Symptoms of SIBO & Best 3 Bacterial Overgrowth Treatment Options

What Causes SIBO?

Many symptoms of SIBO are often confused with those generally associated with some other disease. Clarity on what causes SIBO can lead to a better understanding of the condition known as small intestinal bacterial overgrowth which may present symptoms very similar to other diseases and conditions.

Normally, the bacterial count in the small intestine is quite low, i.e. 10per ml or less. When there is an excess of naturally occurring intestinal bacteria in the small intestine, SIBO (small intestinal bacterial overgrowth) happens. Blind loop syndrome is sometimes used to describe the condition.

Bacteria are found in both the large and small intestines and are essential for the normal functioning of the intestine with regards to digestion and immunity. Under normal conditions, there are more bacteria in the large intestine (colon) than in the small intestine.

In the small intestine digestive juices mix with food which helps it move through the intestines quickly. SIBO develops when stagnant food in the small intestines becomes the breeding ground for bacteria to multiply.

Some of the factors that contribute to the risk of developing an overgrowth of bacteria in the small intestine include, but are not limited to:

Sluggishness of the small intestine: Inadequate propulsion of the contents of the small intestine can lead to bacterial overgrowth over a period of time. Causes are for example:

  • A neurological or motor sluggishness of the muscles of the small intestine in various diseases, such as systemic sclerosis (scleroderma), cystic fibrosis, celiac disease, radiation enteritis, diabetes, Crohn’s disease, a bowel obstruction (subileus)
  • Gastric acid suppression consuming acid blockers. A consequence is an elimination of the bactericidal (bacteria-killing) milieu in the stomach
  • Immune deficiency in severe diseases or diseases of the immune system
  • Small bowel disease, including irritable bowel syndrome (IBS)
  • Liver Cirrhosis: SIBO in cirrhosis is attributed to a motility abnormality. It increases the risk of hepatic encephalopathy and spontaneous bacterial peritonitis
  • A major mechanism leading to the consequences of maldigestion (impaired nutrient digestion) and malabsorption (impaired nutrient absorption) is the bacterial decomposition of food components and bile acids. As a result, sufficient bile acids are no longer available for the digestion and absorption of fats and fatty acids which may lead to a vitamin B12 deficiency.
  • Complications arising from abdominal surgeries such as gastric bypass and gastrectomy
  • The lining of the small intestine is damaged
  • Problems in the small intestine such as intestinal adhesions and intestinal diverticulosis
  • Amyloidosis
  • Parkinson’s disease
  • Hypothyroidism

symptoms of SIBO

Symptoms of SIBO

Bacterial overgrowth of the small intestine can be asymptomatic, but can also lead to variable symptoms:

  • Abdominal bloating may be caused by excess bacteria in the small intestine, the result of food that was only partially digested entering the small intestine. The bacteria feed on the nutrients and may cause malabsorption. This can result in the mucosal barrier of the bowel breaking down and causing inflammation. The symptoms then experienced are bloating, gas, pain, and inflammation.
  • Loss of appetite may be attributed to nausea experienced due to SIBO or a person may be feeling unusually full and uncomfortable after they ate.
  • Abdominal pain which is experienced after a meal is one of the common symptoms of SIBO. During digestion methane and hydrogen, gases build up in the bowel causing abdominal pain.
  • Nausea is not only linked to a blocked intestine but often is one of the symptoms associated with various other conditions such as motion sickness, concussion, appendicitis, migraines, etc.
  • Constipation may be because of methane gas building up in the small intestine
  • Diarrhea may be caused by a bacterial infection known as gastroenteritis. Viral and bacterial gastroenteritis symptoms may include fever, bloody diarrhea, dehydration, electrolyte imbalance, vomiting, and nausea
  • Fatigue due to malnutrition. Malnutrition occurs when vitamins and minerals cannot be absorbed optimally in the small intestine due to excess bacteria. Malnutrition can also lead to NASH (Non-alcoholic Steatohepatitis) which is “A type of liver disease in which fat builds up in the liver of people who drink little or no alcohol. This causes inflammation of the liver and damage to the cells in the liver, which may lead to cirrhosis (scarring of the liver) and liver failure. People with NASH are at increased risk of developing liver cancer.” – Source
  • Unintentional weight loss (losing weight which is noticeable but without any intention to). Losing weight when unintentional may be a symptom of a more serious illness like diabetes or cancer

