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Best Vitamins for Gut Health: How to Support Your Gut Microbiome

Written by Dr. Michael Ruscio, DC on April 28, 2025

Written by Dr. Michael Ruscio, DC on April 28, 2025 — Reviewed by Hannah Wright

• Vitamins for Gut Health|
• Vitamins You’re Not Getting|
• Vitamin A|
• Vitamin C|
• Vitamin E|
• Vitamin D|
• Multivitamins|
• Diet|
• Probiotics|
• Glutamine & Hydrochloric Acid|

Essential Vitamins and How They Affect Gut Health 

A well-functioning gut is key to absorbing dietary vitamins. However, the relationship goes both ways—the gut and its microbiota also need vitamins to function well 1. 

Research into this two-way relationship between the gut and vitamins is still in its early stages. That said, vitamins seem to support gastrointestinal health by influencing the makeup and activity of the gut microbiome, as well as maintaining the integrity of the gut barrier and the immune system 1.

Some vitamins are water-soluble, meaning they dissolve in water and aren’t stored in the body for long, so we need to replenish them regularly 2. They act mainly as cofactors, helping enzymes in the body function properly. 

Water-soluble vitamins are crucial for energy production, cell metabolism, and maintaining healthy skin, nerves, and immune function. They include 1:

• Vitamin C
• B Vitamins (like B1, B2, B3, B6, B12, folate, and others) 

Other vitamins are fat-soluble, requiring fat to dissolve them, and are stored in the body’s fatty tissue and liver 2. We don’t need to consume them as often as water-soluble vitamins because the body can hold onto them for longer periods. 

Fat-soluble vitamins form important parts of cell walls and play key roles in vision, bone health, immune function, and blood clotting. These vitamins include 1:

• Vitamin A
• Vitamin E
• Vitamin D
• Vitamin K 

All our essential vitamins may also keep the gut healthy by increasing the variety of beneficial gut microbes, boosting the immune system, and protecting the gut from harmful damage caused by free radicals 1. 

The following table summarizes how different vitamins may support gut health 1.

The Gut Health Vitamins You’re Not Getting

Eating a diet full of vitamins (or taking supplements when needed) is the best way to avoid vitamin shortages that could compromise your gut health or make gut issues worse.

Unfortunately, the following four vitamins for gut health are often lacking in the diet.

Vitamin A

Vitamin A is necessary for keeping the intestinal barrier healthy, so low levels could play a role in a leaky gut and imbalanced gut bacteria. Studies have found that vitamin A can help improve the gut microbiome, reduce diarrhea, and lower the risk of norovirus 1 3 4. 

Dietary Sources of Vitamin A

Vitamin A in food comes from animal products as retinol (the active form) and from fruits and vegetables as carotenoids (which the body converts to active vitamin A) 1. 

Eating these foods regularly will likely give you enough vitamin A 5:

• Oily fishes like herring and salmon
• Beef liver and other organ meats 
• Green leafy vegetables
• Other colorful (especially orange and yellow) vegetables like sweet potatoes, carrots, broccoli, and winter squash
• Orange fruits like cantaloupe, mangos, and apricots
• Dairy products like milk and cheese
• Eggs

Vitamin A Dosage

• Women need 700 micrograms (about 2,300 IUs) per day 2. 
• Men need 900 micrograms (3,000 IUs) per day 2. 
• Pregnant adults need 770 mcg per day 6.
• Breastfeeding adults need 1,300 mcg per day 6.

Is Testing for Vitamin A Helpful?

No. A blood test can help confirm a vitamin A deficiency—when your blood levels are less than 20 mcg/deciliter—but it may not accurately reflect the true amount of vitamin A in your body 7. 

Vitamin C

We don’t know much about how vitamin C directly impacts the gut microbiome, but lab studies show it has antimicrobial effects on bacteria, viruses, and fungi 1. 

One human study found that delivering vitamin C to the colon may increase healthy gut compounds called short-chain fatty acids 8. Vitamin C might also reduce harmful free radicals in the gut lining and help fight H. pylori infections in the stomach 1.

Dietary Sources of Vitamin C

It’s relatively easy to get enough dietary vitamin C if you eat more fruits and vegetables. Some of the best sources include 2 9:

• Citrus fruits (such as oranges and grapefruit) and their juices 
• Red and green bell peppers 
• Kiwifruit
• Broccoli
• Strawberries
• Cantaloupe
• Baked potatoes
• Tomatoes

Vitamin C Dosage

• Women need 75 mg per day 2.
• Men need 90 mg per day 2. 
• Pregnant adults need 85 mg per day 9.
• Breastfeeding adults need 120 mg per day 9. 

