Can IBS Cause Nutrient Deficiency Symptoms?

No one walks in the door of our clinic with just GI symptoms. In many cases, our clients are unknowingly suffering from nutrient deficiency symptoms. 

Most of our clients who are struggling with IBS, SIBO, reflux and other digestive issues have other symptoms such as fatigue, brain fog, hair loss, migraines, anxiety, depression and skin irritations.  As if having gut discomfort wasn’t enough to deal with!  

What do these other issues have to do with gut health?  Everything!

Nutrient deficiencies can make IBS worse

IBS, (irritable bowel syndrome) and SIBO (small intestinal bacteria overgrowth), are gastrointestinal conditions that can lead to malabsorption and nutrient deficiency symptoms if left untreated.

We find that nutrient deficiencies are often the cause of not only GI symptoms but symptoms that can affect the whole body. It’s the classic chicken and the egg situation where one issue causes another and you’re not sure which one caused which. In either case,  they can be better managed with proper nutritional repletion.

Let me tell you about when I was first diagnosed with SIBO.  I also had iron deficiency anemia, less than optimal zinc levels and was low in vitamin D.  This helped explain why I was feeling fatigue and experiencing increased anxiety.  On top of the bloating and constipation that SIBO caused.  As you know, having SIBO is really challenging to say the least.

Was I surprised?  Nope. We see this situation all the time.  

And I knew that healing from SIBO, increasing energy and feeling less anxious was going to take more than just following a low-FODMAP diet and getting treated for SIBO.  I also had to address my nutrient deficiencies because they were likely contributing to my digestive symptoms, as well. 

This article will discuss how IBS or SIBO can cause nutrient deficiency symptoms, how nutrient deficiencies can cause or exacerbate IBS symptoms, what nutrient deficiencies are most common, and how to correct them.

Why Are You Still Stuck With SIBO?

How Can IBS Cause Nutrient Deficiency Symptoms?

Even if you’re eating a seemingly balanced diet, IBS symptoms such as indigestion, constipation and diarrhea can impact your nutrition status. This is because IBS can disrupt the digestion of your food and can directly interfere with nutrient absorption(1).

What nutrient deficiency symptoms should you look out for? The most common symptoms we see in our practice include diarrhea, fatigue/weakness, muscle cramps, brain fog, hair loss, skin issues and weak fingernails. And tack on the diarrhea and cramping you may already be experiencing, and it can feel like an endless cycle!  If this sounds like you, then it’s time to turn this bus around!

There are five nutrients that we see to be low most often with IBS and other GI conditions like SIBO. If you have IBS, it’s important to get regular bloodwork done, including vitamin and mineral levels. This will help you to determine what you may need to change in your diet and if you need a supplement.

Common Nutrient Deficiencies with IBS

There are several nutrient deficiencies that can occur with IBS, but these five are the most common.

Vitamin B12

Vitamin B12 is one of the most common nutrient deficiencies we see with IBS and SIBO. Low vitamin B12 in itself can further exacerbate IBS symptoms you may already be experiencing such as diarrhea, fatigue, weakness, and brain fog. This combination of symptoms may further increase your B12 needs and require supplementation to treat the deficiency.

Vitamin B12 requires enough stomach acid to be present in order to be absorbed. The problem is there we often see low levels of stomach acid with IBS and SIBO.  Common reasons for low stomach acid include taking acid reflux medication. And one of the biggest reasons for low stomach acid is… STRESS!

The body could be making less of a protein in the stomach called intrinsic factor, which also helps your body absorb B12. Vitamin B12 is also a water-soluble vitamin, and so is more easily lost through bodily fluids such as in the case of diarrhea(2).

So between the lower than optimal stomach acid levels and/or low levels of intrinsic factor, it becomes very difficult for your body to absorb the B12 it needs, which can further aggravate your IBS symptoms.

