Dr. Jennifer Luis ND

SIBO Fatigue – Body Pain, Mood Disorders & More

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The human body is designed to run on food. Without enough nutrients such as vitamins, minerals, protein, fats, carbohydrates and water, any symptom or condition is theoretically possible. The building blocks of neurotransmitters, hormones and immune system components all rely on biochemical structures derived from our food in some capacity. Therefore, if digestion isn’t at a maximal level of strong health, doesn’t it make sense that energy, mental health, pain, and sleep could be affected?

Digestive disorders that limit absorption of nutrients are serious. They can range from diseases such as ulcerative colitis and celiac or conditions like IBS. How do these disorders originate? Many believe that the root to multiple conditions is from inflammation in the gut, caused by imbalanced bacteria and other microorganisms. One such relatively new condition is SIBO.

What is SIBO?

Small intestine bacterial overgrowth (SIBO acronym) is exactly what the name infers. The small intestine is a relatively sterile environment, with very minimal colonies of microorganisms living near the transition zone with the large intestine. Sometimes the valve between the small and large intestine called the ileo-cecal (or IC) value doesn’t fully close when it should and bacteria are able to migrate in the wrong direction instead of being swept down and out.

When these colonies set-up a new living space in the small intestine, the immune system recognizes that this as an invader and launches an attack. This leads to inflammation and it can become chronic if the bacteria outlast the onslaught. More and more colonies can be produced and can move farther up the small intestine towards the stomach. This can be over a few months or a few years and is sometimes traced back to a food poisoning or traveler’s diarrhea event as the initial cause. Other times, multiple antibiotics can be to blame or even low stomach acid production.

Most often SIBO produces symptoms of the digestive system, but sometimes it is silent and symptoms are seen elsewhere. Skin conditions such as acne and eczema, headaches, fatigue, mood changes, hair loss and weight changes can be related to SIBO. More obvious digestive symptoms such as gas, bloating, constipation, diarrhea and heartburn make it easier to identify SIBO and to test and treat quicker.

Why SIBO’s Effects Aren’t Limited to Digestive Issues

Extracting nutrients from food is the main purpose of the small intestine. Stomach acid triggers digestive enzymes and bile to be released and the macronutrients are broken down into amino acids, fatty acids, simple carbs, vitamins and minerals. At various locations in the small intestine, each nutrient has a specific mechanism of absorption into the blood stream and thus into the cells. Nutrient absorption is very complicated and if a barrier to proper transferring of nutrients into the blood stream is impaired, all body systems can be affected.

Inflammation due to bacterial overgrowth makes the lining of the gut swollen and physically challenging to bring nutrients across. Think about the symptom of hair loss. One of the first reasons checked for hair loss is iron deficiency and a simple blood test can identify this cause. However, why is iron low in the first place? Other than diets lacking in iron (vegetarian diets are usually iron-rich if done properly) or heavy periods in women, it comes down to the ability to absorb iron across the lining. This is one example of how SIBO can cause symptoms outside of digestion. In this scenario, it isn’t enough to determine that iron deficiency is the cause, always ask why is iron deficiency present in the first place.

Understanding SIBO Fatigue

Similarly to the example of hair loss, lack of many nutrients can lead to fatigue. B vitamins are responsible for metabolism, hormone and neurotransmitter production and this translates to energy. Vitamin and mineral deficiencies are one reason along with general malnutrition when it comes to fatigue. Depending on the severity or how long SIBO has been present, other nutrients can struggle to be absorbed such as healthy fats and amino acids. These are also required for metabolism and all body processes.

Inflammation of any sort causes stress on the body. Chronic, on-going inflammation such as with SIBO can affect cortisol production which has a cascading effect on multiple other aspects of health. This can lead to fatigue, insomnia, weight gain, mood disorders, menstrual irregularities and even the development of other conditions such as auto-immune diseases.

How SIBO Affects the Human Body

At the local digestive level, SIBO causes excess gas to be produced which can feel like pain and bloating and lead to heartburn, GERD, constipation and/or diarrhea. At the systemic or full body level, SIBO may cause a multitude of symptoms because of nutrient deficiencies and inflammation. Signs may not be as obvious initially, it can be hard to identify that headaches and muscle spasms or nerve pain are due to nutrient deficiencies which are caused by SIBO. However a good physician will trace back the reason for the deficiencies in the first place.

Explaining the Link Between SIBO and Fatigue

Nutrient deficiencies such as iron, Vitamins B5, B6 and B12, and Vitamin D are commonly associated with fatigue. Other nutrient deficiencies can indirectly be involved but difficult to test for. Testing low in a nutrient helps to understand why fatigue is felt, but why is the nutrient low? SIBO is one cause of malnutrition and should be evaluated by the SIBO breath test.

