
Bleeding gums or tooth infections can be a pain in the mouth. Likewise, constipation, diarrhea, or reflux can bum you out. Contrary to what you might think, these problems in the mouth and the gut are intimately related. Their relationship even has a name: the oral-gut connection. The mouth and gut are like two stops on the same bus line. Clinicians and dentists don’t need to treat them separately anymore. They can be treated as one. Treating the oral-gut connection may be the key to helping patients with chronic mouth symptoms, gut symptoms, or both. We review eight natural treatments that can improve oral and gut health at the same time by balancing microbes, improving tissue health, tuning up the immune system, and calming inflammation. By taking these health steps, the mouth and gut can start working again as they should. The gastrointestinal tract will be healthier, stronger, and more comfortable- top to bottom.
We are grateful to Designs for Health for making this blog possible.
Before we dive into the eight supplements I like best for boosting oral health and gut health at the same time, let’s talk about food. Diet is the #1 most important factor for oral and gut health. What you eat all day, every day has a huge overall health impact on your body and your microbes. The following natural treatments should come after a healthy diet and regular water intake are fully in place and part of your daily habits. I recommend a whole foods diet high in fiber, vegetables, fruits, seeds, proteins, and healthy fats. It should be very low in sugar, sweeteners, processed, and packaged foods. Drink half of your weight in ounces of water every day. Avoid sweetened drinks of all kinds. Herbal tea is a good option, too.
Clinicians, if you have a strong background in integrative and functional medicine gut health protocols, you will find this topic to be a breeze. That’s because most of what you need to know to improve a patient’s oral health, you already learned when treating the gut.
8 Supplements for Oral and Gut Health
- Prebiotics
- Probiotics
- Enzymes
- Multivitamin-mineral
- Antimicrobials, as directed
- Soothing, healing supplements
- Fish oil
- Immune support
#1. Prebiotics
Prebiotics are wonderful for gut health and oral health because they provide the fuel needed to grow a healthy, diverse, garden of friendly bacteria. Prebiotics are the hard-to-digest components of plant foods that feed your good bacteria. Our bodies can’t make great use of them, but our microbiome has figured out how to take advantage of them and thrive.
Prebiotics pack a punch for building up good bacteria in both the mouth and the gut. Prebiotics are unique because they don’t just feed one or two good bacteria in the mouth or gut. They feed many, many species. But that’s not all. They also activate the immune system, turn off inflammation, and build up your barriers to better protect you from the outside world.1,2
When you eat more fiber, plants, colorful fruits and vegetables, and cooked then cooled starches, you are eating prebiotics. Prebiotics and probiotics (which we cover next) help to build up your friendly bacteria in the mouth and the gut.
Why should we build up our good bacteria?3
All of the microorganisms in the mouth, or the oral microbiome, live along the same tract as all of the microbes in the gut, known as the gut microbiome. The mouth and the gut house the two most biodiverse microbiomes in the human body. Here are the amazing services that your good bacteria provide to your body 24/7.
- Activate the immune system
- Break down toxins
- Crowd out bad bacteria and pathogens
- Help develop and nourish the lining of the mouth/gut
- Produce antimicrobial substances and antioxidants
- Promote a healthy immune defense
- Synthesize vitamins
What prebiotic foods should you eat to best serve your microbiome? Celery, lettuce, asparagus, banana, and beets are prebiotic foods that are great for the mouth and the gut. Make sure you chew them for extra time, so they can have more contact with your mouth tissues. You can also swish smoothies that are high in prebiotics before swallowing them. Prebiotics that you swish or chew and then swallow will do double duty for the mouth and the gut.
You can also take prebiotic supplements if your microbiome needs a boost or if you have a hard time getting 7-10 servings of veggies and fruits each day. There are prebiotic powdered supplements to add to smoothies or water. Recently, companies have added prebiotics to toothpaste.
Check out my blog, “The Best Prebiotics for the Oral Microbiome” for a full list of prebiotic foods to kickstart a healthy microbiome.

Image by Alicia Harper from Pixabay
#2. Probiotics
Friendly bacteria help to boost the microbiome in the mouth and the gut. This is one of the supplements on this blog that you have certainly heard of. Aside from a long human history of eating fermented foods, now we see commercials and internet ads everywhere about the benefits of probiotics for gut health.
Probiotic foods are fermented foods, such as yogurt, kimchi, or sauerkraut. Probiotic supplements come in the form of capsules or powders.
