What Actually Causes SIBO? [Learn the Main Causes of SIBO to Test For]

What causes SIBO?

If you’ve had chronic bloating and diarrhea and are intolerant of many foods, you may be curious about small intestinal bacterial overgrowth (SIBO). Maybe you’ve been diagnosed with irritable bowel syndrome (IBS) or gluten sensitivity but feel like there is more to your symptoms.

If so, then it’s vital that you understand what causes small intestine bacterial overgrowth (SIBO), to see if one of these issues could be causing your symptoms.

What is SIBO?

SIBO is an overgrowth of bacteria in the small intestine. While we naturally have a vibrant microbiome in our small gut, there should be only about 103 bacteria per mL. In SIBO, this number increases to more than 105 – 10bacteria per mL.1

You can read more about SIBO here.

So, What Causes SIBO?

causes of sibo

Now that we know more about SIBO, let’s get to the meat of the issue: what causes SIBO?

There are two underlying mechanisms that contribute to SIBO by increasing bacteria in the small intestine:

1. Small Intestinal Dysmotility

A healthy GI system is in motion. The gut moves via peristalsis- irregular and forceful movements after eating- and the migrating motor complex (MMC)- coordinated movements every 90-120 minutes during fasting.2

These work in conjunction to move food, bacteria, and debris from the intestines. SIBO occurs if either system is impaired.

Motility disorders, excessive stress, and organ dysfunction can all play a role.

2. Malabsorption

 There are multiple causes. Our stomach acid not only digests our food but also suppresses the growth of ingested bacteria.2

Low levels of gastric acid (called hypochlorhydria) can be caused by Helicobacter pylori infection or acid-suppressing medicines like omeprazole.3

Other underlying causes of malabsorption include decreased secretion of bile acids and pancreatic elastases (which also are vital in absorbing our food) which cause an imbalance in the gut bacteria.

Finally, any process that damages the small bowel mucosa- the site of food absorption- can contribute to SIBO.

Delving deeper, we find there are four main categories of diseases that incorporate one or both of underlying causes in SIBO:

1. Motility Disorders

Motility disorders affecting the gut are a major underlying cause of SIBO. Many metabolic and organ disorders (see below) lead to motility problems. For example, scleroderma is an underlying SIBO cause in up to 62% of patients.3

Neurological disorders like chronic intestinal pseudo-obstruction and gastroparesis also slow small intestine motility. With a slowed gut, bacteria are not cleared out, leading to stasis and bacterial growth.

2. Malnutrition and Malabsorptive Disorders

Any disorder that disrupts absorption can become a SIBO cause. If you can’t absorb your food, the bacteria will feed on it and grow.

A classic example is Celiac disease. Up to 2/3 of Celiac patients with symptoms on a gluten-free diet had SIBO.1

Other malabsorptive disorders include chronic pancreatitis, cirrhosis, and Crohn’s disease.3

Additionally, over time, the Standard American Diet (SAD), which is high in poorly digested carbohydrates and inflammatory fats, can contribute to an unhealthy gut bacteria in both the small and large intestines.

3. Anatomic Disorders

If you’ve had a gastric bypass to lose weight, abdominal surgery or have small intestine diverticula or outpouchings,1 this may be your SIBO cause.

These anatomical lesions cause a “swamp”2 in the small intestines, slowing motility and disrupting food absorption,  which induces bacterial growth.

4. Immune and Organ Dysfunction

A reduced antibody or T-cell response can increase bacterial overgrowth. This lowers small intestine mucosal immunity,  especially immunoglobulin A (IgA),1 allowing bacteria to cling to the intestinal mucosa.2

In addition, the mucosa becomes inflamed and absorbs less nutrients.

Organ dysfunction like diabetes, cirrhosis and renal failure impair the gut’s nervous system, slowing motility.

SIBO also occurs in up to 15% of elderly disabled adults due to increased medicines, health problems, and lowered immunity.1

Learn about SIBO causes with Dr. Weinstock:

Causes that disrupt MMC function

gut function

The small intestine is part of the “rest and digest” system, or the parasympathetic nervous system (PNS). The intestine is rich in nerves, so the gut is often called our “second brain.” Any dysfunction in the PNS affects the MMC, leading to bacterial stasis in the small intestine.

Another SIBO cause may be a loss of neurons that innervate the small bowel.2 Overactivation of the sympathetic nervous system (SNS) promotes the “fight or flight” response. This system kicks into overdrive when we are chronically stressed or in chronic inflammatory conditions. When the SNS is active, MMCs slow down, and bowel stasis occurs.