Many of the symptoms of SIBO may resemble many other gastrointestinal (GI) conditions.

The symptoms of SIBO can differ from one person to another. It depends on the severity of the overgrowth of bacteria and whether a person has any other coexisting condition.

Why Stomach Acid Is Good For You

SIBO Diagnosis

In order to assist with diagnosing SIBO, the doctor will inquire about the patient’s symptoms as well as their medical history.

A physical test involves touching the abdomen to determine the presence of gas or bloating. If the presence of SIBO is suspected, testing to check for bacterial overgrowth will be recommended.

The 2 most common tests are 1) breath testing and 2) small intestine aspirate and fluid culture technique.

Hydrogen-based breath testing

The patient is given a mixture of water and glucose (or lactulose which is a sugar that can only be broken down by the bacteria found in the gut) to drink. The test measures how much hydrogen and methane is present in a person’s breath when they breathe into different tubes at set intervals for a few hours.

While this test proves to be quite popular because it is non-invasive, cheap, and easy to use as a means of testing for SIBO, it is not 100% accurate in confirming bacterial overgrowth.

Hydrogen-based breath test


When using glucose, the breath test has a sensitivity of 62.5% and a specificity of 81.7%. while the lactulose test has a sensitivity of 52.4% and a specificity of 85.7% when compared with the direct aspiration method (small intestinal aspiration and culture technique) – Source.

SIBO may be indicated when there is a quick rise in the hydrogen or methane that is exhaled. Hydrogen and methane are the results of bacteria interacting with sugar.

To obtain accurate results, however, there are some limitations such as:

  • the patient must maintain a low fiber diet for 24 hours before the test
  • sleep, exercise, and smoking may affect the accuracy
  • medications such as laxatives and antibiotics must be avoided before the test
  • the breathing sampling frequency is highly variable
  • the malabsorption of carbohydrates may give a false-positive result

Small bowel aspirate and fluid culture technique

Although invasive, and more expensive, this technique is a more accurate way of checking for small intestine bacterial overgrowth.

In order to acquire the fluid sample, an endoscopy is performed. This means a thin flexible tube (endoscope) is inserted through the mouth down the throat and the upper digestive tract to the small intestine. A sample of the intestinal fluid obtained here is then sent to a laboratory where it is analyzed for the presence of bacteria.


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As with the breathing test, this technique also has its limitations:

  • invasive
  • cumbersome
  • expensive
  • time-consuming
  • technical difficulties with the transport and culture of the aspirate
  • the aspirate may get contaminated by oral bacteria
  • location of sampling and amount of the fluid may be variable, etc.

The treating doctor may opt for other tests when existing tests prove not to be accurate. Other tests that may be performed include:

Other tests
The existing tests for SIBO are not always precise, so a doctor may recommend other tests to get a better picture of someone’s digestive health. These could include:

  • blood tests to check for a vitamin deficiency
  • imaging tests (x-rays, CT scan, MRI) to ascertain if there are any structural abnormalities in the small intestine
  • performing an intestinal permeability test to determine if the intestinal lining is “leaky“
  • stool tests to test for the malabsorption of fat

SIBO Treatment

Most importantly, the treatment of SIBO should have as its main goal to correct the bacteria in the gut to normal levels. Achieving this can bring relief from the symptoms of SIBO as it can lead to the absorption of more nutrients from food.




