5 critical nutrient deficiencies caused by SIBO

Recently I had a client, a young woman in her 30s, who had been grappling with extreme fatigue, constant bloating, and an unexplained rash on her arms. Despite consulting multiple doctors and trying various treatments and diets, her symptoms persisted, leaving her frustrated and exhausted. 

When she came to see me, I noticed a recurring theme — persistent digestive issues that she hadn’t connected to the other problems she was facing. After conducting a stool test and an SIBO breath test, we discovered she had small intestinal bacterial overgrowth (SIBO), which was likely contributing to both her nutrient deficiencies and fatigue and skin issues.

Many people don’t realise that SIBO doesn’t just cause digestive discomfort; it can lead to significant nutrient malabsorption, which can have a ripple effect on the entire body. The impact of SIBO extends far beyond bloating or abdominal pain. It can result in deficiencies of critical vitamins and minerals, affecting energy, cognition, skin, and potentially the development of autoimmune disease. 

In this article, I’ll share insights from my clinical practice on the nutrient deficiencies commonly associated with SIBO, explore the underlying mechanisms that lead to these deficiencies, and explain why stool testing is an essential tool in diagnosing and managing SIBO.

What are the symptoms of SIBO?

In my clinical experience, nutrient deficiencies linked to SIBO often manifest in a variety of ways, sometimes extending beyond the typical digestive complaints. Many clients come to me reporting symptoms of fatigue, weakness, or even cognitive issues like brain fog. 

Fatigue, in particular, is a major red flag for nutrient malabsorption. I experienced this myself when I was diagnosed with Chronic Fatigue Syndrome. My clients often describe it as “never feeling rested,” even after a long night’s sleep. Some also experience anxiety, brain fog or difficulty concentrating, which can be traced back to a deficiency in B vitamins, particularly vitamin B12, which is essential for neurological function.

Skin issues are another common sign of nutrient deficiencies that I’ve seen in clients with SIBO. One client, for example, came in with dry, flaky skin and frequent rashes, which she couldn’t relate to any particular food she was eating or activities she was doing. She was unaware that these symptoms could be linked to poor absorption of fat-soluble vitamins like A, D, E, and K, all of which are often depleted in those with SIBO due to fat malabsorption. 

Additionally, digestive symptoms like diarrhoea or constipation are common but are sometimes overlooked as contributing factors to nutrient loss. Over time, this can lead to significant deficiencies that affect not only the gut but the entire body.

Another frequently missed symptom is anaemia. Clients with SIBO are often unaware that their constant tiredness, which can be accompanied by pale-looking skin, could be linked to low iron levels. Bacteria in the small intestine can compete for iron, leading to iron deficiency anaemia. This was the case with one client who had been struggling with dizziness and shortness of breath for months before we addressed her iron deficiency.

Five critical nutrient deficiencies linked to SIBO

SIBO can severely disrupt nutrient absorption in the small intestine, leading to critical deficiencies that affect the whole body. Here are the five most common nutrient deficiencies I see in clients with SIBO, along with how SIBO contributes to each one:

Vitamin B12

In cases of SIBO, bacterial overgrowth competes with the body for essential nutrients, with vitamin B12 being one of the most affected. B12 is crucial for red blood cell production and neurological health. Unfortunately, the excess bacteria in the small intestine consume this vitamin before the body has a chance to absorb it. As a result, you may experience fatigue, brain fog, and even tingling or numbness in the extremities. I’ve seen many cases where persistent B12 deficiency led to these neurological symptoms, which we were able to trace back to SIBO.

Fat-soluble vitamins (A, D, E, and K)

SIBO often leads to fat malabsorption, which impacts the absorption of fat-soluble vitamins A, D, E, and K. The bacteria in the small intestine disrupt fat digestion by deconjugating bile salts, which are essential for proper emulsification and absorption of fats. 

Iron

Iron deficiency is another common issue with SIBO. The bacteria in the small intestine compete with the body for iron, leading to iron deficiency anaemia. Many clients come to me experiencing extreme fatigue, paleness, and sometimes dizziness, unaware that low iron could be at the root of their symptoms. Rather than just supplementing iron, dealing with the root of the issue leads to longer-lasting results. 

