Bacteria in Your Gut: SIBO Symptoms, Causes, Diagnosis, and SIBO Treatment

Intestines with Gut Bacteria on Blackboard

They say two is a company and three is a crowd. What if there’s more than a million? I am talking about bacteria here, and having that much within your small intestine definitely spells disaster. Even healthy individuals host bacteria throughout their digestive tract. However, there are intrinsic mechanisms that help maintain the delicate balance of the gut flora. Gastric acid destroys many bacteria before they leave the stomach, while the bile and pancreatic secretions control bacterial growth within the small intestine. Intestinal motility, immunoglobulins, and intestinal valves also help maintain just the right amount of bacteria in the small intestine. This part of the digestive tract found between the stomach and colon, where most food is broken down, should not have more than 10 organisms/mL. However, certain conditions lead to a qualitative and quantitative imbalance within the small intestine leading to small bowel bacterial overgrowth syndrome (SBBOS) or small intestinal bacterial overgrowth (SIBO).

What is Small Intestinal Bacterial Overgrowth (SIBO)?

SIBO is a disorder of excessive bacterial presence within the small intestine. On the average, less than 10 3 (mostly Gram-positive) organisms/mL are found in that section of the digestive tract. Many of these bacteria contribute to our body’s normal function like the digestion of food, absorption of nutrients and the inhibition of pathogens. In the case of a person with SIBO, bacterial population may be 100 times more. The type of microbial flora present within our gut also characterizes SIBO. Certain species like Firmicutes and Bacteroidetes, Proteibacteria and Actinobacteria, Veruccomicrobia and Fusobacteria are considered important in fighting inflammation and tumors. However, harmful bacteria like enterobacteria, bacteroids, clostridia, and fusobacteria get to dominate within the small intestine of a SIBO patient. When the ideal microbiome within the gut is altered, small bowel cells get inflamed. This is followed by poor digestion and malabsorption of fats, proteins and carbohydrates. All these can lead to diarrhea and other symptoms.

SIBO Symptoms

It is not easy to identify SIBO based on symptoms because these are often similar to other digestive and even biliary or gallbladder diseases. Typical manifestations include abdominal pain, nausea, vomiting, diarrhea, and bloating. Due to malabsorption of nutrients, SIBO may also lead to malnutrition, weight loss and fat-soluble vitamin deficiencies like iron deficiency anemia, hypocalcemia, neuropathy, and megalobastic anemia. Some patients suffering from bacterial overgrowth indicate the presence of a single symptom while others report overlapping conditions.

The most obvious symptom is often dictated by the predominant type of bacteria present within the small intestine. For example, microorganisms that turn carbohydrates to short-chain fatty acids may produce bloating without diarrhea. On the other hand, if there is abundance of bacteria which metabolize bile salts to unconjugated or insoluble compounds, bile acid diarrhea or fat malabsorption may happen. Some bacterial species may also cause mucosal injury and enhanced intestinal barrier permeability which can bring about systemic sepsis or intestinal failure, if not addressed quickly.

SIBO Causes and Risk Factors

Until recently, SIBO was thought to be a rare condition only affecting a few people. However, due to the availability of tests, the medical community has now admitted that it is more common than it seems. Various studies have also shown that SIBO is prevalent in patients who have existing irritable bowel syndrome, metabolic disorders, dysmotility disease, neuromuscular disease, and other conditions related to the digestive, liver, and biliary system. Statistics show that patients who have undergone abdominal surgery, bilateral truncal vagotomy, gastrectomy and other related surgical procedures have greater risk of developing SIBO. Age-associated decline in gastrointestinal motility also make the elderly a high-risk population.

Gallbladder Removal

All surgeries run the risk of contributing to SIBO but cholecystectomy is not only a surgical procedure which is a risk factor in and of itself, but also affects bile flow along with the quality of bile (i.e. – type of bile acids). And since bile contributes to peristalsis or movement of the intestines, the prescribing of ursodeoxycholic acid (a bile salt) has been shown to improve motility following removal.

Studies show that people who have been through a cholecystectomy, with or without gallstones, run a greater risk of developing SIBO over time. 4-6 months shows no increase in SIBO, but 2 years to 12 years is statistically proven that there is increased incidence of SIBO. The reason given for this is also research based; the motility of the intestines (large and small) decreases shortly after the surgery. This slower transit time of the food through the whole digestive system not only causes constipation but also gives more time for an overgrowth of bacteria to develop in the small intestine.

But causes of SIBO are not usually so simple, rather it is complex and interrelated with other diseases and conditions. In some patients, there can be more than one cause. Some of the known causes are enumerated below:

1. Disorders That Compromise our Body’s Innate Protective Defense

The body has numerous built-in mechanisms to protect itself from SIBO. This includes gastrointestinal tract barriers like gastric enzymes, bile, and intestinal secretions. The exponential proliferation of bacteria may arise from the dysfunction of these natural defenses.

