IBS & Nutrient Deficiencies: Everything You Need to Know

No one walks in the door of our clinic with just GI symptoms. Alas, IBS and nutrient deficiencies can go hand in hand, just like nutrient deficiencies and other digestive conditions. In many cases, our clients are dealing with a LOT of symptoms, including fatigue, brain fog, hair loss, migraines, anxiety, depression and skin irritations. As if having gut discomfort wasn’t enough to deal with!

Luckily, our clients are in good hands to get things sorted out so that they can find lasting relief. If you’re new around here – welcome! I’m Sara Kahn, MS, CNS, CDN. I am a board-certified functional and integrative nutritionist in New York City and I have been serving clients locally and beyond for years. Here at Belly Bliss Nutrition, my team and I use our clinical expertise and personal experience with digestive issues to help our clients get down to the root causes of their digestive issues – including IBS – so that they can finally feel better. Sweet relief!

In this article, I’ll explain to you what IBS is, how it can be connected to nutrient deficiencies (and vice versa), as well as what you can do about it. I’ll also invite you to check out our services if you’d like support.

Let’s start with a super-quick overview of what IBS is.

What is IBS?

IBS – short for Irritable Bowel Syndrome – is a squirrelly condition where your digestive tract might look normal but is not acting like it should. No, your symptoms are not “in your head”, they’re simply not something that can be seen or measured by an endoscopy or colonoscopy.

IBS can be caused by a number of different factors, including genetics, food allergies, food poisoning, food intolerances, various types of dysbiosis, changes in how your muscles contract, and more. It’s complicated!

For many folks who have IBS, the muscles and nerves in your digestive tract are not working like they should be. This can cause anything from gas and bloating to pain, constipation, and diarrhea. In addition to all of those icky symptoms, IBS can cause  – drumroll please – nutrient deficiencies.

To make matters worse: nutrient deficiencies can make your IBS symptoms worse – ACK!

Remember IBS is always caused by something and it’s important to determine and address the root cause.  For a full rundown on IBS, click here: A complete overview of IBS.

Nutrient deficiencies can make IBS worse

If IBS and nutrient deficiencies are going hand in hand, which came first?

Unfortunately, this is a classic chicken or the egg situation; either could have come first. But as a clinician, I’m here to help drill down to the root causes so that we can find the custom solution that will actually work for you.

This is an important problem to solve. A recent study found that folks with IBS were at far greater risk of nutrient deficiencies, including Vitamin B12, Vitamin D, zinc, and more (SOURCE).

Why? Folks with IBS might be following a more limited diet and avoiding whole food groups for fear of disruptive symptoms – who wants to sign up for an afternoon spent running to the bathroom? Plus, if you’re dealing with chronic constipation or diarrhea, you’re probably not absorbing your nutrients as well as you could be.

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 fatigued 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.

How Can IBS Cause Nutrient Deficiency Symptoms?

As we began to explore earlier, IBS can cause nutrient deficiencies.

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 
• weak fingernails

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! (Psst: We can help – click here to find out how)

In the meantime, there are five nutrients that we see to be low most often with IBS and other GI conditions like SIBO:

• Vitamin B12
• Zinc
• Vitamin D
• Magnesium
• Iron

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.

5 Common Nutrient Deficiencies with IBS

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

1.    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 that 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 a water-soluble vitamin, and so is more easily lost through bodily fluids such as in the case of diarrhea(2).

Vitamin B12 is absorbed in the small intestine.  If you have SIBO, the inflammation it causes in the small intestine can impact your body’s ability to absorb it.

So between 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:

• 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, which is another important B vitamin. We like to see Vitamin B12 levels be above 750 pg/mL.  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.

2.    Zinc

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, bacteria 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 plasma 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

3. Vitamin D

Newsflash:  Almost all of our clients are suffering from low levels of vitamin D unless they’re taking a supplement regularly.

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 important 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.

For more info about Vitamin D, check out this article: Vitamin D, Depression, and Gut Health – Is There a Connection?

4. Magnesium

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.

Basically, magnesium is oh-so important for your digestive system and beyond.

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
• Constipation – could your IBS-C be caused by a magnesium deficiency or insufficiency?

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, anxiety, migraines, and muscle twitching.

5. Iron

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 and legumes – 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 when ferritin levels are 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.

Note: This blog post was originally published April, 2022. It was updated and reposted in January 2025.

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