11 Best Supplements to Strengthen Your Microbiome

Sour stomach…Mood swings…Weight gain…Anxiety…Lack of sleep…Does any of this sound like your life? Then you might have some disruptions going on in your gut biome. Microbiome supplements may be the answer.

Our gut biome is the environment of living organisms inside of our gut. The gut biome ranges from the good like beneficial bacteria to benign microorganisms such as some fungi to painful intruders like inflammations.

If you are suffering from an unhealthy microbiome, then you probably experience many, if not all of the symptoms mentioned above. While it takes a bit of commitment, you can easily strengthen your microbiome by taking these 11 supplements.

Top 11 Microbiome Supplements

Knowing where to start when you are trying to improve your gut health can be overwhelming. Luckily, microbiome testing is our area of expertise and we are here to help. So, let’s go over 11 supplements you will want in your house to boost your microbiome’s overall health.

Apple Cider Vinegar

This an old school treatment that still does wonders to this very day. Apple cider vinegar goes a long way in killing off the bad bacteria in your gut. Thus, your helpful stomach bacteria gets an opportunity to set up residence, ultimately improving your intestinal flora.

What gives apple cider vinegar its incredible abilities such as restoring gut flora comes from how the product is made.  Apples are first crushed and then introduced to bacterial yeast. This exposure causes the sugars to ferment and transform into alcohol.

unfiltered apple cider vinegar microbiome

More bacteria are added to the process, causing even more fermentation to transpire. Eventually, an enzyme-rich vinegar is made in the form of acetic acid.

Acetic acid helps break down food in the gut, making the digestion of food easier. Furthermore, it may help ease gastrointestinal distress such as feeling constipated or bloating.

Lastly, apple cider vinegar serves as prebiotics. Prebiotics is food for probiotics, the beneficial bacteria that live in your gut.


This is an amino acid that our body produces on its own.  However, it does get the moniker of being a “semi-essential” amino acid.  This is much due to the fact that preterm infants are unable to produce this protein on their own. Therefore, the infant must get arginine via diet.

What makes arginine one of the best microbiome supplements is that this building block of life supports the cells living within the intestinal wall. Keeping these cells strong is essential for healing Leaky Gut Syndrome and fighting off symptoms of IBS.

Additionally, arginine boosts the immune system, further helping the gut barrier maintain its integrity. Boosting the immune system goes a long way in supporting the microbiome because 80% of our immune cells come from our intestinal flora.

Using arginine supplements can help fight off infection as well as reduce inflammation within the intestines. Arginine’s bioavailability is strengthened when taken in unison with omega-3 fatty acids.

B-Vitamin Complex

B Vitamins are so important for many functions throughout the system, most notably providing the body with energy. Many B-Vitamins are scarce in a lot of foods in our everyday diet, even the best foods for gut health. 

This nutrient deficiency is especially true of Vitamin B-12, which could only be found in animal fats and dairy. Therefore, it is important that vegans and vegetarians supplement with this essential vitamin.

Vitamin B Complex Benefits

With that being said, there are many B-Vitamins that serve a huge role in improving gastrointestinal distress associated with an unhealthy microbiome. Research has shown that those who abuse alcohol tend to have low levels of Thiamine (Vitamin B1) and small-intestinal bacteria overgrowth (SIBO). That means this vitamin plays a crucial role in fighting off foreign substances in the microbiome, and when comprised by lifestyle choices can lead to gastric problems that need extreme interventions like surgery.

Vitamin B6, another essential micronutrient hurt by toxic substances such as alcohol and prolonged use of antibiotics, can help safeguard the body against inflammatory responses in the gut.  Heighten Vitamin B6’s bioavailability by taking in conjunction with magnesium.


There is a battle going on in your gut between beneficial bacteria and bad bacteria. At the middle of this war? Currency called iron.

The tug-of-war over iron in your system may leave your good stomach bacteria low on this pivotal micronutrient. One fascinating study explained how multiple strains of bacteria can gobble up all your iron:

“Bacteria in the Enterobacteriaceae family are particularly good at circumventing host factors that limit access to iron during inflammation, and many strains have accumulated iron acquisition proteins in an “arms race” against other bacteria and the host. The pathogen Salmonella entericaserovar Typhimurium (S. Typhimurium) uses virulence factors to trigger inflammation and has iron acquisition and metabolic capabilities that give it a growth advantage in the inflamed gut. The probiotic Escherichia coli Nissle 1917 strain does not trigger inflammation, but also has an arsenal of iron acquisition elements that is comparable with or superior to many pathogens.”

