Functional Medicine on SIBO

Aug 22, 2019

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.

Hydrogen Sulfide SIBO can cause halitosis and periodontal disease, fibromyalgia and colon cancer. It is associated with Chronic Fatigue Syndrome as elevated hydrogen sulfide is toxic to the mitochondria. Mitochondria are the power plants of our cells and so if they do not work well, we do not provide energy to our bodies well. In effect Brain fog and short-term memory loss can be associated mitochondrial issues within our brain.

Other symptoms we see is Orthostatic hypotension (POTS), Arrhythmias, Low blood pressure, night sweats, hot at night. We also find that patients may suffer with a painful bladder because Hydrogen Sulphide is an irritant to the destrusor muscle of the bladder. Patients could also experience more parts of their bodies that feel numb (paresthesia’s) but also more places where they have pain, especially on the joints.

Bacteria, yeast and fungus can form a biofilm, which is an extracellular matrix (like a really solid house) that protects the bacteria fungus or yeast from our innate immune system killing them and through which nutrients and even DNA are shared. When you have bacterial overgrowth, you likely have fungal or yeast overgrowth as well. If treatments such as antimicrobials, probiotics and diet are not working, we must consider bacterial, fungal or yeast biofilm production. It has been shown clinically that treating the biofilm, in addition to treating the bacteria or fungus, can be the difference between success or failure in clearing the bacteria, fungus or yeast.


How is SIBO treated?

At Functional Medicine Associates the approach to treating SIBO always takes the whole individual into account. This holistic and systemic approach is essential to ensure that all of the possible associations relating to the patient’s health history, symptoms and other possible diseases are considered.

It is important to remember that SIBO is the result of the dysfunction of something else. The first step is to find out if your symptoms are actually caused by SIBO. As explained, this can be done using the SIBO breath test kit. If the patient
tests positive for SIBO then dealing with this bacterial overgrowth would be the first step in treating it.


At Functional Medicine Associates we have developed a simple approach for testing and treating SIBO.

We recognise that it is impossible to have a “one size fits all” approach with SIBO because patient symptoms are along a spectrum and everyone is different. Each patient’s plan should be personalised not formulaic and should be realistic with regards to outcomes. Eliminating the bacteria is not always possible with some patients as there may be another underlying cause of the SIBO. If you have an underlying condition, you will need treatment for this also, if possible.

Based on our experiences with patients many can self-treat by following these recommendations for a DIY type approach at home.

  • Mindful eating, chewing slowly and reducing eating on the run.
  • Taking digestive enzymes.
  • Identify and reduce additional stressors while eating and throughout the day.
  • You will likely want to reduce the amount of fermentable carbohydrates in your diet.

Functional Medicine Associates Approach to Resolving SIBO

Our approach has been honed and consistently researched over the last 5 years. We have also had enough time to work and learn with patients and we have found that there is never a 1 size fits all approach. Because of this we recommend testing and consultations.

This can be arranged by contacting us.

Our SIBO approach in brief

  • Test: Do you have SIBO or Not?
  • Enzymes: Ensure there are sufficient enzymes in order to properly digest your food
  • Starve: Cut off the food chain that feeds the bacteria causing SIBO
  • Liver: Provide the right nutrients for optimal liver function
  • Attack: Use anti-microbial treatments to eliminate the overgrowth of bacteria
  • Restore: Help the gut lining and microbiome recover to full strength

Test: For those who want to test, see detailed description of testing in “How is SIBO Diagnosed” above. For those who do not want to test, follow the recommendations for SIBO DIY. It can be confusing to follow information on the internet because there are so many different recommendations. Try these steps to see if you get alleviation of symptoms. Sometimes, diet is all that needs to be changed to alleviate the bulk of your symptoms. It is important to note that certain antimicrobials may need to be ordered by a licensed practitioner. Thus, we will not make recommendations on antimicrobials here, rather give you information on how to optimize your digestion and motility.

Enzymes: Often stomach acid and pancreatic enzymes can be low because of stress, improper chewing, rushing to eat and previous food poisoning. This leads to food that is not digested which will stimulate bacteria to grow and feed on the undigested food. Enzymes are needed to ensure that foods are digested well in order to reduce this potential as well as to maintain proper enzymatic secretions in general.

Starve: SIBO is an overgrowth of bacteria in the small intestine and the first step in treatment is to starve the bacteria of their food source. Although there are a number of SIBO diet protocols available (see below) the main foods that feed the bacteria in the small intestine are carbohydrates such as sugar, alcohol, certain grains and wheat products. This includes refined carbohydrates such as bread, cookies, cake but also includes complex carbohydrates such as whole grain and legumes which are also broken down into sugar in your gut. This is always on a case by case basis, as some patients are less tolerant to certain carbohydrates than others.

SIBO Diets to consider

There are a number of different dietary approaches to treating SIBO. All of these remove carbohydrates in differing amounts ranging from least restrictive to most. The choice of dietary approach is in part determined by the results of your SIBO test, your symptoms and your ability to tolerate carbohydrates. Start somewhere and personalise your approach with a practitioner. It is important to note that these diets are only meant to be maintained for the duration of SIBO treatment and it might be best to change between diets while treating if the SIBO has not resolved. Keeping a restricted diet like this limit’s macronutrient and micronutrient diversity and ultimately, the biodiversity of the microbiome.

  • Fodmaps
  • Specific Carbohydrate diet
  • Elemental diet
  • GAPS diet
  • Cedars Sinai diet
  • SIBO diets developed by SIBO researchers such as Dr Allison Siebecker, Dr Nirala Jacobi

Liver and Gallbladder: These organs are often sluggish and or congested where SIBO is concerned. The liver doesn’t produce enough bile that ultimately breaks down fats and the gallbladder can become delayed in secreting bile. Bile salts can also be broken apart by the bacteria all of which leads to increased fat malabsorption. Additionally, the liver’s ability to detoxify can be damaged by the presence of gram (-) bacteria that have the ability to cause inflammation with their lipopolysaccharide (LPS) coating that is toxic. This can result in increased level of toxins meant for excretion to come back in the circulation. Thus, optimizing both is essential to treating SIBO successfully.

Attack: Some clinicians use antibiotics to attack the overgrown bacteria however SIBO can be treated successfully using herbal antimicrobials. Depending on the type of gas present, this will be either a mono or dual therapy and there can be a rotation of different antimicrobials for successive rounds if needed.

Restore: SIBO can cause damage to the intestinal wall with their toxic by-products and the endotoxin, LPS, that coats the gram (-) bacteria. Nutrients that may be deficient such as Vitamins A + D and B vitamins can also result in lowered gut integrity. It is therefore important to follow the treatment with a restoration protocol.

In Summary

A recent paper published July 2019 in the Journal Gastrointestinal Disorders questioned the whole idea of IBS. Stating that IBS was likely an umbrella diagnosis for many aspects of GI disorders and can well be treatable.

SIBO is one of the most common causes of IBS, maybe up to 70% of all cases. It is also misdiagnosed and or missed as a symptomatic cause of IBS or another disease process. For all those people who suffer from IBS symptoms or have a diagnosis of IBS and have not responded to their conventional treatments we would recommend testing for SIBO.