Bacteria in Your Gut: SIBO Symptoms and Treatment

They say two is a company and three is a crowd. What if there are more than a million? I am talking about bacteria here, and having that much within your small intestine spells disaster, and that’s what happens with SIBO.

While it is normal for healthy individuals to host bacteria throughout their digestive tract, 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 the right amount of bacteria in the small intestine. This part of the digestive tract 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 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 functions like the digestion of food, absorption of nutrients, and the inhibition of pathogens. In the case of a person with SIBO, the bacterial population maybe 100 times more.

The type of microbial flora present within our gut also characterizes SIBO. Certain species like Firmicutes and Bacteroidetes, Proteobacteria and Actinobacteria, Veruccomicrobia, and Fusobacteria are 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. Small bowel cells get inflamed when the ideal microbiome within the gut is altered. This is followed by poor digestion and fats, proteins, and carbohydrates malabsorption. All these can lead to diarrhea and other symptoms.

SIBO Symptoms

It is difficult to identify SIBO based on symptoms because these are often similar to other digestive and biliary or gallbladder diseases. Typical manifestations include abdominal pain, nausea, vomiting, diarrhea, and bloating. Due to the malabsorption of nutrients, SIBO may also lead to malnutrition, weight loss, and fat-soluble vitamin deficiencies like iron deficiency anemia, hypocalcemia, neuropathy, and megaloblastic anemia. Some patients suffering from bacterial overgrowth indicate the presence of a single symptom, while others report overlapping conditions.

The most apparent symptom is often dictated by the predominant type of bacteria in the small intestine. For example, microorganisms that turn carbohydrates into short-chain fatty acids may produce bloating without diarrhea. On the other hand, if there is an abundance of bacteria that 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 considered a rare condition that 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 with irritable bowel syndrome, metabolic disorders, dysmotility disease, neuromuscular disease, and other conditions related to the digestive, liver, and biliary systems. Statistics show that patients undergoing abdominal surgery, bilateral truncal vagotomy, gastrectomy, and other related surgical procedures have a greater risk of developing SIBO. Age-associated decline in gastrointestinal motility also makes the elderly a high-risk population.

Gallbladder Removal

All surgeries run the risk of contributing to SIBO. Still, cholecystectomy is not only a surgical procedure that 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, prescribing 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 two years to 12 years is statistically proven that there is an increased incidence of SIBO. The reason 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 causes constipation and 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 enzymes 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 maybe a consequence of surgery.

  • Small intestinal obstruction – blockage that keeps food or other liquids from passing through the small intestine or the colon
  • Diverticula – a condition where pouches form in the duodenum, jejunum, or colon wall. These pockets can harbor bacteria and lead to SIBO symptoms.
  • Fistulae – an 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 the small intestine
3. Motility disorders

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

  • Scleroderma – a type of autoimmune disease that involve the hardening and tightening of the skin
  • Gastroparesis – a 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 – increase bacterial colonization in the duodenum and slow intestinal transit. This is one reason why using the best probiotics for SIBO natural treatment is important.
  • Immunosuppressant medications – affect 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 is 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 clinical or research testing:

  1. Bacterial Culture

This is the most direct way to analyze 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 obligate anaerobes cause overgrowth
  • The 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 is 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 provide 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 toward the type, dose, or duration of the antibiotic regimen
  • No consensus on the meaning of clinical response to antibiotics
  • Over-prescribing of antibiotics
  • Risk of severe 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 tools for possible SIBO cases, addressing the condition is a challenge. As SIBO often co-exists with other GI disorders, defining a typical patient and identifying a treatment protocol is difficult. Nevertheless, there are three clear goals to help resolve SIBO:

1. Antibiotic therapy

Antibiotic treatment is still the most popular route to address SIBO. However, a variety of bacterial strains are found simultaneously in a patient, and each one has a different reaction and sensitivity to antibiotics. Therefore, many doctors 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.

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 is believed to be superior to antibiotics used, as exhibited in numerous experiments.

  • Certain probiotics exert anti-inflammatory effects and help reduce the 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 that address motility issues due to SIBO.

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

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 signaling 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 healthier digestion. Since it helps alleviate symptoms like stomachache, dyspepsia, bloating, and heartburn, it may also be prescribed for other digestive and biliary conditions.

Organic Ginger Root is also known to 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 a blood thinner.

You may create an account in Wellevate to order these supplements, or you may just get it from Amazon.

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 address causes like blind loops, bowel obstruction, multiple small intestinal diverticula, fistulae, and many more. Specialized non-transplant surgeries can also improve intestinal motility, normalize intestinal transit, or increase the mucosal surface area of the gut.


One of the most effective natural treatments for SIBO is probiotics.

1. Bacillus coagulans

These gram-positive bacteria can pass through the stomach in their spore form and multiply rapidly in the intestines. This helps eliminate pathogenic organisms while replenishing the number 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, bile, and pancreatic juices. This makes it an excellent support for the microbiome of both the upper and lower gastrointestinal tracts. Saccharomyces boulardii has also been proven to relieve diarrhea, IBS, and other intestinal and bowel infections. Saccharomyces boulardii can be taken with antibiotics with no problem, making 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 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 relieve bloating and abdominal pain and improve bowel movements. This probiotic is named as such because it thrives most in babies’ intestines 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

These probiotic bacteria are present in large amounts within our intestine and colon as it aids in the absorption of nutrients and 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 digestion and helps maintain a healthy gut. Aside from relieving common digestive problems like gas, bloating, cramping, constipation, and diarrhea, it also enhances immune function, promotes brain development, reduces inflammation, and improves cognitive health.


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