Why Gut Issues Can Cause Nutrient Deficiencies

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Some of the biggest, and often overlooked, health issues in people with digestive disorders are nutrient deficiencies. Low nutrient levels can be caused by many factors, including lack of nutrient intake, maldigestion, malabsorption, loss of appetite, and increased energy expenditure. Plus, they’re especially prevalent in people with irritable bowel disease (IBD), including Crohn’s disease and ulcerative colitis. 

Research has shown that up to 85% of people with IBD are lacking critical micronutrients—including during the active phases of IBD and when it’s in remission. The most common deficiencies include B-vitamins, vitamin D, vitamin K2, zinc, calcium, selenium, magnesium, and iron.

That’s why for my patients with GI issues, I will normally recommend two things—daily supplementation and fixing the underlying cause of low nutrient levels.

What Causes Nutrient Deficiencies?

The biggest, and perhaps most direct, reason for nutrient deficiencies in people with gut health issues is malabsorption syndrome. Your body absorbs nutrients from the foods you eat through your small intestine, which is lined with villi and microvilli which produce enzymes that make nutrient absorption possible. If you have IBD, your intestinal lining may be inflamed, which disrupts this important process and makes it much tougher for nutrients to be absorbed.

Another culprit can be a lack of appetite. Symptoms of IBD—including gas, bloating, and indigestion—can reduce your desire to eat, so you’re less likely to eat all the foods you need to keep your nutrient levels where they should be. Plus, if you have had surgery for your IBD, such as having a section of your intestines removed, you have less intestinal capacity to absorb nutrients.

Now, what if you have irritable bowel syndrome (IBS), not IBD? Can IBS also cause nutrient deficiency? While people with IBS are typically less likely to have malabsorption syndrome, IBS can cause loss of appetite due to abdominal discomfort, and make it more difficult for your body to digest foods like gluten, dairy, soy, and corn—which can also lead to nutrient deficiencies.

Plus, if someone with IBS has SIBO (Small Intestine Bowel Overgrowth), which is VERY common in those with IBS, the imbalance of gut flora can cause malabsorption. So, whether you have IBD or IBS, it’s important to pay attention to your nutrient levels.

Here's why these nutrient deficiencies can have a big impact on your health.

B-Vitamins Support Your Heart, Brain & Overall Health

B-vitamins are real powerhouse nutrients inside your body. Vitamin B6, for example, is an essential “cofactor” in the functioning of 140 separate universal enzymes inside your body—without it, many important processes won’t happen. Vitamins B12 and folic acid (vitamin B9) are just as critical.

This important trio of nutrients which can be lacking in people with gastrointestinal issues help to support:

  • Normal Homocysteine Levels: Homocysteine is an amino acid found in your blood that is a byproduct of normal metabolic functions inside your body. While some homocysteine is normal and fine—and your body is equipped to handle it—high levels can cause your body to deposit sticky, artery-clogging platelets in your blood vessels. The combination of folic acid and vitamins B6 and B12 help to support normal homocysteine levels by helping to neutralize excess homocysteine.
  • Healthy HDL Cholesterol Levels: HDL (high-density lipoprotein) cholesterol, often called the “good” cholesterol, helps to clear oxidized LDL cholesterol that can clog your arteries out of your body through your liver. The trio of folic acid, vitamin B12, and vitamin B6 help to support healthy HDL cholesterol levels.
  • Memory: The combination of folic acid and vitamin B12 supports memory by enhancing immediate and delayed recall. Plus, the combination of folic acid and vitamin B12 may support cognitive health.

Two other B-vitamins often deficient in people with gastrointestinal issues are vitamin B1 (thiamine) and B5 (pantothenic acid). Thiamine plays an important role in generating energy in your cells, helps to keep your cell walls strong and functioning, and is essential for healthy brain function. Plus, pantothenic acid helps to convert carbohydrates into glucose, your body’s fuel.

Vitamin K2, Selenium, Magnesium & Iron Are Just as Critical 

  • Vitamin K2 (MK-7): MK-7 helps to promote healthy circulation by helping to keep calcium from building up in your arteries—where you don’t want it—and instead shuttles it to your bones where you need it. Just one note of caution that people on blood thinners should avoid taking vitamin K2.
  • Selenium: This vital trace mineral helps to support normal thyroid function. Plus, it’s necessary for several housekeeping functions inside your body, supporting normal cell growth, keeping your immune system efficient by enhancing T-cells that fight infections, and providing antioxidant support.
  • Magnesium: This essential mineral is a necessary catalyst for hundreds of biochemical reactions inside your body. It does everything from helping your heart to stay in proper rhythm, to supporting healthy arteries and muscle function, to blood pressure, cellular energy, and more.
  • Iron: If you’re frequently tired, you may be lacking iron—also called iron deficiency anemia. Your body needs iron to create hemoglobin, which is the component of red blood cells that carries oxygen from your lungs to cells throughout your body. Since too much iron can be just as harmful as too little, you want to work with your doctor to check your iron levels before taking iron supplements.
  • Vitamin D: The “sunshine vitamin” as it’s commonly called, vitamin D is an immune-modulating vitamin that is also helpful for maintaining a healthy bone structure.  A large percentage of the population is deficient in Vitamin D – fortunately, levels can rise with increased sun exposure and through supplementation.  

How Can You Avoid a Nutrient Deficiency?

Whether you are dealing with maldigestion, malabsorption, loss of appetite, and really any gastrointestinal condition that predisposes you to chronic inflammation, it’s really important to work on the underlying issue at hand to get the nutrient deficiencies under control. 

Taking nutritional supplements without fixing the “leak” so to speak is like filling up the tub to take a bath yet leaving the drain open. A lot of water will be wasted, and the tub may never entirely fill up.  The same concept is true for treating nutrient deficiencies–if the gut is inflamed nutrients may not be absorbed well. So, in addition to supplementing, it’s really important to work with your doctor to identify and treat the underlying cause of your nutrient deficiencies. 

If you have a gastrointestinal issue such as IBD or IBS, I recommend taking B-vitamins, vitamin D, MK-7, selenium, and magnesium daily. It’s also important to get your iron levels checked to make sure you’re not anemic. Plus, I also recommend supplementing with calcium and zinc if you’re low on these nutrients.

Keeping your nutrient levels where they should be is extremely important for your heart, brain, energy levels, and overall health—so it’s not something you want to ignore.

Dr. Drew Sinatra

Meet Dr. Drew Sinatra

Dr. Drew Sinatra is a board-certified naturopathic doctor and self-described “health detective” with a passion for promoting natural healing, wellness, and improving quality of life by addressing the root cause of illness in patients of all ages. His vibrant practice focuses on treating the whole person (mind, body, and spirit) and finding missed connections between symptoms and health issues that are often overlooked by conventional medicine.

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