Probiotics have many, many health benefits supported by scientific research. Probiotic supplements can change the pH and make the environment more conducive to growing good bacteria. They also help to get rid of pathogenic microbes.
In the mouth, dental probiotics are usually a lozenge or a chewable tablet that can be taken after brushing teeth. Dental probiotics can ward off pathogens that cause cavities. They help to reduce bleeding gums, loose teeth, and gum disease. They fight bad breath and tooth stains.4-6 I use the term “dental probiotics” to refer to probiotic lozenges that melt in the mouth for oral health. “Oral probiotics” on the other hand, are capsules taken by mouth and swallowed to support gut health or even whole-body health.
In the gut, oral probiotics calm down inflammation, promote regularity, crowd out pathogens and gut infections. They can reduce constipation and diarrhea. They can even promote brain health and balanced mood.5,7-14
Often found in capsules and powders, now probiotics can be found in toothpaste, mouthwashes, functional foods, and more. Dental probiotics, even if swallowed, will not likely do much for gut health. So, take a dental probiotic and an oral probiotic to support the mouth and gut at the same time.
There are only a few different types of probiotics available on the market: Lactobacillus species, Bifidobacteria species, Streptococcus species, Akkermansia muciniphila, and Bacillus species (often called spore-forming probiotics). Streptococcus salivarius is an oral microbiome probiotic. Saccharomyces boulardii is a friendly yeast that comes in a capsule and sometimes gets grouped together with probiotics. This list of probiotics may seem like a lot, but we carry hundreds of species in our mouths and guts, not just ten or so. I hope that we will have more options in the future. I like all of these and I think rotating them is a good idea to get better exposure to a variety of microbes.
Keep in mind that probiotics do not always stick. Sometimes their health benefits occur only while you take them and they disappear when you stop taking them.

Image by Clker-Free-Vector-Images from Pixabay
#3. Enzymes
Enzymes are critical to help us break down our food into its smallest nutritional components so that our bodies can thrive. Digestive enzymes also help us destroy unwanted organisms and proteins so they can’t hurt us.
If you remember from high school, enzymes are proteins that catalyze reactions, or make chemical reactions happen, throughout the body. However, when we are talking about enzymes in the gut, we are specifically talking about digestive enzymes.
Digestive enzymes are very important for balancing the gut microbiome. They help prevent overgrowth of bad bugs. Example digestive enzymes are amylase, lipase, and protease, which are made in the pancreas. Stomach acid is a key player in the digestive process, too.
Enzymes don’t just work in the gastrointestinal tract to keep us healthy. They also work in our saliva to kill bad bugs and defend us from harm. Digestion starts in the mouth when we chew up foods. We have many enzymes in our saliva that help start the digestive process from the moment we take the first bite. Examples of enzymes that work in the mouth are amylase, lysozyme, and lactoperoxidase. Amylase is made in the mouth and breaks down carbohydrates. Lysozyme in saliva defends you from bacteria by breaking down their cell walls. Lactoperoxidase is antibacterial, antiviral, antifungal, and antiparasitic. It also just so happens to help prevent cavities, gingivitis, and periodontal disease.
While dental enzymes are not as widespread and popular as digestive enzymes for gut health, certain oral health lozenges contain enzymes to freshen breath or enzyme-containing toothpastes alter the oral microbiome or prevent cavities. I expect to see more enzymes in natural oral health products in the coming years.
#4. Multivitamin-mineral
To support oral and gut health at the same time, we need to make sure the body has the vitamins and minerals it needs to work properly. This is critical for anyone struggling with gut health, oral health, or both. The tissues in the mouth and gut need plenty of good nutrition to fight infections, ward off bad bacteria, nourish and heal tissues, and turn off inflammation.
A high-quality multivitamin-mineral provides the bare minimum micronutrients necessary to boost the nutrition of your gastrointestinal tract and mouth. And this assumes you are eating a diet rich in nutrients, like the one I described at the beginning of this blog. However, a multivitamin-mineral doesn’t do a comprehensive job providing you with all of the nutrients you may need. Nutritional testing with an integrative and functional medicine provider can help pinpoint the supplements you specifically need for optimum wellness.
While true “malnutrition” is no longer a threat in most wealthy nations, people in those countries can still experience nutritional insufficiencies that slow down and hamper their health. This problem is exacerbated by the westernized diet, which is high in grain-fed meats, grains, potatoes, and dairy, yet low in fresh vegetables, fruits, fiber, vitamins, and minerals. Depleted agricultural soils mean the food we eat every day is less nutritious.
