What Causes Fatigue? Part 2: Thyroid, Adrenals, Gut & Biochemical Processes

What causes fatigue? Part 2: A Bulletproof functional medicine perspective

In Part One of “What Causes Fatigue?” we talked about optimising diet, sleep and assessing common nutrient deficiencies. This is a good place to start but many people have already done this and still have fatigue and other health issues. In this article, we will discuss some of the other causes of fatigue and how to assess it if this is a problem for you.

Low Thyroid Function

Low thyroid affects 10-12% of the population, especially women, yet 60% of people with low thyroid symptoms go undiagnosed. That means there is a lot of people with sub-optimal or low thyroid function who don’t realise that this is an issue for them, and while low thyroid function can cause many symptoms, from weight gain to skin problems, fatigue is one of the most common.

There are a couple of reasons why so many people are not diagnosed with low thyroid, the main reason is that doctors are only testing TSH levels and while this is an important marker it is only one aspect of thyroid function. The second reason is that the reference range for TSH is between 0.5 and 5.0, yet the optimal range for healthy people is between 1.0 and 2.0, this means that if you are in the reference range for  TSH you are told that everything is “fine,” yet you may still have low thyroid function.

At Planet Naturopath we assess all aspects of thyroid function, this includes, TSH, T4, T3, reverse T3 and the thyroid antibodies. If you are not converting T4 to the active form of T3, it is also important to assess adrenal function, gut function as well as the key nutrients that support thyroid function, this includes iodine, selenium, iron, B vitamins and zinc.

Adrenal Fatigue

Adrenal fatigue, which is also known as Hypothalamus Pituitary Adrenal Axis Dysfunction (HPA-D), whether you call it adrenal fatigue or by the medical term HPA-D, the adrenals are influenced by both physical and mental stress and can have a big influence on fatigue.

The article “Bulletproof and Adrenal Fatigue” describes in more detail the causes of adrenal fatigue, how to test for adrenal fatigue and the steps that you need to take to address it.

The first step to treating adrenal fatigue it to address the underlying cause.  Many people associate stress with mental and emotional stress, but stress can also be from physical stress like gut infections, lack of sleep (lack of sleep affects everything!), overtraining or injuries.

To identify adrenal fatigue the best type of test to do is the DUTCH hormone test, this assesses free cortisol and free cortisone, as well as total cortisol production, as well as a comprehensive assessment of the sex hormones.

Gut Infections

Gut infections like Helicobacter pylori, Small Intestinal Bacterial Overgrowth (SIBO), parasites, candida and other causes of gut inflammation often go undiagnosed as they are not routinely tested in a visit to the doctor. These types of gut infections can cause fatigue for a number of reasons even if you are eating a great diet and doing all the right things.

This article on Optimising your Digestion goes into a lot more detail about digestion function.

Gut infections affect the absorption of nutrients leading to deficiencies in iron, B12, zinc, magnesium and other nutrients, these deficiencies will lead to fatigue. If you have been tested for low iron or low B12, rather than just take supplements to address the problem it is a good idea to do some digestion testing to find out the underlying cause.

Gut infections also cause “leaky gut” and lead to an imbalance between your good and bad bacteria, this is known as dysbiosis which is associated with fatigue, brain fog, mood changes and many other physical symptoms.

The best way to assess gut infections is with a Comprehensive Digestive Stool Analysis (CDSA) Test which can identify bacteria, parasite and candida infections, as well as assess your beneficial bacteria, levels of inflammation and digestive enzymes. To assess SIBO there is a special type of breath test which measures the levels of methane and hydrogen gas which are produced by the bacteria in the small intestine, SIBO is the number one cause of IBS and the many symptoms that this can cause.


Methylation is a complex biochemical process that occurs in nearly all the cells of the body. Methylation influences many aspects of your health including immune function, neurotransmitter production, synthesis of DNA and RNA, gene expression and energy production.

The methylation cycle is essential in the production of Co-enzyme Q10, Carnitine and Creatine which are all important in cellular energy production, defects in these pathways can lead to Chronic Fatigue symptoms.

Genetic defects in the methylation cycle can lead to low levels of active B12 and folate, this also further impacts the methylation cycle and the production of energy. An Organic Acids test is a good way to assess levels of the active B vitamins, as well as Co-enzyme Q10 and Carntine levels.

Mitochondrial Dysfunction

Defects in the methylation cycle and the citric acid cycle also affect mitochondrial function. Your mitochondria is like your cells’ batteries and defects in the mitochondria basically means you’ll have a flat battery. A flat battery equals no energy.

The main role of the mitochondria is the production of ATP, which is what we need for energy!

It used to be thought that mitochondria dysfunction was a rare genetic disease, but now it is commonly accepted that there are different levels of mitochondrial dysfunction which can be caused by nutrient deficiencies such as amino acids, B vitamins, Co-enzyme Q10 and iron.

One of the reasons that some people feel so good, and have a lot more energy on a ketogenic diet is that the mitochondria functions very well when fuelled by fatty acids from ketones. This provides a steady supply of energy compared to glucose.

The Organic Acids test is the best way to assess the citric acid cycle and mitochondrial function. It helps to identify if there are any blocks in the citric acid cycle and what nutrients are needed to optimise energy production.

The Next Step

As you can see there are many different causes of fatigue and the first steps are to optimise your diet, nutrition and sleep. For most people, this is going to be enough to get you feeling great, but for a number of people there is still going to be fatigue and energy issues, no matter what you do nothing seems to help with sleep, or your digestion is still not right despite cutting out the crappy foods.

At Planet Naturopath we specialise in Functional Pathology testing for digestion and hormonal problems, tests such as the DUTCH hormone test, CDSA test, SIBO and Organic Acids test are available to help you identify the underlying cause of your energy or health problems.

Consultations are available via phone or Skype Australia wide, and the specialised test kits can be sent to wherever you live in Australia or overseas, go to Planet Naturopath for more details.