best vitamins for gut health

Best Vitamins for Gut Health

While probiotics often dominate the gut health industry, certain vitamins also play a crucial role in maintaining a strong gut lining, promoting bowel regularity, and reducing inflammation. 
In this article, we’ll review the best vitamins for gut health, food sources of these nutrients, and proper dosing for supplementation.

Vitamin D

An estimated 40 percent of people in certain areas of the United States may be deficient in vitamin D. While this vitamin is well-known for its role in bone strength and immune function, it is also necessary for optimal gut health. For example, supplementing with vitamin D may improve the diversity of your gut bacteria and reduce levels of inflammation in the blood (1, 2). While this benefits any individual, it is particularly important for people with inflammatory conditions, like inflammatory bowel disease (3). Ask your doctor to check your vitamin D levels at your yearly visit. However, keep in mind that a “normal level” does not necessarily mean optimal. In our practice, we prefer vitamin D levels around 50 ng/mL for best outcomes.
Dosing: 2,000 - 5,000 units per day depending on your blood levels. We recommend taking a vitamin D supplement with vitamin K2 to reduce calcium deposits in the blood. Buy Vitamin D + K2 drops.

Food sources of vitamin D: salmon, mushrooms, fortified milk

vitamin D dropper

Vitamin D3/K2 Liquid

Increased energy & improved mood is just a drop away.


While technically a mineral, magnesium has over 300 functions in the body and is particularly important for gut health. Magnesium oxide is the most common supplement form of this mineral, however, it is not well absorbed and often causes diarrhea or GI upset. If you suffer from constipation or hard stools, magnesium citrate is the best option. This form of magnesium works by pulling water into the intestines to make bowel movements softer and easier to pass. However, we often recommend a combo supplement with magnesium citrate and glycinate in order to reap the other benefits of this mineral like supporting healthy sleep and blood sugar balance.
Dosing: start with 200-250 mg of magnesium per day, increasing to 450 mg as needed. Find magnesium in our Root Shop.

Food sources of magnesium: pumpkin seeds, chia seeds, almonds, spinach, cashews, black beans

magnesium combo

Magnesium Combo

Three forms of highly absorbable magnesium in one capsule.

Vitamin C

Vitamin C is a powerful antioxidant known to fight off inflammation. Plus, it is also required for your body to make collagen, a protein essential for the structure and function of skin, muscles, and tissue, like that found in the gut lining. Some studies suggest vitamin C supplements can positively change the bacterial composition in your gut as well (4).
Dosing: 500 - 1,000 mg per day. Start slow and increase as tolerated. Some people may experience diarrhea or other digestive discomfort with high doses of vitamin C. 

Food sources of vitamin C: bell peppers, oranges, kiwi, broccoli, strawberries


Zinc is one of the top mineral deficiencies we see in our practice. This is unfortunate as it is also one of the best nutrients for gut health. For instance, zinc is required to maintain the strength and function of your intestinal cells. When the integrity of your gut lining is compromised, larger food proteins or harmful bacteria may enter into the bloodstream. This is known as a “leaky gut” which may cause food sensitivities and even trigger autoimmune disease.
Dosing: 10 - 30 mg of zinc per day in the form of zinc picolinate, glycinate, or citrate. Find zinc in our Root Shop. Make sure you also take a multivitamin that contains copper, as taking too much zinc for longer periods may cause a copper deficiency.

Food sources of zinc: oysters, beef, pumpkin seeds, pork



A super mineral for skin, hormone, & immune health


While obviously not a vitamin, we would be remiss without mentioning one of our most popular and effective probiotics for overall gut health. Megaspore is a soil-based probiotic, which means it is able to survive the harsh environment of the gut that typically destroys probiotics before reaching their destination. Soil-based probiotics have shown to balance gut bacteria, produce antioxidants, improve leaky gut, and lower inflammation in the body. Read more about Megaspore and soil-based probiotics. 
Dosing: Start with one capsule every other day and slowly increase as tolerated over a few weeks for a goal of two capsules daily. 


The ultimate spore-based probiotic

Fiber for Gut Health

While supplements can serve as an important addition to a functional medicine treatment plan, you cannot out-supplement a poor diet. Your gut requires a variety of whole foods, fiber, healthy fats, and protein. Make sure to include a good source of fiber with every meal and snack. Fruits, vegetables, nuts, seeds, legumes, and whole grains are the best sources of fiber to fuel your healthy gut bacteria. Need some inspiration? Check out our Root Meal Plans, each specifically designed for general health, constipation, or people with symptoms of gas and bloating.

Key Takeaways

Your gut is a complex ecosystem that requires the right fuel and environment to function properly. Some of the best vitamins for gut health include vitamin D, magnesium, vitamin C, and zinc. An effective probiotic, like Megaspore, can provide additional benefits by correcting imbalances in gut bacteria and reducing leaky gut. Finally, you should always include a source of fiber with each meal and snack to promote a robust and diverse gut microbiome. 

Get started with our FREE hormone and gut health friendly recipes

& Sign up to receive tips and updates from Root.

Related Articles

An image of some food.

PCOS and Constipation

Constipation is a fairly common symptom among women with polycystic ovary syndrome (PCOS). In this article, we’ll discuss the relationship between PCOS and constipation, and how you can treat the root cause of both of these conditions with diet, lifestyle, and targeted supplementation.

hashimoto's graves'

Hashimoto's vs. Graves'

Hashimoto’s and Graves’ are both autoimmune disorders affecting the thyroid, a butterfly-shaped gland located at the front of your neck. In both of these conditions, the body creates differing antibodies that attack and damage the thyroid gland.