SIBO Fatigue and Related Non-Digestive Symptoms

SIBO leads to inflammation and lack of proper nutrient absorption into the blood stream. Not only is this a case of feeling both physically and mentally exhausted, but it can lead to other symptoms.

Lack of nutrients means that other body systems do not have the enough of the building blocks required to build hormones, neurotransmitters, to detoxify, to build structures such as proteins, hair, nails, blood cells and much more. This over time can lead to a multitude of symptoms because a multitude of body systems are affected.

Brain Fog

Often described as not able to concentrate or focus, brain fog can be a symptom of SIBO. Low hormones such as estrogen, thyroid, cortisol, and DHEA can be behind brain fog and may be independent of SIBO. Menopause, hypothyroidism and adrenal dysfunction are all changes or imbalances to hormone levels and can affect the brain. But sometimes taking a step further back and asking why did the hormone levels change in the first place, may lead to examining digestion and testing for SIBO for an answer.

It is possible too that low iron (or other nutrient) is contributing to brain fog and that can be tied to SIBO in some cases. A common symptom of iron deficiency is brain fog, along with fatigue, hair loss and shortness of breath with exertion.

Headaches & Memory Loss

One of the gasses that some SIBO bacteria produce is methane. Methane acts not only to slow down digestion but it can cause other body symptoms such as headaches. So, SIBO can directly cause headaches but also indirectly. A lack of iron or magnesium can lead to headaches. Common migraine and headache protocols involve supplementation with magnesium and some B vitamins and have clinical success. The source of the deficiency can sometimes be tied back to SIBO if absorption is limited.

Memory loss is not a common symptom of SIBO. There may be an indirect link due to nutrient deficiencies however any memory loss should be discussed with a physician.

Dizziness / Lightheadedness

Lack of iron can be the primary reason for dizzy and lightheaded symptoms, especially if more common with a change of position or exertion. Low cortisol, low caloric intake, imbalances in blood sugar and inner ear dysfunction would also be to blame. SIBO and malabsorption might be the reason for the low iron or low caloric intake and even low cortisol.

Depression & Mood Disorders

Hormones and neurotransmitters are very important when it comes to mood. Either too little or too much of these chemical messengers can lead to anxiety, depression, irritability and general lack of emotions or apathy. When trying to determine the root cause of mood disorders, it is important to consider reasons why up-regulation or down-regulation of hormones and neurotransmitters are to blame. Taking an even further step back would be to figure out if all nutrients are in well enough levels to allow for production to optimal levels. If the answer is no, digestive conditions such as SIBO should be considered.

Skin Issues (Eczema, Psoriasis, Acne)

Skin conditions can be linked back to digestion in many cases. Sometimes it is a particular food such as dairy that triggers acne or eczema and other times it is due to inflammation from SIBO or other digestive overgrowth. By eliminating bacteria living in the small intestine and re-balancing large intestine flora, many skin conditions are greatly improved or resolved.

Do You Have SIBO Fatigue? Time for a SIBO Test!

A SIBO breath test using a lactulose breath test over a 3 hour collection is the current gold standard for testing SIBO. This test can be ordered through a naturopathic physician and performed at home. After eating a very plain diet for 1-2 days prior to testing, a 3 hour breath collection (1 sample every 20 minutes for a total of 10 samples) is analyzed by the lab to determine the amount of parts per million of hydrogen and methane gasses.

The report will give a baseline amount followed by 9 challenged amounts. It takes between 2-3 hours for food to make it through the mouth, stomach and small intestine into the large intestine so completing the test over 3 hours will ensure all parts of the small intestine are evaluated.

Causes for SIBO Fatigue

Whether it is from iron deficiency or other nutrient deficiencies, lack of important micro and macronutrients can easily cause fatigue. Tiredness is sometimes related to caloric restriction when severe SIBO symptoms make it difficult to eat anything. In this case, weight loss can be reported too.

Inflammation results in an imbalance of hormones and can also create pain and discomfort. This overtime can be another cause of exhaustion and may be from SIBO alone or additional digestive or hormonal imbalances.

Chemical Imbalance Caused by SIBO

Biological chemicals such as hormones and neurotransmitters send signals to organs and tissue so that other bodily processes can be initiated or maintained. When nutrient deficiencies are so strong that altered amounts of these messengers are produced, many varied symptoms can occur. 

Mood imbalances such as anxiety and depression can be heightened if not enough dopamine, serotonin or thyroid and progesterone hormones are synthesized. The brain is an important location for neurotransmitter (NT)  production, but equally important is the second “brain” of neuroendocrine production around the digestive system. Considering that in close proximity SIBO is creating inflammation of the small intestine, it is possible that these effects are influencing NT production surrounding the gut. There is a great amount of research being conducted at this time surrounding the gut/brain/neurology connection.

