Small Intestinal Bacterial Overgrowth (SIBO) – A Common Cause of IBS & other Health Problems

September 18, 2020 Dr. Martin Gleixner, MSc, ND No comments exist

By Dr. Martin Gleixner, MSc, ND

Digestion issues have ramifications in all aspects of our health. Despite the crucial role that digestion has on our wellbeing, chronic digestive problems are often under-diagnosed, missed or allowed to proceed without treatment for far too long. In many cases, palliative options such as laxatives or antacids aimed to alleviate symptoms are often recommended. Meanwhile, the actual cause (i.e. the main reason) for their digestive problem is neglected.

For those who have digestive issues such as irritable bowel syndrome (IBS) or gastroesophageal reflux disease (GERD) identifying the root cause is paramount. Whether someone has heartburn, constipation and/or diarrhea, gas (bloating, belching, flatulence), indigestion (nausea, food sits in stomach, fullness feeling), abdominal discomfort or cramps, among others digestive symptoms, bacterial overgrowth in the small intestine is often involved. This health condition is named small intestinal bacterial overgrowth or SIBO for short. It is estimated that 60% of IBS may be due to SIBO. For those with inflammatory bowel disease (e.g. Crohn’s disease), addressing SIBO can alleviate symptoms and substantially improve quality of life.

SIBO is recognized as a standard medical condition by conventional medicine worldwide. Despite this recognition, the diagnosis and treatment options for SIBO are not presently conducted by our conventional health care system in New Brunswick. A diagnostic breath test for SIBO is now available at the Moncton Naturopathic Medical Clinic. This standard lactulose breath test verifies for both hydrogen and methane gases. This test can also be helpful to analyze for the presence of hydrogen sulfide gas producing bacteria.


What is SIBO? Is it an infection?

SIBO is defined as an “abnormally large numbers of bacteria present in the small intestine leading to impaired digestion and absorption”. It is important to note that the bacterial colonization of the small intestine is composed of bacteria that are normally found in the large intestine and are actually not considered pathogenic such as some commonly known ‘bad’ species such as Salmonella or C. difficile. Therefore, SIBO is actually not an “infection” per se. The key issue regarding the excess amounts of bacteria is the location: the small intestine should only have low bacterial counts (note: in contrast, it’s the large intestine that naturally contains an abundance of bacteria). Because SIBO is not like a typical infection, the immune system does not mount a full-fledged response against it. Because we don’t have the immune system to help us fight off SIBO-related bacterial overgrowth, the eradication of such bacterial species and preventing relapses can be more difficult than acute infections.


What’s the problem with having too many bacteria in the small intestine?

First, because the small intestine is where most of the digestion and absorption of nutrients occurs, a surplus of bacteria in that area leads to the malabsorption of carbohydrates. In other words, the bacteria are able to eat your carb-rich foods before you do. Normally, carbs are broken down into simple sugars (e.g. glucose) and then easily absorbed into the bloodstream. When this doesn’t occur because bacteria are taking their share, it creates problems in maintaining your own blood sugar levels. Furthermore, when bacteria have unlimited food sources, it leads to excess fermentation (think ‘gas’) which causes various unpleasant digestive symptoms.

Secondly, the surplus of bacteria also causes chronic low-grade inflammation of the small intestine lining leading to reduced production of digestive enzymes which are required to breakdown and digest food particles. This in turn results in further malabsorption. Dysfunctions of the gut lining can also lead to nutritional deficiencies, increased intestinal permeability (“leaky gut”), and can create or worsen food intolerances/sensitivities.

Because of such issues, SIBO causes not only digestive problems, but also contributes to body-wide symptoms such as mood changes (anxiety, depression), skin problems, headaches, fatigue, brain fog, hypoglycemic episodes (sweating, feeling shaky, etc.), weight issues, among others.


After eradication - why is it important to go one step further?

So far, we’ve discussed how the bacterial overgrowth involved with SIBO can cause a host of health problems. Therefore, eradicating the bacteria is no doubt a priority (see below for info regarding the use of pharmaceutical antibiotic medications and/or herbal antibiotics). Unlike infections, once eradication of the bacterial overgrowth is confirmed, additional steps are needed to heal from SIBO. One of the most important concepts to understand in order to fully address SIBO, is to determine WHY the bacteria got there in the first place. In other words, it’s essential to fix the actual cause of the bacterial overgrowth.