Is Testing for Vitamin C Helpful?

No. Blood tests aren’t great for diagnosing a chronic vitamin C deficiency (less than 0.2 mg/deciliter in plasma). Plus, it’s easy to get enough vitamin C by adding more fruits and vegetables to your diet. Most people will also respond quickly to vitamin C supplements 10.

Vitamin E

Vitamin E is a fat-soluble antioxidant that helps repair cell membranes to keep them healthy 1.

Some studies have suggested that vitamin E also has the potential to shape the gut microbiome 11. With its antioxidant capabilities, vitamin E might help combat free radical damage in the gut and maintain the integrity of the gut wall 1.

Dietary Sources of Vitamin E

The richest sources of vitamin E are foods that contain unsaturated fats, so low-fat diets may not meet your vitamin E needs. Most people will be able to get enough if they eat nuts or vegetable oils daily, especially as 12:

• Hazelnuts, almonds, peanuts, or sunflower seeds
• Wheat germ oil, sunflower oil, or safflower oil

Leafy greens, including spinach and broccoli, also provide some vitamin E 2. 

Vitamin E Dosage

• Adults (including pregnant) need 15 mg per day 2.
• Breastfeeding adults need 19 mg per day 12.

Is Testing for Vitamin E Helpful?

No. True Vitamin E deficiency (less than 0.5 mg/deciliter) is rare. Testing has little to offer unless you have 13:

• Genetic mutations that limit your ability to absorb or make use of vitamin E 
• Fat malabsorption issues caused by conditions like cystic fibrosis or chronic pancreatitis

Vitamin D

Early evidence suggests that vitamin D from sunshine may help regulate the gut microbiome 14. Some studies also link vitamin D supplements to changes in gut microbiota, though the results aren’t consistent 15. 

Overall, the evidence is mixed. One meta-analysis (study of studies) showed that vitamin D supplements probably won’t improve irritable bowel syndrome (IBS) symptoms unless your vitamin D levels are very low (less than 20 ng/mL) 16. 

Meanwhile, a systematic review (methodical summary of studies) hinted that vitamin D might be linked to fewer relapses in people with inflammatory bowel disease (IBD) 17. 

Dietary Sources of Vitamin D

It’s hard to get enough Vitamin D from the diet alone. Sunlight is usually the best source, with diet playing more of a supporting role. 

Still, here are some of the best dietary sources, though you’d need to eat a lot of them daily to meet your needs:

• Fatty fish like trout, salmon, tuna, and mackerel, and fish liver oil 18
• Fortified milk: Most of the U.S. milk supply, along with many plant-based alternatives, is fortified with about 3 mcg (120 IU) of vitamin D per cup 18.
• Mushrooms 18 
• Beef liver, egg yolks, and cheese 18

Vitamin D Dosage

• Most adults (including pregnant and breastfeeding) need 10–15 mcg (400–600 IU) per day 2.
• Older adults (over 70) need 20 mcg (800 IU) per day 18. 

I usually suggest my clients try to keep their blood levels of vitamin D between 100–125 nmol/L (40–50 ng/mL)—a bit higher than the standard 75 nmol/L (30 ng/mL)—because in my experience, most people do better at this range. For clients with autoimmune conditions, I often recommend aiming even higher, up to 125–150 nmol/L (50–60 ng/mL).

As I discuss in Healthy Gut, Healthy You, here are some general supplement guidelines:

• A typical maintenance dose for adults is 50 mcg (2,000 IU) per day.
• A treatment dose to correct a deficiency is 150 mcg (6,000 IU) per day.

In the clinic, I use vitamin D3 combined with vitamin K₂ 19, and I usually recommend a moderate daily dose of 50–100 mcg (2,000–4,000 IU). 

If you’re on blood thinning medications like warfarin, check with your doctor before taking anything with vitamin K.

The Sunshine Vitamin

Vitamin D is unique because you don’t need to get it from food if you get regular sun exposure. In fact, research suggests that safe, non-burning sun exposure is the best way to meet your vitamin D needs 20. Vitamin D from the sun might also benefit the gut microbiome more than supplements 14 21 22.

How much sun you need depends on factors like your current vitamin D level, your skin color, and where you live 23. Sunlight access can be limited, but here are some general daily guidelines:

• Darker skin (phototypes V–VI): 25–40 minutes of midday sun on about 35% of your skin, without sunscreen 24 
• Lighter skin (phototypes I–IV): Around 9 minutes of sunlight on about 35% of skin around noon (without sunscreen) from March to September, or 13 minutes daily from June to August 25

Given that food sources of vitamin D are limited and less effective, aim for healthy sun exposure when possible. 