The initial method, most widely used, is to modify GI (gastrointestinal) microbiota by taking antibiotics. Treatment by antibiotics largely depends on the results obtained from the test(s) performed to measure the bacterial overgrowth.

Which antibiotic to take is largely determined by whether the sample indicated higher levels of hydrogen or more methane.

When hydrogen is at a higher level, the antibiotic rifaximin (Xifaxin) is generally prescribed. For higher levels of methane, rifaximin taken together with neomycin (Mycifradin) is the choice of antibiotic treatment.

The consulting doctor may switch between different kinds of antibiotics; thus preventing bacterial resistance. Antibiotic treatment may turn out to be long-term for some as bacteria can return once a patient stops taking antibiotics.

Other antibiotics used include Amoxicillin-clavulanic acid (Augmentin), Ciprofloxacin (Cipro), Metronizadole (Flagyl), Norfloxacin (Noroxin), and Trimethoprim-sulfamethoxazole (Bactrim).

Antibiotics will reduce bacteria in the gut, but will, unfortunately, not cure the condition that initially caused the bacterial overgrowth. Once an underlying condition (see causes of SIBO) has been determined, that condition needs to be treated.


The use of probiotics, (fungi and bacteria that have a beneficial effect on the microbiome) as an effective way of bacterial overgrowth treatment, is still controversial.

Probiotics, can, however, stabilize the intestinal wall and improve the symptoms of SIBO in some instances.

On the other hand, probiotics may cause or worsen bacterial overgrowth in people with low motility.

More research is necessary to demonstrate the effectiveness of probiotics.

SIBO Diets

When a small intestinal bacterial overgrowth diet is considered as a treatment for SIBO, there are a few things you should know. The diets have the main objectives of reducing symptoms and learning which foods trigger the symptoms of SIBO.

At this time there are 2 diet treatments for SIBO available, namely the low-FODMAP diet and the elemental diet.


This is an eating plan that is supposed to be followed temporarily only. FODMAP refers to a diet low in short-chain carbohydrates (sugars) that can cause intestinal distress because they are poorly absorbed by the small intestine. FODMAP stands for “fermentable oligosaccharides, disaccharides, monosaccharides, and polyols”.

The FODMAP diet works by avoiding high FODMAP foods during what is known as the elimination phase. The duration of the elimination phase is largely determined by the extent of the SIBO symptoms and could be as short as 2 weeks or as long as 8 weeks.


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Foods that contain any one of the 5 different types of FOPMAPs are regarded as high-FOPMAP foods. Foods that contain either 1. fructans (found in a variety of fruits and vegetables), 2. fructose (found in corn syrup and honey), 3. galactans (legumes), 4. lactose (dairy products), or 5. polyols (found in some fruits and veggies) and must be avoided during the elimination phase include, but are not limited to:

  • dairy products contain lactose (milk, ice cream, and yogurt ),
  • beans, lentils, chickpeas contain galactans
  • veggies (asparagus, garlic, onions, cauliflower, peas, butternut squash, mushrooms, artichokes),
  • wheat-based foods (crackers, bread, barley, grains, cereal),
  • fruit (pears, peaches, apples, cherries), etc.

During the elimination phase, the symptoms of SIBO should decrease. Foods that you can include in your diet during the elimination phase are low-FOPMAP foods such as:

  • Dairy (almond milk, hard cheeses, soy milk, feta)
  • Fruits (grapes, kiwi, cantaloupe, strawberries)
  • Grains (oats, quinoa, corn pasta, corn flakes, rice cakes, barley-free bread)
  • Nuts and seeds (macadamia nuts, peanuts, sunflower seeds)
  • Protein (eggs, tempeh, seafood, firm tofu)
  • Vegetables (cucumbers, eggplant, green beans, lettuce, potatoes, tomatoes, zucchini)

Once the elimination phase is complete, the reintroduction phase starts. During the reintroduction phase, you slowly (every few days so you can check if symptoms occur), and one by one, start to add the different FODMAP types back into your diet. It is done this way to help pinpoint which of the FODMAPs trigger your SIBO symptoms. This is best monitored by keeping a diary of what you eat.

