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SIBO Fatigue [Explained by a Dietitian]

If you’ve been diagnosed with SIBO you’re likely to experience a range of digestive symptoms, including gas, bloating, abdominal distension, and more. However, patients with SIBO often experience another non-digestive symptom: fatigue!

If you’re wondering if what you’re experiencing is SIBO fatigue, and if so, what you can do about it, this article is for you!

Let’s start by understanding what SIBO is and its impact on your body. 

Overview of SIBO

SIBO’s name is quite literal, it stands for small intestinal bacterial overgrowth. If you are diagnosed with SIBO, it means that there is an overgrowth of bacteria in your small intestine. The term “overgrowth” is used because the small intestine should generally have a low level of bacteria, especially compared to the colon, where we find all the microorganisms that comprise the intestinal microbiome and are responsible for certain aspects of digestion. 

This overgrowth is associated with the following symptoms:

  • Gas
  • Bloating
  • Nausea
  • Fatigue
  • Loss of appetite
  • Feeling of fullness
  • Constipation
  • Brain fog 
  • Joint pain
  • Abdominal pain
  • Abdominal distension

In order to understand how these symptoms are generated, it’s helpful to understand a little about the function of the small intestine. First, your small intestine is the primary site of absorption of nutrients in your body. Did you know that 90% of the calories we consume are absorbed through the small intestine? In order to accommodate all that absorption, the small intestine needs a permeable and complex lining. Such a lining is delicate in nature.  In addition, your small intestine contains more immune cells than any other organ in the body, which means that what happens in the small intestine can impact your immune system [1, 2]. The many complex reactions of digestion and absorption combined with the outsized immune system involvement creates a delicate balance, which can easily be thrown off by something like SIBO. 

Thus, the symptoms we see with SIBO can be related to any of the following issues:

  • Bacterial metabolism: production of gas and other byproducts of metabolism
  • Immune system: production of mediators, which trigger reactions in target tissues
  • Inflammation: causes symptoms, such as pain, swelling, etc.
  • Lining damage and/or dysfunction: tight junctions may loosen, allowing more passage of particles across the membrane. Conversely, lining may lose permeability, resulting in imparied absorption [3]. 

These issues are important to keep in mind as we explore what causes SIBO fatigue.

What Causes SIBO Fatigue?

Bearing in mind the role of the small intestine in digestion and absorption, and the impact on immune function, we can appreciate how SIBO fatigue can stem from divergent underlying causes: 1. nutrient deficiencies, 2. hormonal imbalances, 3. Mental health status, 4. Inadequate or poor quality sleep. Other issues can be at play of course. But, this provides a good starting point.

Let’s take a look at how these conditions play out in SIBO.

Nutrient Deficiencies

We already learned that the small intestine absorbs 90% of our nutrition. That’s bonkers for a relatively small organ. That also means that any damage, imbalance or dysfunction in the small intestine is going to have an outsized impact on nutrient status. Common nutrient deficiencies seen with SIBO include the fat soluble vitamins, especially vitamin D, as well as iron and B vitamins.

B vitamins are relatively well known for their role in energy and metabolism. Clearly, deficiencies in B vitamins can cause fatigue. Vitamin D deficiency is another potential culprit when it comes to fatigue. 

The good news is that treating SIBO and healing the gut will improve absorption and likely lead to better energy levels.

Hormonal Imbalances

Another important process that happens in the small intestine is the conversion of the main thyroid hormone (T4) to active thyroid hormone (T3). If this pathway is impaired, as could be the case with SIBO, T3 levels could be low. Low T3 levels, even with normal TSH levels, can lead to symptoms of hypothyroidism. In addition to weight gain and constipation, another hallmark complaint with hypothyroidism is fatigue.

Once again, treating SIBO, while also healing and rebalancing the gut is the first line of defense against this type of hormone imbalance, and likely others. 

Mental Health and the Gut-Brain Connection

You may have heard of something called the gut-brain connection. This is a simple way of referring to a complex set of interactions in which the health and function of one organ affects the other[4]. Chemical messengers, known as neurotransmitters are produced in the gut and travel to the brain via a system of neurons. These messages influence mood, appetite, memory and pain! Messages coming FROM the brain TO the gut, on the other hand, influence gut motility, mucus secretion, gut lining function, and more!

Clearly treating SIBO is one way to address mood disorders, thereby improving SIBO fatigue [5].

Inadequate or Poor Quality Sleep 

SIBO patients can struggle to fall asleep and/or be awoken by some symptoms of SIBO, such as abdominal pain, nausea, and/or joint pain. However, the mood disturbances associated with SIBO are also known to result in poor sleep quality or inadequate sleep. 