Other Comorbid conditions that could be SIBO causes

  • IBS-Diarrhea and IBS-MixedIBS affects up to 15% of the population.4 There is a link between IBS-D and M and SIBO, and some believe that IBS simply functions as a method to classify the symptoms. Meanwhile,  the underlying mechanism of these two diseases may be related to autoimmune nerve damage that can occur after food poisoning. (See below) Up to 84% of people with IBS had a positive lactulose breath test, suggesting SIBO,1 and up to 60% of IBS-D patients are positive for autoimmune antivinculin,2 a newer test for diagnosing SIBO.4
  • Mast cell activation syndromeMCAS is a newly discovered disorder that affects 1-17% of the population.2,5 It causes an over-activation of mast cells, inflammatory cells that release histamine and other chemical messengers to activate our immune system. The two most common symptoms are fatigue and muscle pain,2 but other common symptoms include hives, syncope, and headache. MCAS also activates the SNS, slowing the small intestine, creating an underlying cause of SIBO.
  • Postural Orthostatic Tachycardia Syndrome (POTS): this is a rare disorder that affects 170 per 100,000 people.5 It is related to MCAS and is caused by SNS overactivation when standing up. Patients can have symptoms of palpitations, syncope, headache, memory problems, and blurred vision. Underlying causes of POTS include autoimmune disorders, Lyme’s disease, Epstein Barr Virus (EBV) vaccines, Traumatic Brain Injury.2
  • Inflammation: A critical SIBO cause is chronic inflammation. It wears down our immune system, increasing organ dysfunction and illness. Systematically, it appears as fatigue and widespread muscle pain, while in the small intestine, it may manifest as SIBO. Other inflammatory conditions that coexist with SIBO are fibromyalgia, restless leg syndrome, chronic prostatitis, rosacea, eczema.2 Besides, SIBO patients may have an increased risk of anxiety and depression. Scientists are beginning to understand the importance of the gut-brain axis, a connection between the gut microbiome and cognitive brain centers 7 which explains the link between inflammatory bowel conditions and mental illness.

A special note about food poisoning

food poisoning causes sibo

After food poisoning, we all develop antibodies to the bacteria so we don’t get sick again.

Unfortunately, in about 10 percent of people with severe food poisoning, the antibodies mistake the tight junction (connections) between our gut cells for the infectious bacteria, causing our immune system to attack the interstitial cells of Cajal (the gut cells that coordinate muscle movement in the small intestine).4

Therefore, in this case, an autoimmune condition causes SIBO.

People who develop long-term IBS-D and M symptoms after food poisoning have antibodies to cytolethal distending toxin B (CdtB) and vinculin (the tight junction of our gut cells). That’s why so many IBS-D patients are positive for antivinculin, making it an excellent diagnostic test for SIBO.

A ray of hope is that about 50% of people have spontaneous resolution of their symptoms.

A Summary of Underlying Causes in SIBO

Anatomical disorders
  • Small intestine diverticula
  • Gastric resection
  • Surgical blind loops
  • Adhesions
Motility disorders
  • Gastroparesis
  • Small bowel dysmotility
  • Celiac disease
  • Chronic intestinal pseudo-obstruction
Irritable Bowel Syndrome
  • IBS-Diarrhea
  • IBS-Mixed

*Both suspected to occur from impaired motility following food poisoning

Metabolic disorder
  • Diabetes
  • Hypochlorhydria
Organ system dysfunction
  • Cirrhosis
  • Renal failure
  • Pancreatitis
  • Immunodeficiency
  • Celiac Disease
  • Crohn’s Disease
  • Recurrent antibiotics
  • Gastric acid suppression


What tests identify the underlying causes of SIBO?

tests for SIBO

Before you undergo testing, consider your symptoms:

  • Do you have inflammatory symptoms like hives?
  • Are you taking medicines or have other medical conditions that affect your gut?
  • Also, do not forget about food poisoning or other illnesses that could be a SIBO cause.

Two classic diagnostic tests are:

1. Upper GI Bacterial culture

This involves taking samples from your small bowel and culturing the bacteria. It is invasive and requires an upper GI endoscopy, and many bacteria do not grow on standard culture media, making the test often inaccurate.1

2. Breath testing

This test measures the gas produced in the intestine. After drinking a substrate (such as lactulose), your breath is analyzed for hydrogen and methane.6

Generally, a rise of 20ppm for hydrogen and 10 ppm of methane is considered diagnostic,8 but new information suggest that high methane levels may be caused by LIBO.

A new breath test will analyze hydrogen sulfide,9 which may be more diagnostic of IBS- D and SIBO and is common if you have elevated Desulfovibrio piger bacteria.

The hydrogen sulfide breath test is not yet widely available, but there is also a stool test.

Other important tests to consider:

3. IBS check test (anti-vinculin and anti-CdtB)

This test is specific for post-infectious IBS also known as SIBO that occurs after food poisoning. Remember, around 60% of IBS is estimated to be caused by food poisoning and SIBO. This will allow you to see if you developed IBS and SIBO from food poisoning.

4. Stool tests (measures large intestine microbiome)

A DNA analysis of your large gut bacteria (called polymerase chain reaction or PCR) may be especially useful for diagnosing LIBO6 (helping you to differentiate from SIBO) as it determines your gut microbiome.

However, science is still in the early stages of understanding the gut microbiome and these tests are not known as clinically valid yet.

Currently, a commercially available test is uBiome.

5. Other tests

Other tests that are important are:

  • Gluten sensitivity (celiac disease)
  • Pancreatic elastase (pancreatitis)
  • Blood count and Ig panel (immune deficiency)
  • Small bowel follow through (anatomical problems)

SIBO always occurs because of another malfunction

There are many SIBO causes, but they do not act in isolation. For example, MCAS and histamine release causes inflammation, chronic stress decreases MMC motility and diabetes can damage gut nerve cells. Many people have multiple factors that work together to create a perfect storm which causes SIBO.  It is vital that we discover the underlying causes of SIBO to stop the vicious cycle.

Go to your doctor prepared to talk about underlying causes that may be contributing to your condition. Ask him to check you for all of the potential causes that we discussed above.


SIBO has many causes, so the question: “what causes SIBO?” is essential. This is an exciting time in IBS and SIBO research because researchers and doctors alike are actively learning about the underlying causes of SIBO.

With this new knowledge, we can look forward to an improvement in the diagnosis and treatment of IBS and SIBO so we can get back to living and enjoying life.

To learn more about underlying causes, treatment, and prevention from an expert doctor click here or on the image below:

sibo master series image


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