Learn more about the best vitamins for oral health in my blog.
#5. Antimicrobials
When the microbiome is out of balance and bad bacteria are causing symptoms, it may be time for an antimicrobial treatment. Dysbiosis or microbial imbalance can strike the mouth microbiome and the gut microbiome. An infection, or an overgrowth of bad bacteria, can cause cavities, bleeding gums, bad breath, or root canal infections in the mouth. On the other hand, an infection in the gut can cause diarrhea, abdominal pain, inflammation, gas, bloating, or vomiting.
There’s a time and a place for antimicrobials, so consumers should work with a qualified healthcare provider before going after bad bugs on their own. I recommend finding an integrative and functional medicine provider or a biological or holistic dentist to work with, preferably one who understands how to build up the microbiome, not just how to kill it.
The downside of antimicrobials is that they can harm the good bacteria that we want to build up as microbiome heroes. Some providers will choose antimicrobial herbal formulas for a mouth infection or gut infection. In more serious infections that don’t respond to herbal treatments, health providers may choose antibiotics. Capsules are taken by mouth for gut dysbiosis. Antimicrobial rinses are used in the mouth. Hydrogen peroxide or iodine can be diluted to a 1% solution to swish to kill microbes in the mouth. Antimicrobials or antibiotics taken by mouth can reduce mouth and gut infections at the same time.
Clinicians and consumers need to remember that antimicrobials leave you vulnerable to another infection. When straightening out dysbiosis with antimicrobials, remember to rebuild the microbiome right after. Instead, use a healthy diet, probiotics, and prebiotics (mentioned earlier) to rebuild a strong, healthy microbiome that crowds out infection-causing pathogens for the long haul.
Designs for Health tackled this dilemma with their PeriobioticTM Silver Toothpaste, which combines a probiotic and remineralizing toothpaste with the antimicrobial activity of silver, as well as nutrients such as CoQ10.
#6. Soothing, Healing Supplements
After weeks, months, or even years of illness, there are damaged tissues that need repair. “Gut healing” is a well-known and popular step of a gut health protocol, practiced widely by integrative and functional medicine practitioners. Healing the gut is important because after dealing with dysbiosis in the gut, replacing critical factors like enzymes and stomach acid, and rebuilding the microbiome, the damaged gut lining needs repair. Gut-healing supplements do exactly that: they heal and seal the gut lining. Healing supplement ingredients include aloe vera, deglycyrrhizinated licorice (DGL), and the amino acid glutamine. Zinc carnosine, slippery elm, and okra may also be found in these formulas for gut health. The idea is to soothe the gut lining and cool off inflammation so that it can heal. Nutrients, which we discussed earlier, also play a role here to promote tissue healing.
Likewise, cooling, soothing herbs and nutrients can benefit the mouth, too. After all, bleeding gums are a sign of damaged gum tissues and leaky gums. Once other factors have been addressed in the mouth with a qualified practitioner, healing and soothing agents can be used to rinse the mouth and gums. Aloe vera juice is present in The Natural Dentist mouthwash at 20%. Clinicians, you may simply ask your patient to swish a gut healing formula in the mouth before swallowing it, as a way to target the mouth and gut tissues at the same time.

Photo by Louis Hansel on Unsplash
#7. Fish oil
Fish oil for oral health?! This might not be the number one supplement you think of for health of the mouth-gut axis, but fish oil supplements can work wonders for oral and gut inflammation.
Let’s start with fish oil and the gut. Fish oil is nature’s anti-inflammatory. It is high in certain fatty acids that shift the body toward less inflammation. It also improves the gut lining, a barrier that is critical for immune health.15 When someone has diarrhea, abdominal pain, or gut inflammation, fish oil is a great natural treatment to lower inflammation in the gut. That’s nothing to speak of its benefits for the heart, brain, joints, and skin.
For the mouth, there have been very intriguing studies on a fish oil component called specialized pro-resolving mediators. These specialized pro-resolving mediators are one important part of what makes fish oil so beneficial.16 Pro-resolving mediators essentially tell the body to turn off (or resolve) inflammation. When someone has gum disease, microbial imbalance sets off an immune reaction in the mouth that destroys gums and bone. These pro-resolving mediators from fish oil help to turn off inflammation and turn diseased gums into healthy, happy gums. They promote tissue healing and help balance the oral microbiome. 17-19
Fish oil and specialized pro-resolving mediators are usually taken as capsules orally. You can take fish oil as a liquid, such as cod liver oil. You can also eat more servings of fatty fish per week to increase these anti-inflammatory substances in the diet.