Clearly, if you’re not sleeping well, you’re going to feel tired. Whether it’s SIBO that is negatively impacting your sleep, it’s important to understand that it’s not only duration of sleep that matters, but also quality of sleep. Waking frequently throughout the night is considered poor quality sleep. This can happen for light sleepers, parents of babies, those with sleep apnea, as well as others. Below, we’ll look at some strategies for improving sleep.  

SIBO Testing

SIBO is diagnosed via a hydrogen breath test [6]. For this test, you drink a sugary liquid and then breathe into a balloon every 15 minutes. Each time you breathe into the balloon, the levels of hydrogen and methane are measured. The levels of these gases reflects the amount of bacteria present in the small intestine. 

While this test will indicate whether or not you have SIBO, it won’t tell you WHY you have it. In order to treat SIBO properly, it’s important to know what is causing it. For this reason, other tests are often ordered alongside a hydrogen breath test. Other tests might include:

  • Blood tests to look for deficiencies and/or imbalances
  • Stool tests to identify infections, parasites and/or fat malabsorption
  • Imaging such as ultrasound, CT, MRI and X-rays to examine the organs and tissue 

SIBO Treatments

When it comes to SIBO treatment, we need to think about treating the underlying cause along with, if not before, treating the overgrowth itself. 

  1. Treat underlying cause: this will depend on what the underlying cause is for you. You will need to work with your doctor and other health care providers to determine the cause and establish a treatment plan. 
  1. Diet: a low FODMAP diet is the most common diet used to improve SIBO symptoms [Staudacher]. This diet is intended to be short term. You should only be on this diet for 3-6 weeks, before beginning the reintroduction phase, which is outlined in my previous article on Reintroducing FODMAPs.
  1. Antimicrobials– if you’re looking for a gentler, more natural approach to treating SIBO, antimicrobial agents are an option worth considering. Examples include: oregano, berberine, and peppermint. When using antimicrobial agents, individuals should work with a doctor, registered dietitian or other healthcare provider.
  1. Antibiotics– traditional antibiotics are generally effective at treating SIBO. If you choose this treatment method, simply keep the above considerations in mind.

How to Reduce SIBO Fatigue

Eat a Balanced Diet

To support optimal energy levels, you need to fuel your body with the right mix of macronutrients (protein, carbohydrates, and fats). This exact mix depends on age, health status, and activity levels. So, it’s not possible to give general advice on this. However, an inadequacy in any macronutrients will have downstream effects on your energy levels. 

Macronutrients, however, are only half of the nutritional picture. We also need to consistently nourish our bodies with precious micronutrients to ensure that all of our complex body systems are finely tuned. Micronutrients are primarily the vitamins and minerals that we find in whole, unprocessed foods. Avoiding packaged and processed foods will ensure that your diet is high in micronutrients.

Get Adequate Sleep

Improving your gut health and healing from SIBO will likely improve your overall sleep, assuming you have decent sleep habits. However, if you’re dealing with SIBO now, here are some strategies that may help: 

  • Abdominal massage before sleeping
  • Hot shower or bath before bed
  • Consistent waking and sleeping schedule
  • Outdoor movement in the morning

Work with a Professional to Address Underlying Causes

Other issues that contribute to SIBO fatigue likely require professional care. Your doctor can evaluate the status of the thyroid hormones by ordering a thyroid panel (blood test). You can also talk to your doctor about whether you’re a good candidate for mental health counseling. You can also reach out to a therapist on your own to discuss your needs and goals. A registered dietitian can help you understand how to improve your diet to meet your nutritional needs. 


SIBO itself is fairly straightforward. However, the symptoms and the underlying causes can be quite complex. The causes of SIBO fatigue itself can stem from: nutritional deficiencies, mental health status, hormonal disturbances and sleep disturbances. You can use diet and lifestyle to support your overall energy levels. However, working with a professional is your best bet for treating the underlying cause and getting to the root of the problem.

For more information and help with gut health visit:


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  2. Lazar V, Ditu LM, Pircalabioru GG, Gheorghe I, Curutiu C, Holban AM, Picu A, Petcu L, Chifiriuc MC. Aspects of Gut Microbiota and Immune System Interactions in Infectious Diseases, Immunopathology, and Cancer. Front Immunol. 2018 Aug 15;9:1830. doi: 10.3389/fimmu.2018.01830. PMID: 30158926; PMCID: PMC6104162.
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