  • Immunodeficiency syndromes – diseases that compromise the immune system response
  • Low stomach acid – the absence or insufficiency of hydrochloric acid in gastric secretions of the stomach and other digestive organs allows for the growth of bacteria
  • Pancreatic insufficiency – occurs when the pancreas does not make enough enzyme for the digestion and assimilation of nutrients
2. Anatomical Abnormalities

Anatomical abnormalities in the GI tract provide a conducive environment for the colonization of bacteria. These abnormalities may be a complication of other diseases, in-born, or may be a consequence of surgery.

  • Small intestinal obstruction – blockage that keeps food or other liquids from passing through the small intestine or the colon
  • Diverticula – condition where pouches form in the wall of the duodenum, jejunum or colon. These pockets can harbour bacteria and lead to SIBO symptoms.
  • Fistulae – abnormal connection between the colon and the small bowel
  • Surgical blind loop – may cause stagnation of bacteria, abnormal motility and ineffective flow of food and other liquids
  • Previous ileocecal resections – this can increase the risk of SIBO as it allows the movement of bacteria from the colon to small intestine
3. Motility disorders

Normal gastrointestinal motility is designed to effectively move food and other materials through the tract. However, some disorders disrupt those tightly coordinated series of events, causing delayed or suppressed movement of food and bacteria.

  • Scleroderma – type of autoimmune disease that involve the hardening and tightening of the skin
  • Gastroparesis – disorder of delayed gastric emptying
  • Enteropathy – malabsorption syndrome characterized by inflammation of the small intestine and the loss of microvilli structure.
4. Use of certain medications
  • Proton-pump Inhibitors – increases bacterial colonization in the duodenum and slows intestinal transit. This is one reason why it is important to use the best probiotics for SIBO natural treatment.
  • Immunosuppresant medications – affects the body’s natural immune response to fight harmful bacteria


Diagnosis and Tests

The nonspecific symptoms of SIBO make it a commonly misunderstood and underdiagnosed disease. It also doesn’t help that there are substantial disagreement among medical practitioners and researchers regarding the gold standard for SIBO diagnosis.

Two tests are commonly conducted to confirm bacterial overgrowth – breath tests and bacterial culture. Nevertheless, there are more than two options that may be employed. Below is the list of all available technology for the purpose of clinical or research testing:

  1. Bacterial Culture

This is the most direct way to analyse the quality and quantity of the bacterial population. For this procedure, liquids are taken from the proximal jejunum through a catheter and an endoscope. Samples were also previously collected by intubating the small bowel. However, the old method was cumbersome and time-consuming so more diagnostic centers are taking advantage of endoscopy.


  • Expensive and time-consuming
  • Possibility of contamination during transport and culture of the aspirate
  • No clarity and standard on sample handling and microbiological techniques
  • Culturing only reveals about 20% of microbiota compared to genomic methods
  • SIBO occurring more distally in the small intestine may be missed
  • False-negative results may occur where overgrowth is caused by obligate anaerobes
  • Location of sampling and the amount of fluid recovered can be variable
2. Breath Testing Technique

Because of the non-invasive nature and ease of use of various breath testing techniques, it is now becoming the more popular choice for SIBO diagnosis. These methods all rely on the modification of a substrate by bacteria. Lactulose, glucose, sucrose, or xylose are often used. Hydrogen and methane breath tests are currently the most important diagnostic methods.


  • Despite the use of several substrates, none has been identified to be the best among the rest
  • The differences in bacterial flora among subjects may produce inaccurate results
  • There is no standard protocol for the administration, timing, and collection of breath specimens
  • Low fiber diet required for 24 h before the test
  • Smoking, sleep and exercise can affect test accuracy
  • Antibiotics and laxatives taken before the test affect the results
  • Rapid transit time can give a false-positive result
  • Delayed gastric emptying/slow transit can give a false-negative result
3. Therapeutic Trial Approach

When a patient’s symptoms clinically suggest SIBO, doctors may also opt to proceed with an antibiotic trial. Through this, they can use the patient’s response to antibiotics to confirm the extent and nature of the condition. This procedure is often used in association with other diagnostic tests.


