Follow on

How A Hidden Gut Infection Can Cause Your Chronic Fatigue

Chronic fatigue is a debilitating condition characterized by persistent and unexplained exhaustion, which significantly impacts daily life and overall well-being. In recent years, researchers and healthcare practitioners have been exploring the connection between chronic fatigue, particularly Small Intestinal Bacterial Overgrowth (SIBO) and yeast overgrowth. (*),(*),(*)

Chronic fatigue, also known as chronic fatigue syndrome (CFS), is a complex and challenging condition characterized by extreme fatigue that cannot be explained by any underlying medical condition. Individuals with chronic fatigue often experience symptoms such as prolonged tiredness, physical and mental exhaustion, brain fog, sleep disturbances, reduced concentration, and muscle pain.

Today’s article will delve into the relationship between chronic fatigue, SIBO, yeast overgrowth, and the persistent feeling of tiredness, shedding light on an important but overlooked cause behind this condition.

Transcript of video 

Chronic Fatigue

If you recently went to the doctor because you are always tired, feeling run down, and experiencing post-exercise fatigue, your doctor may have tested your thyroid gland for something called hypothyroidism. After ruling out that your thyroid wasn’t a problem, you were probably sent home without any answers guidance, or direction. You are not alone, many of my patients find themselves in the same boat! According to the U.S. Centers for Disease Control and Prevention. Chronic fatigue syndrome affects about 1 million Americans every single year and usually affects more women than men. (*)

I’m Dr Hagmeyer clinic director here at Dr. and today I’m going to explain how your chronic fatigue syndrome may be caused by a hidden gut infection or by an overgrowth of bacteria called SIBO. (*) It’s also possible that an overgrowth of Yeast could be the cause behind your chronic fatigue. (*),(*),(*)

Chronic Fatigue and SIBO

What is SIBO

SIBO stands for Small Intestinal Bacterial Overgrowth. It is a condition characterized by an abnormal increase in the number and/or types of bacteria in the small intestine. Normally, the small intestine contains a relatively low amount of bacteria compared to the large intestine. However, in cases of SIBO, bacteria from the large intestine move upward into the small intestine and proliferate, causing an overgrowth. The overgrowth of bacteria in the small intestine can interfere with normal digestive processes as absorption issues. In addition to the toxins produced by bacteria and yeast that lead to chronic fatigue syndrome, overgrowth can also lead to malnutrition and malabsorption of critical nutrients. One of the most common vitamin deficiencies is B12 but there are many other nutritional deficiencies that I have talked about in this article.

Chronic Fatigue and SIBO

If you are experiencing chronic fatigue along with the symptoms of bloating, gas, constipation or diarrhea, acid reflux, and brain fog you may want to consider a gut problem known as SIBO or small intestinal bacterial overgrowth or SIFO if the overgrowth is caused by yeast.(*) If these symptoms occur regularly or intensify when you eat fruit, fiber, sugars, or starches I would be even more concerned that an underlying gut issue is contributing if not causing your fatigue.

For many with CFS it’s also very common to suffer from muscle and joint pain, difficulty thinking and focusing, and finally sleep problems.

When it comes to chronic fatigue and SIBO, multiple studies have already found district differences in the gut microbiome in patients who suffer from chronic fatigue syndrome and those who don’t. (*),(*) These studies confirm the link between yeast or bacterial overgrowth in the gut with chronic fatigue syndrome.

Our microbiome is a community of bacteria, yeast, and even viruses living on and in your body and they influence everything from how we feel, how our immune system responds to our environment, and our body’s ability to resist disease. There’s not a whole lot that the microbiome is not involved in.

Over my 20-plus years in clinical practice, one thing I can tell you that I have seen over and over again as a root cause of chronic fatigue is something called SIBO or SIFO, if in the small intestines or dysbiosis of large intestines. SIBO is bacterial overgrowth, while SIFO is fungal or yeast overgrowth.

Typically, these kinds of problems are identified using either a Functional Stool Test (FST) or a Hydrogen Breath test (also known as a Lactulose Breath Test or Glucose Breath Test.

Let’s talk about how this yeast or bacterial overgrowth or infection happens. Keep in mind….Like most chronic health problems there is no one singular reason. SIBO or yeast overgrowth can be caused by things like diets high in sugars, carbohydrates, and starches, it can be caused by thyroid disease, diabetes, it can be caused by scarring from past surgeries, or gut inflammation like we see in Crohn’s disease and IBD, it can be caused by low stomach acid, and it can even be caused by stress, medications, and neurological imbalances.

  • Hypothyroidism
  • Low stomach acid
  • Medications such as antibiotics, Antidepressants, NSAIDs, and acid-blockers
  • Stress
  • Neurotransmitters
  • Scarring from surgeries or Crohn’s disease
  • Dysmotility caused by diabetes, scleroderma, or neurological conditions
  • Stuck Ileocecal valve

Common causes of SIBO and fatigue

Typically, more often than not it’s a combination of these factors that leads to this overgrowth of bacteria or yeast in your small intestine or gut dysbiosis in the large intestines. Now…Because your gut is the gatekeeper to many aspects of health, this becomes an important area especially when you are chronically fatigued, and because your gut is the gateway to health it’s not an area that should be ignored.

As I already mentioned, if you have the symptoms of chronic fatigue and you have a problem digesting fruits, Fiber, sugars, and starches, then It’s time to look at this gut-fatigue connection.

