S, et al. Hydrogen and Methane-Based Breath Testing in Gastrointestinal Disorders: The North  American Consensus. Am J Gastroenterol. 2017 May;112(5):775–84.
7. Saad RJ, Chey WD. Breath testing for small intestinal bacterial overgrowth: maximizing test accuracy. Clin Gastroenterol Hepatol  Off Clin Pract J  Am Gastroenterol Assoc. 2014 Dec;12(12):1920–64.
8. Erdogan A, Rao SSC, Gulley D, Jacobs C, Lee YY, Badger C. Small intestinal bacterial overgrowth: duodenal aspiration vs glucose breath test. Neurogastroenterol Motil  Off J Eur  Gastrointest Motil Soc. 2015 Apr;27(4):481–9.
9. Boltin D, Perets TT, Shporn E, Aizic S, Levy S, Niv Y, et al. Rifaximin for small intestinal bacterial overgrowth in patients without irritable bowel syndrome. Ann Clin Microbiol Antimicrob [Internet]. 2014;13(1):49.
10. Bohm M, Siwiec RM, Wo JM. Diagnosis and Management of Small Intestinal Bacterial Overgrowth. Nutr Clin Pract [Internet]. 2013;28(3):289–99.

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