  • No standardized approach towards the type, dose or duration of the antibiotic regimen
  • No consensus on the meaning of a clinical response to antibiotics
  • Over-prescribing of antibiotics
  • Risk of serious side effects from antibiotic treatment
  • Difficulty in identifying patients without SIBO vs. those with SIBO caused by an antibiotic-resistant organism

SIBO Treatment

Due to the lack of standardized investigative tool for possible SIBO cases, addressing the condition is a challenge. As SIBO often co-exists with other GI disorders, it is difficult to define a typical patient and identify a treatment protocol. Nevertheless, there are three clear goals to help resolve SIBO:

  • Identify and correct the underlying cause/disease.
  • Treat the bacterial overgrowth and maintain a healthy gut flora with good bacteria with the aid of the best probiotics for SIBO. 
  • Provide nutritional support. Resolve nutritional deficiencies.
1. Antibiotic therapy

Antibiotic treatment is still the most popular route to address SIBO. However, there are a variety of bacterial strains found simultaneously in a patient, and each one has a different reaction and sensitivity to antibiotics. Therefore, many doctors will prescribe broad-spectrum antibiotics and adjust based on the observed response to sensitivity tests. Cyclical antibiotic treatment is also employed to prevent tolerance

2. Probiotics

Probiotics are often called the “good bacteria” as it helps control the proliferation of harmful bacteria.

The use of this treatment approach aims to restore balance within the microbiome by “replacing” the missing bacteria and altering the composition of the gut flora. The use of the best probiotics for SIBO are believed to be superior to antibiotics use as exhibited in numerous experiments.

  • Certain probiotics exert anti-inflammatory effects and help reduce relapse rate.
  • By reducing inflammation, probiotics may reduce pain by diminishing visceral (organ) hypersensitivity.
  • Probiotics improve gut motility and perception, addressing bloating and flatulence.
  • Probiotics alter the composition of stool and gas and increase intestinal mucus secretion, thus modulating symptoms like constipation and diarrhea.
3. Prokinetics

Prokinetic agents are medications used to address motility issues that arise due to SIBO.

  • They increase the frequency of contractions within the small bowel to strengthen the lower esophageal sphincter.
  • They cause the contents of the stomach to move faster, addressing constipation, obstruction, and other dysmotilities.

Your doctor may prescribe a prokinetic drug to increase gut motility. There are, however, some natural prokinetics that you may want to try on your own as well.

Pure Encapsulations’ MotilPro is a hypoallergenic nutritional supplement free from gluten, soy, and dairy, which supports gut signalling and boosts gut movement. Aside from helping prevent and address SIBO, it is also recommended for those with IBS, reflux, gastroparesis, dyspepsia, and other similar symptoms.

Another natural prokinetic option is the use of Iberogast. It consists of nine different herbal extracts which all contribute to a healthier digestion. Since it helps alleviate symptoms like stomachache, dyspepsia, bloating, and heartburn, it may be prescribed for other digestive and biliary conditions too.

Organic Ginger Root is also known as a help for gut motility, usually in high amounts like 1000 mg. It is just important to note though, that ginger is contraindicated for those on blood thinners.

4. Digestive Support

Low stomach acid and enzyme deficiency may affect the innate ability of our gastrointestinal system to protect itself. Therefore, taking supplements such as Betaine HCL and Digestive Enzymes may help support

5. Surgical Treatment

Surgical treatment is considered when the underlying cause of SIBO has something to do with anatomical abnormalities. This method can be used to address causes like blind loops, bowel obstruction, multiple small intestinal diverticula, fistulae, and many more. Specialized non-transplant surgeries can also be used to improve intestinal motility, normalize intestinal transit, or increase the mucosal surface area of the gut.


One of the most effective natural treatment for SIBO is the use of probiotics.

1. Bacillus coagulans

This gram-positive bacteria has the ability to pass through the stomach in its spore form and multiply rapidly in the intestines. This helps in the elimination of pathogenic organisms while replenishing the quantity of desirable microorganisms.

2. Saccharomyces boulardii

There are numerous studies published on the benefits of this non-pathogenic yeast. It is resistant to stomach acid as well as bile, and pancreatic juices. This makes it an excellent support for both the upper and lower gastrointestinal tracts’ microbiome. Saccharomyces boulardii has also been proven as a relief for diarrhea, IBS, and other intestinal and bowel infections. Saccharomyces boulardii can be taken along with antibiotics with no problem which makes it especially useful for SIBO.

3. DDS -1 Lactobacillus acidophilus

This is the most stable bacterial probiotic resistant to heat, humidity, oxygen, and light. It helps digest protein, fat, and lactase while producing folic acid and vitamin B12. This specific strain actually produces a natural antibiotic (called acidophilin) that fights 23 different toxin-producing microorganisms. Another of its by-products is hydrogen peroxide which fights adverse bacterial and yeast overgrowth.

4. Bifidobacterium infantis 35624

This probiotic strain is well-tested and known to provide relief from bloating and abdominal pain as well to improve bowel movements. This probiotic is named as such because it thrives most in the intestines of babies to help break down lactic acid within breast milk. However, it can still give great overall benefits for infants and adults alike.