Vitamin B12 has many important benefits in the body, and so it’s important to ensure you’re getting enough. It is involved in red blood cell and energy production, bone health, as well as in gut health. A recent study shows that vitamin B12 is used by bacteria in the gut, and is required for over a dozen enzymes that support a healthy gut environment(3).

So how do you know if you have low vitamin B12?

Vitamin B12 Deficiency Symptoms:

  • Nausea
  • Decreased appetite
  • Fatigue
  • Brain fog
  • Constipation, diarrhea, or gas
  • Muscle weakness, numbness or tingling
  • Shortness of breath

Foods High in Vitamin B12:

Vitamin B12 is mainly found in animal foods, oral supplements or injections.

  • Meat – fish, red meat, and poultry
  • Eggs
  • Dairy products

If you have IBS or SIBO, be sure to get your vitamin B12 levels tested via blood work. Additionally, ask your doctor about testing your folate and methylmalonic acid levels, which is a substance that is often high in B12 deficiency.

If your vitamin B12 levels are below 400pg/mL, which is still considered in the normal range, and you are experiencing symptoms, then you may benefit from a B-complex supplement.


Zinc is an essential mineral that helps wounds heal, supports our immune system (which is mostly in our gut), helps to make proteins and new DNA, and most importantly as it relates to gut health, it helps repair and protect our intestinal barrier. You may have heard of “leaky gut”. This is a common phrase for a compromised intestinal barrier that allows toxins, bacterial and allergens to enter the bloodstream. Having a gut that is more permeable means more food sensitivities, irritation, and inflammation. 

Further, stomach acid production requires zinc.  Having robust stomach acid levels is our first line of defense against bacteria entering the digestive tract through food (think food poisoning!).  We also need stomach acid to help digest protein, help absorb vitamin B12 & iron and to activate digestive enzymes.  

Studies have shown zinc deficiency is fairly common in IBS(5). And this is why it’s so important to get your zinc levels tested.  Ask your doctor to test for zinc.

You can also look at an indirect marker of zinc called alkaline phosphatase, which is commonly included in a Complete Metabolic Panel blood test. If one of these markers is low or at the lower end of the normal range, you may benefit from a zinc supplement. 

Zinc Deficiency Symptoms:

  • Poor wound healing
  • Diarrhea
  • Frequent infections
  • Acne
  • Ridges on fingernails

Foods High in Zinc:

  • Meat and seafood – Oysters, crab, lobster, chicken, turkey
  • Dairy, nuts, seeds and beans
  • Grains – Fortified cereals or bread

Vitamin D

Newsflash:  Almost all of our clients who are not supplementing with vitamin D and who live in the Northern parts of the United States are suffering from low levels of vitamin D. 

Vitamin D is a fat-soluble vitamin, which means that it needs fat to be absorbed in the intestine. With IBS and SIBO, inflammation in the intestines is common, which can affect vitamin D absorption.

Vitamin D plays a role in calcium absorption, bone health, and the prevention of muscle spasms and cramps.

Why vitamin D is crucial for gut health

Vitamin D helps maintain the intestinal barrier, so you are less likely to have “leaky gut” and inflammation.  Vitamin D also increases the diversity of the microbiome, which is the collection of good gut bacteria in the digestive tract that plays a huge role in digestive function, neurotransmitter production (hello good mood), and immune system regulation. 

Studies show that healthy people have a diverse array of microbes co-existing in their gut(7). We need to keep these critters happy and healthy!  

As I mentioned earlier, no one walks in the door with just IBS.  Almost every single client has some degree of anxiety and/depression.  And no wonder, chronic digestive symptoms can certainly affect your mood.  But gut health and mental health are intrinsically linked, and this is where your vitamin D status may be playing a role.

Studies show that those with vitamin D insufficiency or deficiency have higher rates of mental health conditions(9). Remember, the microbiome regulates neurotransmitter production and vitamin D levels contribute to a healthy microbiome.

Further, vitamin D receptors are in the parts of the brain that regulate emotions and neuron production, so you want to have enough vitamin D in the body so those receptors can latch on to them.