With SIBO, the bacterial overgrowth in the small intestine is actually not the main issue, it is the end-result of the illness. The illness (or actual problem) is predominately caused by the lack of the migrating motor complex (MMC). Normally the MMC involves nerves and muscles that work together in order to promote stomach emptying and move any contents in the small intestine forward in the direction to the large intestine. Food contents in the gut after all should always be going in a one-way direction! When these coordinate contractions work efficiently, our gut motility is an action. Damage to the nerve complex and muscles of the small intestine allows bacteria from the colon to go backwards up into the small intestine and proliferate there. This in turn leads to bacterial overgrowth known as SIBO.

In summary, once you get a diagnosis of your health issue (e.g. IBS), it’s important to ask WHY (e.g. why do I have IBS symptoms?). Various causes for IBS exist including food intolerances, SIBO, colonic bacterial imbalances, etc. If SIBO is found, it’s important to ask WHY again (why is SIBO found in my gut)?


Overview of SIBO

  1. Inflammation and/or damage of the small intestine (e.g. as caused by food poisoning) -->
  2. Lack or impaired migrating motor complex (MMC): nerve/muscle that coordinate bowel contractions towards the rectum become dysfunctional -->
  3. Colonic backwash: bacteria move backwards from the colon into the small intestine -->
  4. Leads to overgrowth of bacteria in the small intestine (SIBO) -->
  5. These bacteria cause gas by fermenting certain fibers, carbohydrates & sugar (e.g. lactose, fructose, etc.) -->
  6. Carbohydrate malabsorption occurs because bacterial fermentation (i.e. the bacteria get to eat your carbs before you do) -->
  7. Symptoms include: a combination of gas/bloating, burping, heartburn, constipation, and/or diarrhea, etc. -->
  8. The overgrowth of bacterial leads to ongoing chronic inflammation and mild damage in the small intestine -->
  9. The resulting damage to the small intestinal lining alters the function of the small intestine (such as reduced production of digestive enzymes) -->
  10. This leads to further indigestion and malabsorption problems and the cycle continues.


Causes of SIBO

The most common cause of SIBO is food poisoning also known as gastroenteritis, stomach flu, or traveler’s diarrhea. Such pathogenic ‘bad’ bacteria create an infection in the small intestine leading to acute inflammation of the gut lining which in turn damages the MMC (as already discussed). After the infection has passed, the nerves and muscles of the small intestinal lining can remain paralyzed which leads to the backward migration of colonic bacteria into the small intestine. Since motility is impaired, the daily ‘sweeping’ action that cleans out the small intestine is reduced, such that these new bacterial residents are no longer cleared out.

Other than food poisoning, SIBO can be caused by certain co-existing illnesses which also result in MMC dysfunctions such as scleroderma, diabetes, Ehlers-Danlos syndrome, hypothyroidism, Parkinson’s disease and Lyme disease (and Lyme related co-infections). Stress can also affect the MMC for people who dealt with past severe episodes of stress or those with ongoing chronic stress.

Other causes of SIBO include medication side-effects (e.g. proton pump inhibitor medications, antibiotics, opioids), decreased pancreatic enzymes (resulting from a pancreatic disease), slow gallbladder functioning, anatomical irregularities such as narrowing of the small intestines (e.g. which can be seen in Crohn’s disease), scars and adhesions from abdominal surgery, among others. During your appointment with your naturopathic doctor, a full review to evaluate will be conducted in order to determine which cause(s) pertain to you. Addressing the underlying cause of SIBO is an essential part of your healing.


Summary of what contributes to SIBO symptoms

SIBO symptoms are due to a combination of 3 different factors as summarize by SIBO expert Dr. Allison Siebecker ND (2019):

  1. Gas that is created by the bacterial fermentation of carbohydrates in the small intestine. Gas can include one or a combination of hydrogen (H2), methane (CH4) and hydrogen sulfide (H2S). Even low levels of methane gas, for example, can cause constipation.
  2. Damage to the small intestinal lining caused by the bacteria which alters the function of the small intestine (such as reduced production of digestive enzymes).
  3. The remaining underlying cause of SIBO which includes slow motility (MMC damage), structural alterations, low stomach acid production and diseases which also create their own list of symptoms.

It is helpful to highlight these 3 main issues so that both doctors and patients can better navigate and understand how different treatments work (or don’t work). For example, some patients expect all their symptoms to go away after taking an antibacterial treatment which is aimed to address the bacteria overgrowth. However, if their main cause of their symptoms is because the small intestine doesn’t produce sufficient digestive enzymes (for example), they may only feel better once this secondary issue is addressed.


