Top 11 Microbiome Supplements for Immune System, Weight Loss, and Good Bacteria

11 Best Supplements to Strengthen Your Microbiome

Our gut microbes depend on nutrients from our diet to grow strong and keep bad bacteria at bay. Unfortunately, poor diets are void in these nutrients. Here are the best microbiome supplements to improve gut health.
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 microbiome. Therefore, microbiome supplements may be the answer.


How Microbiome Supplements Can Improve Your Gut Health

Our gut biome is the environment of living organisms (gut microbiota) present inside our gastrointestinal tract. The gut biome ranges from: 
• The Good (Beneficial Bacteria)
• The Benign (Some Fungi, Yeast)
• The Painful (Viruses, Inflammation, Fungal, Yeast, Bacterial Infection)
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 eventually strengthen your microbiome. 
Many people turn to probiotic supplements as the sole answer. Don’t get us wrong; probiotics are the most effective for reinoculating your gut microbiome with good bacteria. However, they’re just one of the many pieces in a large puzzle of a microbiome diet. Strengthen your gut health with these 11 microbiome supplements.
Apple Cider Vinegar for Microbiome Supplements
Knowing where to start when you are trying to improve your gastrointestinal 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 balance and overall health.


Apple Cider Vinegar

This old school treatment has a myriad of health benefits 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.
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, bloating, or abdominal discomfort.
Lastly, apple cider vinegar serves as prebiotics. Prebiotics are food for probiotics, the beneficial bacteria that live in your gut [1].



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 [2]. 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, vegans and vegetarians must supplement with this essential vitamin.
With that being said, many B-Vitamins 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) [3]. 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 [4]. Heighten Vitamin B6’s bioavailability by taking in conjunction with magnesium citrate.



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 could 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 [5].”

Br J Nutr

This analysis 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 feel back to your healthier self, you should be able to get enough iron through leafy greens and grass-fed protein.




Magesnium microbiome supplements

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, magnesium is the 13th most abundant element in the universe. Yet so much of the world is suffering from a magnesium deficiency [6]. That’s because many of us don’t follow a healthy diet of fresh produce and dietary fiber. 
Research indicates that low levels of magnesium can ultimately lead to depression. This unfavorable side effect is because low levels of this element in your system can cause a catastrophic change in microbes within your own internal ecosystem [7].
Altering the microbiome 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 [8].
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. s and pea is also efficient [9]. Animal liver is also a viable option as it contains small amounts of this mineral.



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 [10].
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

Microbiome Supplements Vitamin A, Vitamin E
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 [11].
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 [12]. 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 the gut lining. This action is essential for those who are looking for healing a Leaky Gut. Vitamin E’s ability to rejuvenate cells is why this essential vitamin is found in a lot of burn and wound healing creams and oils.



Zinc is essential for the bioavailability of many vital vitamins and minerals. This mineral also plays a massive role in the digestion of food.
That’s because this vitamin stimulates digestive enzymes [13]. 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 critical supplements in strengthening your microbiome.


Microbiome Testing, Personalized Probiotics, and a Healthy Diet

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. 
Unfortunately, the Western Diet is not laden with probiotic foods fit to feed the human microbiome. It’s burdened with fatty meats, artificial sweeteners, and dairy products.
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 common strains found in a healthy gut microbiome, these dietary supplements may not be the exact answer you are looking for. Generic blends don’t have the specific strains needed to help rebuild intestinal flora in your particular gastrointestinal tract.
That is why at Thryve, we do microbiome testing. With our At-Home Gut Health Test Kit, we determine which gut bacteria is causing you gastrointestinal distress. Thryve is a three-phase program for helping an unbalanced gut microbiome. Here’s how.


Test for Microbial Diversity

gut health test kit
The kit has everything you need to safely, quickly, and securely collect a stool sample from your toilet paper with a sterile swab. Immerse the swab in our proprietary preservative liquid in the enclosed vial. 
Mail the vial back to us in the enclosed envelope. Our laboratory uses DNA extraction to isolate the different types of bacteria found in your sample. Based on these clusters of living beings, we can make an educated determination of the ratios of each intestinal microbiota present in your gut. 