Be sure to ask your doctor to test your vitamin D levels and if it’s low or on the lower end of normal, you may benefit from a vitamin D supplement. This is especially since vitamin D is found naturally in only a few foods, so it’s a bit harder to get enough in the diet compared to some of these other nutrients.

Vitamin D Deficiency Symptoms:

  • Weakness
  • Muscle cramps and spasms
  • Fatigue
  • Depression
  • IBS symptoms, especially chronic constipation (10)

Foods High in Vitamin D:

  • Salmon
  • Sardines
  • Tuna
  • Mushrooms
  • Egg yolks
  • Fortified foods – orange juice, milk, and cereal grains

So how can you naturally boost your vitamin D levels? 

Getting regular sun exposure, when possible, is your best defense against vitamin D deficiency. If that is not enough, a combination of diet and supplements can get your levels back up where they need to be.


Magnesium is another essential mineral that tends to run low in those with IBS and SIBO. It plays a role in over 300 enzyme reactions in the body, many of which are involved with digestion.  It is a co-factor in the activation of digestive enzymes, it helps maintain appropriate pH levels of stomach acid and it helps improve muscle function of the digestive tract. 

Magnesium deficiency has also been linked to a potential increased risk of depression(12).

We rarely see low magnesium in blood test results since magnesium deficiencies are rare. We do know however that most of our clients are not meeting their magnesium needs through diet. 

Magnesium Deficiency Symptoms

  • Muscle twitches and cramps
  • Fatigue and weakness
  • Nausea and vomiting
  • High blood pressure
  • Irregular heartbeat
  • High blood sugar

Foods High in Magnesium

  • Almonds
  • Peanuts
  • Pumpkin Seeds
  • Popcorn
  • Spinach
  • Dark Chocolate
  • Fortified cereals and grains

We find that certain symptoms respond well to magnesium supplementation such as constipation, insomnia, migraines, and muscle twitching.


Iron is another very common nutrient deficiency in IBS and its absorption is affected by your gut health. Like vitamin B12, adequate stomach acid is needed for iron to be absorbed. It’s is also an essential nutrient needed for gut bacteria, and so when there is not enough of it this can disrupt gut balance even further(14).

This essential mineral is needed for red blood cell production as well as proper growth and development throughout life. Iron carries oxygen from the lungs to all parts of the body. Your body also needs iron to make hormones, including ones involved in digestion and gastrointestinal health(15).

Iron Deficiency Symptoms:

  • Fatigue
  • Weakness
  • Shortness of breath
  • Hair loss
  • Brittle nails
  • Cold hands and feet

Foods High in Iron:

  • Meat and seafood – Clams, beef, liver, oysters
  • Tofu
  • Beans – white beans, chickpeas, lentils
  • Spinach

If you are experiencing any of these symptoms, ask your doctor to order an iron panel with ferritin. Ferritin is a protein that stores iron, and so it is one of the most accurate ways to test your iron stores. Reference ranges for ferritin vary across medical practices, but the American Gastroenterology Association diagnoses iron deficiency with a level less than 45 ng/mL(16).

We don’t typically recommend iron supplements in all cases, especially for men or post-menopausal women in our practice. This is because in these cases, daily iron needs are lower. With all of our clients, we work to determine the underlying cause of iron deficiency in order to properly address it.

Key Takeaways – How Can IBS Cause Nutrient Deficiency Symptoms?

IBS, SIBO and GI issues can cause multiple nutrient deficiency symptoms (and nutrient deficiencies can cause GI symptoms), which can make for a never-ending cycle of misery. If your IBS has worsened, speak to your doctor to get your nutrient levels checked.

Managing digestive conditions takes a holistic approach, and proper nutrition guidance can help you reduce symptoms across the whole body. Knowing your numbers and optimizing your nutrition is part of our core focus in our personalized gut healing program.

And if you need a high quality, professional grade supplement, you can purchase them using our discount through our dispensary.

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