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By now you know that your gut—and more specifically, your microbiome, the trillions of microorganisms such as bacteria, viruses, and fungi that live in your gut and body—has a huge impact on your overall health, not just your digestion.

“The balance of microbes in your gut effects body functions such as hormone production, blood sugar balance, heart health, weight, mood, and immune function,” says Rebekah Blakely, RDN, registered dietitian nutritionist with The Vitamin Shoppe.

Stress, lack of sleep and even taking antibiotics, for example, can knock your gut health out of whack. When that happens, your overall health can go down the crapper.

“An overabundance of bad bacteria in the gut can cause conditions such as diarrhea, malnutrition, and even inflammatory bowel disease and obesity,” adds Jonathan Valdez, RDN, registered dietitian nutritionist and owner of Genki Nutrition.

You don’t want that.

“Eating a high-fiber diet and getting enough of the right vitamins are some of the best ways to keep a balance between good and bad microbes, which can result in a strong gut,” says Blakely.

Some of the vitamins below can help maintain microbial diversity, others may assist in repairing gut tissue and restoring microbial balance.

Best Vitamins for Gut Health

1. Probiotics

Probiotics are living microorganisms (such as bacteria and yeast) that populate your microbiome. They may help bolster your immune system (1) and there is some evidence that they may help protect against mental health troubles like depression, says Valdez (2).

But their real claim to fame is promoting a leveling up of gut bacteria to support your digestive health (3). Probiotics have been found to help improve the symptoms of various gut diseases (45), including inflammatory bowel disease (IBD) and irritable bowel syndrome (IBS).

There are 7 core categories most often used to make up the strains in probiotic products: Lactobacillus, Bifidobacterium, Saccharomyces, Streptococcus, Enterococcus, Escherichia, and Bacillus.

Four of those—Lactobacillus, Bifidobacterium, Bacillus and Saccharomyces boulardii—are often used in studies. There is a growing body of evidence that probiotics may offer benefits for your gut health.

Your goal: 5 billion colony-forming units (CFUs) or higher (6)

Best food sources: Fermented foods like some kimchi, yogurts, and aged cheeses

What to look for in a supplement: Buy a probiotic that contains at least 1 billion CFUs of the strains that help with gut health (see above).

“Choose a product with multiple strains of bacteria, since different strains offer different benefits, and multi-strain products are generally more effective than single strains,” says Valdez.

Expert Pick:

Garden of Life Dr. Formulated Probiotics

2. Prebiotics

AKA: food for probiotics.

“Prebiotics are non-digestible foods that support the growth of good bacteria in your gut,” says Valdez.

There are different types of prebiotics, but most are a subset of carbohydrates called oligosaccharide carbohydrates (OSCs), which are made up of simple sugars eaten by gut bacteria.

“After your gut bugs feast on prebiotics, they release short-chain fatty acids (SCFAs) that can help improve gastrointestinal discomfort from digestive conditions like IBD and IBS,” says Valdez.

Your goal: Up to 25 g per day (7)

Best food sources: Garlic, onions, bananas, tomatoes

What to look for in a supplement: Go with a mix of prebiotic fiber. The label may list inulin, oligofructose, FOS, acacia, XOS, GOS or resistant starch, says Valdez. “All of these have all been shown to increase healthy bacteria in the gut.”

“Dosages vary depending on the type of prebiotic fiber used and the effects will vary from person to person, so you might have to experiment with different types to find the one that is right for you.”

Expert Pick:

Garden of Life Dr. Formulated Organic Fiber Supplement Powder


3. B Complex

B vitamins help improve microbial diversity while helping to suppress the growth of bad bacteria, says Valdez.

A B complex supplement will contain all of the 8 B vitamins, all of which play a role in gut health, says Valdez.

Your goal (8)

Best food sources: Meats, chicken, fish, eggs

What to look for in a supplement: Pick a supplement that provides 100% or less of the RDA for all eight of the B vitamins, says Valdez. You don’t want to go overboard—too much of some B vitamins (like B12) can cause issues such as diarrhea.

Some brands contain B12 as methylcobalamin but you should go with on that has B12 in the form of cyanocobalamin, which is better absorbed.