Treatments must be conducted in a stepwise process

SIBO is first addressed by eradicating the bacterial overgrowth of the small intestine by using herbal antibacterials (as recommended by ND) and/or pharmaceutical antibiotic medications (as prescribed by an MD). Eradication is assessed based on symptom improvement and mainly on repeating the breath test to confirm. Multiple rounds of antibacterial treatments may be required, especially for those that have higher levels of gas as diagnosed via their initial breath test.

Many people feel better during/after the course of antibacterial treatments because the gas production in the small intestine has reduced significantly. However, not everyone feels better at the end of antibacterial treatments because the other causes of symptoms are still remaining (as mentioned above): e.g. damage to the small intestine lining and underlying problems/diseases that lead to SIBO in the first place.

It is therefore important to follow a step-by-step protocol so that treatments are successful.

Based on clinical evidence and research, both herbal antibiotics and pharmaceutical antibiotics have been shown to eradicate bacterial overgrowth in the small intestine. Because each person responds differently to each type of medications/supplements, the treatment protocol can be changed if someone does not respond to the initial treatments.

In certain situations, an elemental diet may also be considered to eradicate SIBO (e.g. where antibiotic treatments have failed, or when the patient responds poorly to them). An elemental diet consists of a medical food beverage of predigested, easily absorbed nutrients. This type of diet starves off the bacteria but feeds the person because these nutrients are absorbed within the first 2 feet of the small intestine (typically, SIBO is found lower along the small intestine). By reducing bacterial overgrowth via a different mechanism compared to antibacterial agents, the elemental diet can often be an efficacious intervention in antibiotic-resistant cases. For IBS with SIBO, the elemental diet is typically followed for 2 weeks, while for IBD (e.g. Crohn’s disease), it is usually followed for 4 weeks.

Even once antibacterial medications or an elemental diet are successful to eradicate the initial overgrowth, relapses can occur which can lead to chronic cases of SIBO. In such situations, the key is to reduce the intensity/frequency of relapses and if the underlying reasons for the dysfunctional MMC are addressed, SIBO can be cured over time.

Preventative treatments are essential to prolong remission and prevent relapses

Important considerations once eradication of the bacterial overgrowth is confirmed, includes:

  1. Adopt nutritional strategies that aim to reduce the risk of relapse by preventing any remaining bacteria to repopulate again and which supports digestive tract function. Your naturopathic doctor will help you determine the most appropriate dietary guideline for you (such as SIBO diets, a SCD diet, a low FODMAP diet, etc.). Meal spacing is also important. Eating three main meals per day and avoiding snacking is essential. The migrating motor complex (MMC) of the digestive system only begins 90 minutes after eating. Therefore, if you eat all the time and graze throughout the day, the gut can’t initiate the MMC as effectively and therefore food won’t be swept along as well. When the sweeping action of the gut is less active, bacterial overgrowth has a higher likelihood of reoccurrence.
  2. Continue working on addressing the underlining causes that created the bacterial overgrowth in the first place (MCC problem, certain illnesses, etc.). This is especially important for those that have a relapse (such that a bacterial overgrowth returns again in the small intestine).
  3. Based on each person’s unique situation, different naturopathic supplements and lifestyle recommendations can be considered if/when needed.
  4. Stress management is always an important aspect of the healing process.
  5. Ensure forward motility and prevent re-occurrence of colonic backwash: stool needs to evacuate well on daily basis and therefore treatment options will be considered for those prone to constipation.
  6. Heal the nerve and muscle cells of the small intestinal wall (i.e. "Migrating motor complex" or MMC). Prokinetic treatments are an essential part of addressing SIBO as they help to re-activate, stimulate and repair the MMC. For best results, a combination of pharmaceutical and herbal prokinetics are often advised. Prokinetics are used between antibacterial treatment rounds and after eradication to prevent relapse.
  7. Digestive aids such as digestive enzymes or HCl (stomach acid) also can be considered to prevent a relapse by helping with digestion.
  8. Reduce inflammation and heal the lining in the small and large intestine (e.g. by adopting an anti-inflammatory diet and by taking naturopathic supplements formulas aimed to sooth and heal).
  9. Support colonic good bacteria.

Although SIBO is a complex condition, a methodical approach will optimize how you navigate through your healing journey. Recommendations must be individualized at every step of the process.


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