Presence of Bacteria and Toxins in Small Intestine

SIBO represents an abundance of bacteria living in an overgrown manner in the small intestine. These bacteria are of many different species, some are normal body bacteria just living in the wrong place. Others are what is termed dysbiotic, or imbalanced and lead to further imbalances or inflammation. Depending on the bacteria type, different by-product gasses are released by the bacteria. The 3 gasses identified in SIBO are methane, hydrogen and hydrogen sulphide. Each gas can create different effects and symptoms. For example methane gas can cause constipation, odorous breath and in rare cases heart palpitations. Hydrogen gas often stimulates digestion leading to diarrhea or loose stools. Hydrogen sulphide causes very odorous, rotten-egg like flatulence and often causes a high sensitivity to garlic and onions in the diet.

Bacteria can also release toxins to fight off other bacteria and the host immune system. Some of these toxins cause an immune response from the body and lead to further inflammation and worsening of the condition. Clues about the types of overgrowths can be seen with a microbiology stool analysis which may lead to alternative methods for treatment.

Nutrient / Vitamin Deficiency

With inflammation in the gut lining from SIBO comes an inability to fully absorb nutrients into the blood stream. This potentially could lead to deficiencies in any vitamin or nutrient and is common amongst those with SIBO. Iron, magnesium, zinc, Vitamin B12 and Vitamin D are the easiest nutrients to test for by blood and can confirm sub-optimal or deficient levels. Supplementation may be required to bring levels back up to healthy amounts.

Overgrowth of Yeast in Small Intestine

SIFO, or small intestine fungal overgrowth is a very similar condition to SIBO and causes all of the same symptoms. This is not identified on a breath test but can be inferred through other tests such as stool cultures and candida antibody testing. For the most individualized and well-rounded protocol to treat gut health, SIFO should be considered and additional testing along with the SIBO breath test administered.

How to Improve SIBO Fatigue & Other Non-Digestive Issues

Simply test and treat SIBO to improve related symptoms. Finding a qualified physician to order a SIBO breath test is the start. In conventional medicine, SIBO breath tests are not covered under public health care but often can be included with extended health insurance. Once a positive breath test is interpreted, eradication protocols can be initiated involving herbs and possible pharmaceutical interventions for 4-8 weeks. Changes to fatigue and other symptoms when related to SIBO can be felt in the first few weeks and usually continue to improve at a steady rate.

Replacement of nutrients deemed to be deficient should also be consumed through diet and sometimes supplementation.  Changes to diet to include a wide array of vegetables, healthy fats and protein will improve the rate of recovery back to a healthy baseline.

Improve Gut Health

Gut health starts with removing the overgrown flora that cause inflammation. Once SIBO has been treated, a continuation of gut healing protocols should be maintained for several months. This includes a healthy diet, in addition to omega 3s, L-glutamine and probiotics. Replacing the pH balance in the stomach to a strongly acidic level is often required along with enhancing digestion with enzymes.

Sticking to a SIBO-Friendly Diet

A SIBO diet is not always required. Years ago, an anti-SIBO diet was always implemented for at least 1 month after eradicating the overgrowths. This was put in place to ensure no extra food sources could feed any left over colonies. In more recent medicine, this practice has fallen out of favour and rarely suggested. A SIBO friendly diet now means eating with distinct breaks between meals. Being a grazer and not allowing a solid 3 hours between meals or snacks may increase the risk of a recurrence of SIBO.


Interestingly, in a person with SIBO, probiotics can either aggravate symptoms or have no positive benefit. Generally probiotics are given after the overgrowth has been cleared to help restore any imbalances in the large intestine. Although herbs are used to kill SIBO, there will be casualties of good flora in the large intestine and probiotics can help promote healthy and strong new colonies.

The strains and amounts of colony forming units will differ depending on the whole microbiology picture. Generally advisable are probiotics that contain both bifido bacteria and lactobacillus in amounts of 50 billion or more per day.

Digestive Enzymes

During the healing phase, it can be beneficial to add full spectrum digestive enzymes with meals to enhance the breakdown of nutrients. Ensuring food is properly digested will help prevent fermentation which acts as a food source for any backwards flowing bacteria that made it across the valve. Not always are enzymes required, it is best to have an individualized protocol created which will consider enzymes and other digestive enhancements when needed.

Stomach Acid Support

This can be very important and required if SIBO relapses are to be avoided. Low stomach acid leads to undigested food which ferments and feeds SIBO. By doing a simple at home test with baking soda, it can be determined if acid support is required. 1 cup of baking soda and 1/4 teaspoon of water mixed together and consumed at once with an empty stomach should cause a big belch before 2 minutes. If it takes longer or there is no belch, then an under production of acid in the stomach is present. Using apple cider vinegar with meals or capsules of acid, the stomach acid levels will improve over time.