Vitamins for Gut Health

By: David Meine

| December 10, 2021

One of the best things you can do for your health–especially for the health of your gut microbiome–is to supplement your diet with essential vitamins and minerals. They’re called “essential” for a reason. Read on to learn more about the best vitamins for gut health.

Do vitamins really make a difference?

I used to believe that supplements just made for expensive urine. I thought my body didn’t really absorb much, and that I was flushing most of the benefits away. But then I started measuring their effects.

Turns out, I was wrong. For the past three years, I’ve had extensive bloodwork done. And, with proper supplementation, I’ve watched my bloodwork change for the better. At each appointment, I can see the difference in the lab reports that proper supplementation has made in my life. But, more importantly, I can absolutely feel the difference!

Why do I need to take supplements?

A supplement, as its name describes, is meant to be supplementary to a nutritious diet. But the sad truth is, it’s fairly impossible to get all the nutrients we need from food alone. 

Before we’d begun to think of genetically modifying food or the use of chemical fertilizers and pesticides, our soil was severely depleted. The US Senate published this fact clear back in 1936. A study published in 2003 confirmed that our soil was significantly more depleted then than it was in 1940.

This means that if you live in the US, even the healthiest eater simply isn’t getting all of the minerals and nutrients they need from food alone. Most of us are deficient in vitamin D3, the B vitamins, omega-3s, and magnesium, to name a few. 

What vitamins are best for gut health?

Vitamins and minerals are essential for gut health. They help reduce inflammation in the body and repair damage to your gut microbiome that causes leaky gut syndrome. 

Here’s a list of vitamins that most people need and feel noticeable benefits from when added to their daily regimen.

Vitamin D3

D3 is where we are most commonly deficient. If you only take one vitamin, this should be it. Vitamin D3 is necessary for our bodies to be able to absorb calcium and phosphorus. But its equally important as a boost to our immune systems. 

We need more vitamin D than we think. Dr. Gundry estimates that most Americans have very low levels of vitamin D. He practices in California, where there is plenty of sunshine. But 80% of his patients are vitamin D deficient. If a patient has an autoimmune issue, that percentage increases to 100%. We simply don’t get enough Vitamin D through foods and sunshine alone. 

Vitamin D is a super vitamin for gut health. Plus, it’s an easy one to add. Start by adding 5,000 IUS of vitamin D3 daily. If you’ve been diagnosed with an autoimmune disease, start with 10,000 IUs a day. 

A simple blood test will show the vitamin D levels in your body. You can order a finger poke test here and do it from home. My wife Carla, a Certified Functional Nutrition Counselor, likes to see her clients’ bloodwork above 70ng/ml.

The B Vitamins

Many of Carla’s clients are dealing with leaky gut syndrome. This means the microbiome in their gut has been compromised. Because many B vitamins are produced by good gut bacteria, these clients are usually deficient in their B vitamins.

Vitamin B complex is composed of eight B vitamins, and they are the building blocks of a healthy body, directly impacting energy levels, brain function, and cell metabolism. Vitamin B does not stay in the body long, which makes daily supplementation important.

We recommend taking a 1,000-microgram methylfolate tablet each day and putting 1,000 micrograms of methyl B12 under your tongue daily as well. 

Vitamin C

Vitamin C brings a wealth of health benefits. It contributes to the production and formation of collagen, helps wounds heal, strengthens bones and blood vessels, assists in iron absorption, is an antioxidant, and boosts your immune system. 

Figuring out how much vitamin C you need is easy. Start with one tablet a day. Wait a few days. As long as you don’t experience any diarrhea, you can add another tablet. Your body will tell you (through your bowel movements) when you have enough vitamin C.

We like the brand EZ Melt because it dissolves in your mouth, but there are lots of good brands on the market.


Another supplement that provides a host of benefits are omega-3 fatty acids. These, like vitamins, are very important for gut health, as they help repair the gut wall. 

Studies show that most people are profoundly deficient in omega-3s. This is especially worrisome as omega-3s are directly related to brain health. Studies show that the higher the levels of omega-3 fats in your blood, the bigger your brain is, and the better your memory is. 

We encourage taking 1,000 mgs of DHA a day. This typically means taking four soft gels of 1,400-mg fish oil capsules each day. We’ve seen remarkable results and improvement in brain fog, which is something so many of us have struggled with.

There are many other helpful vitamin and mineral supplements to take for your overall health. We detail these, including magnesium, pre and probiotics, and blood sugar managers in our book, Eating to Live: Unlocking the Leaky Gut Code.

Your Body and the Vitamins You Need for Gut Health

This list provides an excellent starting point, but everybody’s body is unique. Every client my wife works with is different, with different supplementation and dietary needs. We strongly encourage you to work with your doctor and find out which vitamins and minerals you’re deficient in. Your bloodwork will tell you. And then, you can watch your bloodwork improve as you add the right supplements to your regimen. Even better, you’ll feel the improvement!

Gain energy, boost your immune system, and start healing your gut as you add vitamins and minerals to a healthy diet and lifestyle.