Expert Pick:

Nature Made Super B Energy Complex

4. Vitamin C

It has a reputation as an ace immunity booster but vitamin C (most commonly found in fruits and veggies) can be a good source of fiber that promotes the growth of beneficial gut bacteria.

“Vitamin C has known antioxidant and anti-inflammatory properties which help protect against oxidative stress from free radicals,” says Blakely.

And, accumulating evidence suggests that oxidative stress can be damaging to the intestinal lining (9).

A pilot study also suggests supplementing with vitamin C may lead to potential beneficial shifts in gut bacteria.

Adds Valdez, “Vitamin C increases short-chain fatty acid production (SCFA), which play an important role in gut health.

Your goal: 90 mg

Best food sources: Citrus fruits, bell peppers, tomatoes, broccoli, Brussels sprouts, strawberries, white potatoes

What to look for in a supplement: Go with one that contains ascorbic acid, the purest form of vitamin C, says Valdez.

“If you have trouble with absorption due to gut conditions like Celiac or Crohn’s diseases or loose stools from vitamin C supplementation, opt for a blend like calcium ascorbate – the calcium can help buffer the vitamin C to potentially reduce side effects,” says Blakely. “Liposomal vitamin C is also a great option as it has increased bioavailability and absorption.”

Expert Pick:

MegaFood Complex C

5. Vitamin D

The sunshine vitamin may be as good for your gut as it is your bones. And there’s a solid chance you’re not getting enough.

“Approximately thirty-five percent of Americans are vitamin D deficient,” says Valdez. “Many people don’t get enough since food sources of Vitamin D are minimal and a lot of people spend a good portion of their days inside (your body makes vitamin D from soaking up the sun’s rays).”

“Vitamin D deficiency has been associated with gut dysbiosis (an imbalance in the gut microbiome) and inflammation,” says Blakely. Recent studies have suggested that vitamin D supplementation may increase microbial diversity in the gut (10).

Your goal: aim for 600 IU (15 mcg) daily

Best food sources: Salmon, Vitamin D fortified milk, cod liver oil, egg yolks

What to look for in a supplement: Go with a vitamin D3 (cholecalciferol) supplement over D2 (ergocalciferol). “Vitamin D3 has been shown to be more effective than vitamin D2 at raising vitamin D levels,” says Blakely.

“Take it with a meal containing fat for better absorption,” she says.

Expert Pick:

Nature Made Extra Strength Vitamin D3

6. Magnesium

“Magnesium is important for hundreds of enzymatic processes in the body, including producing energy from foods,” says Blakely. “It can also help you if you’re constipated. Magnesium draws water into the colon, helping to soften and bulk stools.”

Your goal: 400-420 mg/day

Best food sources: Whole grains, dark leafy greens, legumes, nuts, seeds, bananas, avocado

What to look for in a supplement:
“If you’re constipated, choose magnesium citrate, which has some laxative properties,” says Blakely. “Both magnesium citrate and glycinate are well-absorbed, but glycinate is gentler on the stomach and has less laxative effect.”

Expert Pick:

The Vitamin Shoppe Magnesium Citrate

The Vitamin Shoppe Magnesium Glycinate

7. Zinc

The lining of your gut is like a gatekeeper; it determines which substances are allowed to enter the bloodstream from the digestive tract.

Leaky gut syndrome is a theory that if your gut lining weakens or becomes permeable that it may let toxins leak through the intestinal wall into the bloodstream and trigger inflammation, which may be linked to a number of chronic diseases including metabolic disorders such as diabetes, arthritis and obesity.

“Zinc deficiency can contribute to increased permeability in the intestines,” says Blakely. “Getting adequate amounts of zinc may therefore help protect your gut lining.”

Zinc also plays a role in other ways, such as the production of digestive enzymes, growth of cells, healing of damaged tissue and supporting a healthy immune system.

Your goal: 11 mg/day

Best food sources: Meat, poultry, seafood, eggs, legumes, nuts, seeds, soy

What to look for in a supplement: Look for zinc gluconate, zinc picolinate, or chelated zinc, which are all easily absorbed.

Expert Pick:

The Vitamin Shoppe Zinc Picolinate