Magnesium

Magnesium absorption is also often compromised in clients with SIBO, especially when the gut lining becomes inflamed. The bacteria in the small intestine can damage the mucosal barrier, leading to impaired absorption of this essential mineral. Low magnesium can manifest as muscle cramps, fatigue, and even heart palpitations. 

In my clinical practice, clients with low magnesium due to SIBO often report poor sleep, irritability, and frequent muscle spasms, and although supplementing magnesium can be helpful, addressing the SIBO can have much quicker and longer-term results in relieving symptoms. 

Zinc

Zinc deficiency is also prevalent in those with SIBO and can have a significant impact on immune function and skin health. Similar to magnesium, zinc relies on a healthy mucosal barrier for absorption. The inflammation caused by bacterial overgrowth can impair this process, leading to low zinc levels. Many clients experience poor wound healing, frequent colds, and skin issues, not realising that low zinc levels may contribute to their symptoms. 

Each of these deficiencies can compound the symptoms of SIBO, further complicating the health picture for clients. By addressing SIBO and focusing on nutrient repletion, I’ve seen many clients regain energy, improve their immune function, and resolve a range of symptoms that had plagued them for years.

What causes SIBO?

The development of SIBO can be linked to several underlying causes, many of which I have seen in my clients. One common factor is gut motility disorders. Conditions like irritable bowel syndrome or hypothyroidism can slow down the movement of food and bacteria through the small intestine, allowing bacteria to accumulate. You can find out whether this is an issue for you by doing your colon transit time to get a more accurate picture of how long it takes food to move through your digestive tract. 

Another frequent cause I’ve encountered is low stomach acid. With reduced stomach acid, the body’s natural defence against bacterial overgrowth is weakened, allowing bacteria to thrive in the small intestine. Common signs of low stomach acid include bloating, heartburn, indigestion, a feeling of fullness after eating small amounts, and flatulence. 

Previous surgeries, such as gastric bypass or abdominal operations, can also create structural changes in the digestive tract that promote bacterial overgrowth. In some cases, a dysfunctional immune system also plays a role, as the body’s ability to keep bacterial populations in check becomes weakened.

How can stool testing help?

In my clinical experience, stool testing has been an invaluable tool for understanding the full impact of SIBO and guiding treatment plans. It provides a comprehensive snapshot of the gut’s bacterial composition, helping to identify dysbiosis or bacterial imbalances that are often at the root of SIBO. 

Stool testing also helps assess digestive function, particularly fat absorption. Many of my clients with SIBO experience fat malabsorption, which can be confirmed through stool tests showing unabsorbed fats. This information allows me to target therapies more effectively. Stool tests can also reveal markers of intestinal inflammation, giving insight into the degree of gut damage caused by SIBO.

Stool testing can identify bacterial imbalances and assess digestive function, giving clues about nutrient absorption. Evaluating short-chain fatty acids, digestive enzymes, and signs of inflammation helps to paint a complete picture of how SIBO or gut health is contributing to symptoms. 

Nutrient deficiencies are a common but often overlooked consequence of SIBO. As I’ve seen time and again in my practice, addressing these deficiencies is crucial to restoring overall health and improving both gut and systemic function. Stool testing provides vital insights into the bacterial imbalances and nutrient malabsorption caused by SIBO, allowing for a more targeted and effective treatment approach.

Breath testing is also valuable for diagnosing SIBO because it provides a non-invasive, straightforward way to detect bacterial overgrowth in the small intestine. By measuring the levels of hydrogen and methane gas in your breath after ingesting a specific sugar solution, the test reveals whether bacteria ferment carbohydrates too high up in the digestive tract. This information helps pinpoint SIBO as the root cause of symptoms like bloating, gas, and nutrient deficiencies and can help to rule out other possible causes of nutrient deficiencies. 

If you’re struggling with persistent fatigue, digestive issues, or symptoms that don’t seem to have a clear cause, it’s worth considering the role of SIBO and nutrient deficiencies in your health. Addressing the root cause of your nutrient deficiencies can make a significant difference in your health, allowing you to truly benefit from all the time and effort you’re putting into your diet and lifestyle changes.