Functional Medicine Associates on SIBO

Small Intestinal Bacterial Overgrowth (SIBO)

Everything you need to know

Do you feel uncomfortable within hours of eating a meal?

Does your stomach get so bloated that you feel you have to unbutton your trousers?

Do you regularly wake up with a flat stomach and by the end of the day look as if you are 6 months pregnant?

Swelling, bloating, gas, belching and abdominal pain are all signs that your intestinal tract is not functioning as it should.

These signs and symptoms are commonly attributed to IBS of which you may have been diagnosed with. But did you know that the majority of IBS sufferers could be strongly linked to SIBO, Small Intestinal Bacterial Overgrowth.

SIBO is a condition that we, at Functional Medicine Associates are seeing and having to treat more and more.

What is Small Intestinal Bacterial Overgrowth? (SIBO)

Where does the bacteria come from?

What can SIBO do to you?

What are the symptoms of SIBO?

How is SIBO treated?

Functional Medicine Associates Approach to Resolving SIBO

What is Small Intestinal Bacterial Overgrowth? (SIBO)

Small Intestinal Bacterial Overgrowth (SIBO) as the name simply suggests, is the overgrowth of bacteria in the small intestine. The gastrointestinal (GI) tract normally contains many different species of bacteria and other micro-organisms (collectively known as the gut microbiome), with the largest numbers of bacteria found in the colon (end part of the large intestine) and lower amounts in the small intestine.

SIBO is not a diagnosis of a disease but rather it is a consequence of other bodily dysfunction or existing disease. This means that you ideally need a two phased approach for treating SIBO:

· treat the excess bacteria

· then find and try to treat the root cause of the SIBO.

This may mean that you can have relapses if the underlying condition is something that you cannot fully resolve and therefore has to be managed.

Where does the bacteria come from?

SIBO is the overgrowth of non-pathogenic, opportunistic bacteria in the small intestine as a result of many causes but most commonly, post-infectious IBS (food poisoning) where the motility of the gut has been damaged, but can also occur under high stress with or without the post infectious IBS. In fact, you may have been on holiday and had food poisoning and seemingly recovered but that could have been the start of the development of SIBO.
Other causes of SIBO are an imbalance of good and bad bacteria (dysbiosis), or an overgrowth of bacteria. It may also be caused by a dysfunctional ileocaecal valve (the valve that attaches the small intestine to the large intestine). When this valve is not functioning optimally it allows bacteria to move from the large intestine back up into the small intestine. We call this retrograde bacterial growth.

We must also consider things that cause dysbiosis, such as:

  • Other infections from fungus.
  • Parasites.
  • Mold.
  • Environmental toxins.
  • Stress.
  • Bacteria can also come from the mouth via infection or poor oral health. Over the last few years at Functional Medicine Associates, we have become more involved with oral and dental health. Now that we can test the bacteria in the mouth, we cannot overstate the importance of keeping your mouth and teeth clean through good lifestyle habits and choices. The health of the mouth and teeth influence the health of the body. If you want to know more about testing the bacteria in the mouth click here to see our recent article on the subject.
  • Low stomach acid.
  • Dysfunctional or improper chewing and of course eating too quickly as most of us do.
  • Medications used to treat high stomach acid.
  • Low amounts of other digestive enzymes can cause food to accumulate and feed bacteria.
  • Adequate fluids and unrestricted gut motility are an essential part of making sure that contents such as food and bacteria are moved along and out of the gastrointestinal tract.

In many cases, there can be so many causes of SIBO that cannot be separated. Because of this it is often misdiagnosed and/or missed as a symptomatic cause of IBS or other disease processes. It is therefore important to consider SIBO when other GI treatment plans have failed or are not progressing.

What can SIBO do to you?

You have Small Intestinal Bacterial Overgrowth if the numbers of bacteria on test results in your small intestine are significantly higher than normal.
The excess bacteria feed off undigested or recently ingested food (particularly sugar containing foods such as carbohydrates) in your small intestine, fermenting the sugars in them to produce hydrogen gas. Hydrogen that is produced is used by another species of bacteria called Archae to make another gas Methane. Other bacteria such as Sulphur reducing bacteria make Hydrogen Sulphide (HS2) which can also cause SIBO.

Any of these gases individually or combined can cause the bloating, constipation and/or diarrhea and tummy pain which are common symptoms of SIBO, thus making it the most common cause of Irritable Bowel Syndrome (IBS) ~60-70%.

Aside from the IBS symptoms we have discussed, these overgrown bacteria can wreak havoc because they absorb the nutrients meant for us. These nutrient deficiencies can lead to:

  • restless leg syndrome,
  • pain issues from B12 deficiency,
  • increased levels of the B vitamin Folate,
  • rashes and eczema,
  • gross malnutrition,
  • weight loss,
  • anemia,
  • thyroid problems,
  • poor sleep
  • anxiety

The above conditions are seen commonly in many of our patients at Functional Medicine Associates.

What are the symptoms of SIBO?

Some people with SIBO may not have any symptoms at all whilst, others will experience symptoms similar to irritable bowel syndrome as stated above.

We have seen a few cases where we only discovered the SIBO due to their link with other systemic issues such as Iron deficiency anemia and fat malabsorption issues. While symptoms predominantly affect the gut, SIBO can also cause symptoms in other systems of the body and even in the brain.

The SIBO bacteria also excrete acids that are toxic to the brain and can cause neurological and cognitive problems. Many patients experience what they describe as brain fog and we find this a very consistent symptom in SIBO patients.