It is not recommended to stay on the FODMAP diet long-term. A lot of the high-FODMAP foods are essentially good for a person’s overall health. Many of these foods are regarded as prebiotics which means they improve the balance of intestinal bacteria.

SIBO Elemental Diet

Since this diet carries some risks it should only be followed under medical supervision.

The elemental diet involves the consumption of a special liquid formulation containing nutrients that are in their elemental (primary) form (or as close as possible to it) and in an easy-to-digest form. The formula is designed to replace solid foods and become a person’s only source of nutrients for a period of up to 4 weeks, depending on the severity of the SIBO symptoms.

Since the symptoms of SIBO are related to the overgrowth of bacteria in the small intestine, the main objective is to no longer feed the bacteria and cause the overgrowth to worsen. One wants to, however, still make sure the patient consumes those nutrients that are required to maintain a healthy body.

elemental diet

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For those patients who are reluctant or unable to commit to the full elemental diet (and with the approval of the medical professional under whose care the patient is), there is the option of a partial elemental diet. In this instance, the nutritional requirements of patients come from both the liquid part and from foods that they know they can tolerate.

Elemental formulas contain proteins, carbohydrates, fats, minerals, and vitamins. The formulas are available over the counter as well as on prescription. It is strongly advised to only follow the elemental diet under medical supervision as the medical professional can determine which formula will provide enough nutrition to adequately address your specific symptoms.

The elemental diet can also benefit people afflicted with other digestive issues apart from SIBO.  These are eosinophilic esophagitis, Crohn’s disease, ulcerative colitis, cancer, and radiation-induced diarrhea.

NOTE: SIBO cannot be cured by following a particular diet. Following a diet, may provide some welcome relief from the symptoms of SIBO but does not treat the underlying condition that caused it.

When you follow a SIBO diet is it recommended to drink more water as this will ease digestion and also reduce pain.

In the event, your symptoms worsen after implementing any of the SIBO diets, immediately seek medical attention.

Complications associated with SIBO

Treatment of SIBO is possible, but the condition may recur. When left untreated, SIBO may lead to dehydration, nutritional deficiencies, weight loss, and malnutrition. It is, therefore, vital to get treatment as soon as possible to avoid these complications.

These complications can subsequently affect other aspects of a person’s health, such as energy levels, mental health, and hormones.

Can One Prevent SIBO from Coming Back?

One cannot always prevent SIBO from recurring, but there are a few things one can do to keep our gut healthy and so minimize the recurrence. Some of these include:

  • Regularly follow a nutrient-rich diet with lots of fiber and probiotic-rich foods to maintain gut health.
  • Refrain from eating between meals. Spacing meals with 3-5 hours between them gives the small intestine time to push the food through to the large intestine.
  • Do not eat before bedtime for a minimum of 3 hours. This will improve motility and allow MMC (migrating motor complex) to take place in the small intestine by clearing it out while a person sleeps.
  • Get moving throughout the day. No use killing yourself with 20 minutes of intensive training and then sitting for the rest of the day. Take a short walk every 20 minutes if possible.
  • Maintain healthy stress levels. When a person is stressed, a variety of hormones are released. These then trigger the contraction of the muscles in the GI sphincter which in turn reduces motility and causes the transit of food in the stomach and small intestines to slow down.
  • Quit smoking. Products like cigarettes that contain nicotine may alter the composition of the flora in a person’s gut.
  • Manage any other condition you may have. When someone has a condition that is related to SIBO, such as diabetes or hypothyroidism, the effective management of these could reduce the impact they may have on the person’s digestive system.



You are encouraged to talk to your doctor before taking dietary supplements. Any mention in this article of a specific product does not represent an endorsement of that product.