5. Bifidobacterium lactis

This probiotic bacteria is present in large amounts within our intestine and colon as it aids in the absorption of nutrients as well as the breakdown of body waste. Aside from its digestive benefits, it is also proven to increase immunity, lower cholesterol, and fight cancerous tumors.

6. Lactobacillus plantarum

This beneficial gram-positive bacteria aids in digestion and helps in maintaining a healthy gut. Aside from giving relief from common digestive problems like gas, bloating, cramping, constipation and diarrhea, it also enhances immune function, promotes brain development, reduces inflammation and improves cognitive health.


With all the brands available in the market, it may be a challenge to find the best probiotics for SIBO. Good thing, we have Probiotics-GI Elite.

Probiotics-GI Elite is an expertly formulated full-spectrum blend of probiotics, prebiotics, and enzymes. These efficiently-blended probiotics with the most widely-researched strains of good bacteria help maintain the proper balance of intestinal microflora to support.

The 11 probiotic strains included are: L. acidophilus, L. casei, L. rhamnosus, L. lactis, L. plantarum, L. brevis, L. salivarius, S. thermophiles, B. bifidus, B. coagulans, S. boulardii.

The Prebiotic Blend and Elite Enzyme Blend found in Probiotics-GI Elite also promote overall colon health by supporting intestinal cleansing through the breakdown of accumulated leftover food, destruction of microbes like yeast (Candida), protein digestion boost, and the management of inflammation in the gut.



Andrei, M., Nicolaie, T., Stoicescu, A., Teiusanu, A., Gologan, S., and Diculescu, M. (2015). Intestinal Microbiome, Small Intestinal Bacterial Overgrowth and Inflammatory Bowel Diseases – What are the Connections?. Current Health Sciences Journal, 41(3), 197-203. doi:10.12865/CHSJ.41.03.01

Bures, J., Cyrany, J., Kohoutova, D., Förstl, M., Rejchrt, S., Kvetina, J., … & Kopacova, M. (2010). Small intestinal bacterial overgrowth syndrome. World J Gastroenterol, 16(24), 2978-2990.

Enko, D., & Kriegshäuser, G. (2017). Functional 13C-urea and glucose hydrogen/methane breath tests reveal significant association of small intestinal bacterial overgrowth in individuals with active Helicobacter pylori infection. Clinical Biochemistry, 50(1/2), 46-49. doi:10.1016/j.clinbiochem.2016.08.017

Fialho, A., Fialho, A., Thota, P., McCullough, A. J., & Bo, S. (2016). Small Intestinal Bacterial Overgrowth Is Associated with Non-Alcoholic Fatty Liver Disease. Journal Of Gastrointestinal & Liver Diseases, 25(2), 159-165. doi:10.15403/jgld.2014.1121.252.iwg

Grace, E., Shaw, C., Whelan, K., & Andreyev, H. J. N. (2013). Review article: small intestinal bacterial overgrowth–prevalence, clinical features, current and developing diagnostic tests, and treatment. Alimentary pharmacology & therapeutics, 38(7), 674-688.

Lykova, E. A., Bondarenko, V. M., Parfenov, A. I., & Matsulevich, T. V. (2004). Bacterial overgrowth syndrome in the small intestine: pathogenesis, clinical significance and therapy tactics. Eksperimental’naia i klinicheskaia gastroenterologiia= Experimental & clinical gastroenterology, (6), 51-7.

Nababan, T., & Fauzi, A. (2015). Diagnosis and Treatment of Small Intestinal Bacterial Overgrowth. Indonesian Journal Of Gastroenterology, Hepatology & Digestive Endoscopy, 16(2), 105-111.

Quigley, E. M. (2015). Prokinetics in the management of functional gastrointestinal disorders. Journal of neurogastroenterology and motility, 21(3), 330-336.

Quigley, E. M. (2016) Chapter 39 – Probiotics, Prebiotics, Synbiotics, and Other Strategies to Modulate the Gut Microbiota in Irritable Bowel Syndrome (IBS). Probiotics, Prebiotics, and Synbiotics. Academic Press.

Quigley, E. M., & Quera, R. (2006). Small intestinal bacterial overgrowth: roles of antibiotics, prebiotics, and probiotics. Gastroenterology, 130(2), S78-S90.

Tunkel, A.R. (2017) Host Defense Mechanisms Against Infection. R

Zhang, Y., Liu, G., Duan, Y., Han, X., Dong, H., & Geng, J. (2016). Prevalence of Small Intestinal Bacterial Overgrowth in Multiple Sclerosis: a Case-Control Study from China. Journal Of Neuroimmunology, 30183-87. doi:10.1016/j.jneuroim.2016.11.004.