Personalized Probiotic Supplementation 

From there, we can recommend a probiotics supplement custom to a person’s microbiome. This allows us to fill in the missing pieces of your gut with loads of good quality probiotic bacteria it is definitely missing. 


Dietary Changes and Food Sensitivities 


Thryve Probiotics and Microbiome Testing

Our program also has an in-depth microbiome diet database. It’s laden with prebiotic-rich foods matched up to the bacterial species in your personalized probiotic supplement. The foods we suggest provide dietary fiber to the good bacteria we’re trying to help you grow. 
We also use the case report on your gut health test to determine which food sensitives you might have. Gut microbes prefer specific food components. So, we can tell you which foods are allowing for the overgrowth of bad bacteria. That way, you can make the necessary dietary changes to prevent food sensitivities.
A mixture of probiotic therapy and the right foods could help increase your energy levels, maintain a healthy weight, boost your mental health, improve your immune response, and more!


Click Here To View Resources



[1] Gunnars, Kris. “6 Proven Benefits of Apple Cider Vinegar.” Healthline, Healthline Media, 4 Mar. 2020,
[2] Xia, M., Ye, L., Hou, Q., & Yu, Q. (2016). Effects of arginine on intestinal epithelial cell integrity and nutrient uptake. The British journal of nutrition, 1–7. Advance online publication.
[3] Martin, Peter R., et al. “The Role of Thiamine Deficiency in Alcoholic Brain Disease.” National Institute on Alcohol Abuse and Alcoholism, U.S. Department of Health and Human Services, 2003,
[4] Lotto, V., Choi, S. W., & Friso, S. (2011). Vitamin B6: a challenging link between nutrition and inflammation in CVD. The British journal of nutrition, 106(2), 183–195.
[5] Lotto, V., Choi, S. W., & Friso, S. (2011). Vitamin B6: a challenging link between nutrition and inflammation in CVD. The British journal of nutrition, 106(2), 183–195.
[6] “Office of Dietary Supplements – Magnesium.” NIH Office of Dietary Supplements, U.S. Department of Health and Human Services, 24 Mar. 2020,
[7] Winther G, Pyndt Jørgensen BM, Elfving B, et al. Dietary magnesium deficiency alters gut microbiota and leads to depressive-like behaviour. Acta Neuropsychiatr. 2015;27(3):168-176. doi:10.1017/neu.2015.7.
[8] Kim, K. H., Funaba, M., Yoshida, M., & Matsui, T. (2013). The effects of magnesium deficiency on molybdenum metabolism in rats. Biological trace element research, 151(1), 100–104.
[9] Swain, M. R., Anandharaj, M., Ray, R. C., & Parveen Rani, R. (2014). Fermented fruits and vegetables of Asia: a potential source of probiotics. Biotechnology research international, 2014, 250424.
[10] Tinggi U. (2008). Selenium: its role as antioxidant in human health. Environmental health and preventive medicine, 13(2), 102–108.
[11] Liu, J., Liu, X., Xiong, X. Q., Yang, T., Cui, T., Hou, N. L., Lai, X., Liu, S., Guo, M., Liang, X. H., Cheng, Q., Chen, J., & Li, T. Y. (2017). Effect of vitamin A supplementation on gut microbiota in children with autism spectrum disorders – a pilot study. BMC microbiology, 17(1), 204.
[12] “Office of Dietary Supplements – Vitamin E.” NIH Office of Dietary Supplements, U.S. Department of Health and Human Services, 31 July 2020,
[13] Jing, M. Y., Sun, J. Y., Weng, X. Y., & Wang, J. F. (2009). Effects of zinc levels on activities of gastrointestinal enzymes in growing rats. Journal of animal physiology and animal nutrition, 93(5), 606–612.

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