10 Symptoms of SIBO
  • Diarrhea
  • Flatulence
  • Tummy pain
  • Bloating
  • Constipation
  • Belching
  • Nausea
  • Reflux – heart burn
  • Malabsorption of food and nutrients – especially fats
  • Weight gain, weight loss
10 Extra systemic Symptoms of SIBO
  • Rash (rosacea)
  • Headache
  • Body pain
  • Fatigue
  • Depression
  • Anxiety
  • Brain Fog
  • Tingling and numbness in arms and legs
  • Anemia
  • B12 deficiency
10 ways the body naturally protects from SIBO?
  • Normal forward-moving muscular waves of the intestines called the migrating motor complex.
  • Adequate levels of stomach acid and bile acid secretions which destroy microbes before leaving the stomach.
  • Pancreatic juice, enzymes and bile also act to further destroy bacteria in the small intestine.
  • Correct gut motility, by nerves and interstitial cells.
  • A properly functioning Ileocecal valve which prevents bacteria moving from the large intestine back into the small intestine.
  • A good level of intestinal mucus that traps bacteria.
  • Normal levels of immune proteins that prevent the growth of bacteria.
  • Reducing the amount of stress.
  • Chewing foods well.

What are the risk factors for SIBO?

There are many diseases and disorders that are associated with SIBO, 90% of which comprise disorders that slow down the small intestines’ ability to move things along the gastrointestinal tract.

10 risk factors associated with SIBO
  • Leaky gut and a slowing down of gastric motility of the gut which can both be caused from stress and anxiety.
  • Reduced or low stomach acid levels. This is also known as hypochlorhydria.
  • Disorders of the gut which reduce blood into the area.
  • Medications such as Antacids and antibiotics.
  • Age related changes.
  • Dysfunction to the valve that separates the large and small intestine, the ileocaecal valve. This valve should stop the contents of the large intestine coming back into the small intestine. For some people the valve does not shut as it should.
  • Fibromyalgia.
  • Under active thyroid.
  • Structural abnormalities (which are all associated with a small intestinal obstruction and stagnation).
  • Chronic fatigue syndrome.
10 diseases associated with SIBO

Certain chronic conditions and diseases are associated with a higher risk of having SIBO in part due to their effect on the GI tract.

  • Autism
  • IBD
  • IBS
  • Liver disease
  • Connective tissue disorders
  • Short or excess bowel
  • Structural abnormalities of the Gut
  • Diabetes
  • Auto- immune disease
  • Celiac Disease
How is SIBO Diagnosed?

Testing for SIBO is not always essential and many clinicians may look to simply diagnose based on a patient’s symptoms. The previous “gold standard” for testing for SIBO is a procedure where a tube is put down the mouth into the small intestine from which a sample of bacteria is taken. This is an invasive procedure and as such is not usually performed.

A less invasive procedure, the SIBO breath test, is more commonly used to diagnose SIBO. This simple test can be performed at home by the patient using the test kit and is designed to test for Hydrogen and Methane (humans do not produce these gases, they can only be produced by the bacteria present in SIBO). SIBO can also be inferred but not diagnosed from performing a stool analysis.

A SIBO breath test result

At Functional Medicine Associates, we use a SIBO breath test that requires the patient to drink a sugar solution and then perform a series of breath tests over a 3hour period. If there are higher than normal levels of bacteria in the small intestine these bacteria will ferment the sugars and create the gases hydrogen and/or methane, which in turn will be present in the patient’s breath at specific parts per million (ppm) indicating a positive SIBO result.

Sometimes there can also be Hydrogen Sulphide gas produced, resulting in a “flat line” (0 to 3ppm) for all of the gases.

In our experience testing is very motivational for patients who prefer to know that there is actually something causing their symptoms. We also find that tracking through testing reduces the number of patients who relapse. Testing also makes the strategy more accurate as the respective gases present help to determine the priority and order of the supplements used because different gases respond to different treatments. The gases also have certain symptoms that are more common to each. Testing also helps to clearly identify SIBO or rule it out as a symptomatic cause.

Some Common Characteristics of the Three Gases

Hydrogen dominant SIBO

Is more associated with diarrhea in about 40% of IBS related patients.

Provides the Hydrogen needed for archaea to make methane (CH4) and sulfur reducing bacteria (SRB) to make hydrogen sulfide (H2S).

People with Hydrogen dominant SIBO can be the most reactive.

Methane dominant SIBO

Is more associated with constipation and is generally slower to respond to treatment because it takes time for the archaea to convert the Hydrogen gases. Methane is also produced by the commensal Archaea bacterial family. Decreased motility of the gastro intestinal tract and lactose malabsorption are associated with increased archaea. They are very challenging to kill and typically respond to stronger herbals like Allicin.
Its prevalence is about 35% in people with SIBO. Methane naturally slows everything down decreasing gut motility, increasing constipation and further bacterial overgrowth.

We also have to consider that yeasts like Candida in SIBO as it can be a substrate for Methane production.

Hydrogen Sulfide SIBO

Associated with a flat line on lactulose test.

Produces “rotten egg” smelling wind and defecation that can increase with Sulphur containing foods like brassica vegetables (broccoli, cauliflower, Brussel sprouts).

Patients develop an intolerance to Sulphur containing foods, supplements, and medications, which increase symptoms, one of which is reddish face.

Are you looking to boost your overall health? Interested in how functional medicine can help you? Sign up to our free 5 steps to a healthier you here.

Sign up to receive my 5 steps to a healthier you!


* indicates required

By clicking the subscribe button you agree to our privacy policy.


When you sign up to receive these 5 steps, you will also be signed up to our newsletter. You will receive occasional functional medicine news and advice.*