Is Testing for Vitamin D Helpful?

Yes. Testing your vitamin D level once or twice a year is worth it because low levels are common and testing is fairly affordable (usually less than $50). It gives you a clear picture of whether you need supplements and how much. If you have liver or kidney disease, you may need testing more often—check with your doctor for guidance 26.

With regular testing, you can adjust your daily dose as needed based on your test results.

Can Multivitamins Improve Gut Health?

Eating a whole-foods diet is generally the best way to get the nutrients your body needs. If gut issues are preventing your digestive tract from absorbing nutrients, it’s better to focus on healing your gut and eating well than to rely on vitamin supplements long-term.

Some nutrient-dense diets to consider include: 

• Mediterranean diet
• Paleo Diet
• Low FODMAP Diet

Still, I sometimes recommend a temporary multivitamin for clients dealing with digestive issues. A full-spectrum multi can help cover nutritional gaps when your digestion is impaired or your diet is limited 27, but it does have some downsides. 

For example, multivitamins can meet most nutrient needs, but they typically lack potassium and fiber 28. Plus, you might get more of some nutrients than you need, which could push you over safe upper limits 29. 

That’s why it’s helpful to calculate how much you’re getting from food first—then you can decide whether a multivitamin or individual vitamin supplements make more sense for you.

Probiotics 

Before increasing their vitamin intake, I usually suggest my clients start with probiotics, and for good reason. Not only do probiotics improve digestive symptoms, but they can also improve your ability to absorb nutrients, including key gut-supporting vitamins.

When my clients have digestive symptoms, I typically recommend multi-strain probiotics first. These can help relieve symptoms of IBS gas, bloating, abdominal pain, diarrhea, and constipation, with very few side effects 30.

Probiotics can also correct gut problems like dysbiosis (microbial imbalance), leaky gut, and inflammation, which in turn can improve nutrient absorption and reduce your need for vitamin and mineral supplements.

Research backs this up:

• A meta-analysis showed that probiotics can increase iron absorption 31.
• Two randomized controlled trials (gold-standard studies) showed that synbiotics—a combo of probiotics and prebiotics—can improve micronutrient absorption 32 33.
• A systematic review showed that probiotics can improve the absorption of vitamins B12 and B9 (folate) 34. 
• Other studies have shown that probiotics may boost the absorption of calcium and zinc 34.

Plus, the beneficial bacteria in a healthy gut can actually make B vitamins and vitamin K, which may improve overall nutrient status 1 35.

For some clients who struggle with absorption, I may also recommend:

• L-glutamine: This amino acid may help keep the gut lining strong 36—especially if stress, illness, or intense exercise have taken a toll 37.
• Hydrochloric acid (HCl): Without enough stomach acid, you can’t digest food or absorb nutrients properly—betaine HCl might help if other gut treatments haven’t worked 38.

Ways to Support Gut Health Naturally–Beyond Vitamins

Here’s a quick rundown of simple habits to support gut health:

• Eat more fiber: Both soluble and insoluble fiber feed beneficial gut bacteria and keep you regular.
• Manage stress: Ongoing stress can alter your gut microbiome and disrupt digestion. Practices like deep breathing, meditation, and movement can help bring balance.
• Use antibiotics only when needed: Overusing antibiotics can throw off the balance of your gut microbiome. Always follow your doctor’s guidance.
• Limit processed foods: Highly processed foods with added sugars and preservatives can harm your gut flora.
• Eat fermented foods: Foods like kimchi, kefir, and sauerkraut naturally contain probiotics that help balance gut bacteria.
• Chew your food well: Digestion begins in the mouth. Chewing food thoroughly helps your gut digest and improves nutrient absorption.
• Stay hydrated: Drinking plenty of water supports your gut lining and helps waste move smoothly through the digestive tract.

Vitamins For Gut Health: Let’s Summarize

If your gut is healthy and you eat a variety of whole foods, you’re likely getting most of the vitamins your gut needs—except for Vitamin D, which mainly comes from sun exposure. 

It’s usually easy to get enough gut-friendly B vitamins and vitamin K, and a nutritious diet should also cover vitamins A, C, and E (and a bit of D). Sunlight is best for meeting your vitamin D needs, but supplements are there if you need them.

As your gut gets healthier, it’ll absorb nutrients better, so your need for extra vitamins will likely decrease.

If you are looking for a comprehensive plan to improve gut health, you’ll find a step-by-step guide in my book, Healthy Gut, Healthy You. Or, for more complex gut health problems, you can make an appointment with one of our experienced health practitioners.

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