Problems Associated with SIBO

Some common signs and symptoms of SIBO and yeast overgrowth include:

Digestive Issues:

SIBO and yeast can cause gas, bloating, abdominal pain, and discomfort. These symptoms are often worsened after meals, particularly those containing carbohydrates that the bacteria feed on.

Diarrhea or Constipation:

SIBO can contribute to changes in bowel movements, leading to frequent loose stools or alternating between diarrhea and constipation.


The overgrowth of bacteria or yeast in the small intestine can impair the absorption of important nutrients, leading to deficiencies in vitamins, minerals, and other essential compounds. This can result in symptoms like fatigue, weakness, and unintended weight loss.

Nutritional Deficiencies:

SIBO can interfere with the breakdown and absorption of carbohydrates, fats, and proteins, resulting in a deficiency of certain nutrients. This can lead to symptoms such as anemia, osteoporosis, and impaired immune function.

Other Symptoms:

SIBO and yeast overgrowthh has also been associated with symptoms beyond the digestive system, including fatigue, brain fog, joint pain, skin issues, and mood disturbances. These systemic symptoms occur due to the impact of an overgrowth of bacteria on overall health and the production of certain toxins.

How Do I Know If I Have SIBO?

One of the ways we identify a hidden gut infection is through the use of a breath test. A SIBO breath test is a diagnostic tool used to determine the presence of Small Intestinal Bacterial Overgrowth (SIBO). This non-invasive test measures the quantity of specific gases produced by the fermentation of carbohydrates by bacteria in the small intestine. The test helps identify if there is an abnormal bacterial overgrowth in the small intestine.

During the SIBO breath test, the patient is asked to follow specific dietary guidelines in the days leading up to the test. These guidelines typically involve avoiding certain foods that can impact the accuracy of the test, such as high-fiber foods, simple sugars, antibiotics, and some medications. Fasting prior to the test for a specific period may also be required.

On the day of the breath test, the patient will consume a solution containing a specific type of sugar, typically lactulose or glucose. These sugars are not well absorbed in the small intestine and are known to be fermented by bacteria. As the bacteria metabolize these sugars, they produce gases, such as hydrogen and methane.

The patient breathes into a collection device, typically a small tube, at regular intervals, such as every 15 to 20 minutes, over a period of two to three hours after consuming the sugar solution. The breath samples collected during the test are then analyzed to measure the levels of hydrogen and methane gases.

Elevated levels of hydrogen or methane can indicate the presence of bacterial overgrowth in the small intestine. Normally, these gases are produced in the large intestine, but their presence in the breath during the early intervals of the test suggests that bacteria have migrated to and are residing in the small intestine.

Based on the pattern and levels of gases detected, healthcare professionals can assess the presence and severity of SIBO. This information helps guide appropriate treatment approaches, such as dietary modifications, antimicrobial therapy, or other interventions aimed at reducing bacterial overgrowth.

Let’s Look at A Patient SIBO Breath Test

Remember a problem in the gut can quickly become a problem that affects the whole body. Now let me show you an example of a lactulose breath test that helped me identify this bacterial overgrowth in a past patient.

This patient is 46 years old and has a history of chronic fatigue syndrome, and chronic pain in her lower back and neck, she was diagnosed by her doctor with Chronic fatigue syndrome after thyroid disease was ruled out.

She had a lot of brain fog and complained of irritability and being short-tempered with her family. If you look at this test, along the bottom, you see it says collection times, along the left-hand side it says total hydrogen and methane PPM.

A positive test is where we see a rise of ≥ 20 ppm from baseline in hydrogen by 90 min.

A peak methane level ≥ 10 ppm at any point is indicative of a methane-positive result.

As you can see from this test this patient’s hydrogen levels went from a baseline of 6 ppm up to 37 at 120 minutes.

This is considered a positive hydrogen breath test and indicates a Bacterial Overgrowth in the Small Intestines or SIBO. You will also notice this patient also tested positive for Methane gas.

So, now imagine if this is happening to you. What if your chronic fatigue was coming from bacterial overgrowth?

Gut issues are incredibly common based on the fact that our modern society causes us to eat on the run, we are chronically under stress, and most doctors are antibiotics happy. The average American has been on 6 or more antibiotics within their lifetime.

With this patient we worked on eradicating the gut overgrowth/infection, we used a 4R protocol that I personalized for this patient, and we made changes to the diet. Once we addressed these areas, it took about 6 months for this patient to notice changes. But by 6 months, she had a 90% improvement in fatigue, 90% improvement in chronic pain, and 100 resolution of brain fog.

Closing Thoughts and things to remember about chronic Fatigue Syndrome and Gut Infections

  1. Chronic fatigue and hidden gut infection or gut overgrowth are more common than you think.
  2. If you have any of the bloating, belching, or gas and you suffer from CFS it’s important to consider SIBO as well as the integrity of the gut microbiome. Bacteria and yeast are common culprits of Chronic fatigue syndrome.
  3. While there are multiple reasons for chronic fatigue, a doctor who is Certified in Functional Medicine would be the best kind of specialist to help you investigate the reasons behind persistent fatigue. A Functional Medicine Practitioner can also determine the most appropriate testing for the symptoms you have.
  4. With the right treatment plan, your chronic fatigue syndrome could be improved in 6 months and sometimes even sooner.


See Other Recent Post!

Creating health doesn't have to be a guessing game!

Our Team will help you harness your health so you can trust your body and feel like YOU again. We can help find your Root Cause.