This means you should take iron supplements along with other supplements on this list. Doing so will ensure that the new intestinal flora generated in your gut gets plenty of iron. Once you are feeling back to your healthier self, you should be able to get enough iron through leafy greens and grass-fed protein.


Magnesium plays a role in over 300 essential functions in the human body. As we mentioned earlier, one function is to improve the bioavailability of Vitamin B6.  Sadly, it is the 13th most abundant element in the universe and yet so much of the world is suffering from a magnesium deficiency.


Research indicates that low levels of magnesium can ultimately lead to depression. This because low levels of this element in your system can cause a catastrophic change in microbes within your own internal ecosystem. This alteration is one of the main reasons why the gut brain connection is illustrated through depression and the human microbiota.


Speaking of magnesium, deficiencies in magnesium hurt the production of this trace mineral. Low levels of magnesium cause the liver to cease secreting molybdenum.

Not many have heard of this trace mineral. However, molybdenum is essential for many functions in our gut biome. This mineral acts as a co-factor alongside four important enzymes. When working in unison, molybdenum and these enzymes act as a catalyst for cells to produce energy. In turn, your body uses that energy to detoxify from:

  • Alcohol
  • Drugs
  • Gaseous Byproducts of Mold
  • Noxious Byproducts of Yeast

To get the best molybdenum supplements, be sure they are soaked in fermented grains or seeds. Fermenting in soy and pea is also efficient. Animal liver is also a viable option as it contains small amounts of this mineral.

Microbiome Testing & Personalized Probiotics

We may be biased, but we believe this is the most important supplement of them all. Probiotics are living cultures that promote a healthy gut biome. When everything is going smoothly, probiotics live happily in your gut, feeding on the prebiotics they get from your food.

Thryve Probiotics

However, as poor gut health reigns supreme, probiotics start to die, and inflammations begin to pop up. This lets bad bacteria, yeast, and fungi to prosper, further hurting your overall gut health. The best way to fight off the bad guys is to add more good guys.

Although you can get many probiotics supplements with popular good strains of bacteria, it may not be the exact answer you are looking for. These generic brands don’t have the specific strains needed to help rebuild intestinal flora in your gut biome. 

That is why at Thryve, we do microbiome testing. With our At-Home Gut Health Test Kit, we determine which stomach bacteria is causing you gastrointestinal distress. 

From there, we can formulate a personalized probiotics supplement. This allows us to fill in the missing pieces of your gut with loads of healthy probiotics it is definitely missing.


This is one of the most important microbiome supplements because it’s such a strong antioxidant. Selenium is found at the heart of antioxidant enzymes that are responsible for getting free radicals out of the system.

While there are no symptoms that point to a selenium-deficiency, research has shown that those who have long-term gut health conditions or an autoimmune disease are a greater risk of lacking the nutrient.

Vitamin A

Speaking of antioxidants, you can’t get much more healing done than with Vitamin A. This essential vitamin works in unison with Vitamin D and Vitamin E to boost your immune system and repair your gut barrier.

Vitamin A also acts as a peacekeeper. It works to keep harmony between the microbes in your gut. In order to keep the peace, be sure to supplement Vitamin A with zinc and iron. Vitamin A uses these two minerals as a chauffeur as it moves throughout the body.

Vitamin E

Vitamin E is a fat-soluble antioxidant. Therefore, it helps manage bad cholesterol levels that clog up your gut health and may lead to cardiovascular disease.

As we mentioned before, Vitamin E also works in repairing gut lining. This action is essential for those who are looking for healing a Leaky Gut. The ability of Vitamin E to rejuvenate cells is why this essential vitamin is found in a lot of burn and wound healing creams and oils.


Last is definitely not least. Zinc is important for the bioavailability of many important vitamins and minerals.  This mineral also plays a huge role in the digestion of food.

That’s because this vitamin stimulates digestive enzymes. In turn, these enzymes break down our food sources so that nutrients can become dispersed into the bloodstream.

Secondly, zinc plays a role in strengthening the gut barrier. This ensures waste and excess acid doesn’t leak out into the bloodstream. That makes zinc one of the most important supplements in strengthening your microbiome.