#8. Immune Support
The immune system is front and center in the mouth-gut axis. We have talked about good bacteria, nutrition, enzymes, and other key ingredients for a healthy mouth and gut. However, we would be remiss in our duties if we didn’t highlight the immune system as foundational in gut and oral health. After all, the immune system decides whether your body’s inflammatory response is in an uproar or in peaceful harmony. The immune system can be happy and calmly monitor the comings and goings of foreign organisms. Or it can send the whole body into red alert, causing unending tissue destruction and pain.
Secretory IgA (sIgA), a marker of immunity, is present both in the mouth and in the gut.20,21 It binds, neutralizes, and clears toxins, pathogens, and allergens. Given its critical role in keeping us safe, treatments to raise it can help balance microbes and promote health throughout the gastrointestinal tract.
Supplements to raise sIgA and promote gut immunity include colostrum and immunoglobulins. Serum-derived immunoglobulins can reduce diarrhea, improve nutrition, balance the microbiome, and improve the barrier.22,23 These are usually available as capsules or powder to be taken orally. Building a healthy microbiome with probiotics and reducing stress can also help build sIgA in the mouth and gut.
The benefits of immunoglobulins for oral health have not been studied like they have been for gut health. However, probiotics have been shown to raise sIgA in the mouth and fight cavities.24 I expect there will be more to come on immunoglobulin treatments for oral health in the future. In the meantime, clinicians can treat patients with immunoglobulins to support gut and oral health.
Designs for Health has developed an innovative oral health product that gets at the immune system imbalance common in gum disease. Their PeriommuneTM orange-flavored lozenge calms down the immune system in the mouth while supporting healthy gum tissues with a patented dental probiotic.
Boost Oral and Gut Health at the Same Time
The mouth and gut are two stops on the same bus line, so why not treat them as one? Clinicians and dentists don’t need to see them as separate anymore. They can treat them in tandem. In addition to a whole foods diet and daily hydration, these eight supplements can do wonders for the oral-gut axis. The supplements covered here balance the oral and gut microbiomes, nourish tissues for optimum performance, heal damage, and turn off inflammation. Whether you have mouth symptoms like tooth decay or bleeding gums, or gut symptoms such as constipation, diarrhea, or abdominal pain, these supplements can get your entire gastrointestinal tract working and feeling better- top to bottom!

In 1989, Designs for Health began as a family-owned company offering nutritional counseling and educational services with deep roots in natural medicine and functional nutrition. Three decades later, we have stayed committed to the integrity of our products, customer service, company operations, and family values.
Renowned as a leading innovator and the fastest-growing brand of high-quality nutritional supplements in the healthcare practitioner channel, Designs for Health offers one of the most extensive and diverse ranges of nutritional supplements available. Our focus is squarely on facilitating successful patient outcomes, exclusively serving health professionals.
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Our “Science-First” philosophy is guided by evidence, not trends, ensuring the use of high-quality ingredients that are proven to be effective. This focus on quality over convenience and cost exemplifies our commitment to delivering exceptional care to our partners, contributing to our primary goal of improving health and well-being for all.
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- Bengmark S. Gut microbiota, immune development and function. Pharmacol Res. Mar 2013;69(1):87-113. doi:10.1016/j.phrs.2012.09.002
- Kverka M, Tlaskalova-Hogenova H. Two faces of microbiota in inflammatory and autoimmune diseases: triggers and drugs. APMIS : acta pathologica, microbiologica, et immunologica Scandinavica. May 2013;121(5):403-21. doi:10.1111/apm.12007
- Simren M, Barbara G, Flint HJ, et al. Intestinal microbiota in functional bowel disorders: a Rome foundation report. Gut. Jan 2013;62(1):159-76. doi:10.1136/gutjnl-2012-302167
- Liu X, Cao S, Zhang X. Modulation of Gut Microbiota-Brain Axis by Probiotics, Prebiotics, and Diet. Journal of agricultural and food chemistry. Sep 16 2015;63(36):7885-95. doi:10.1021/acs.jafc.5b02404
- Partty A, Kalliomaki M, Wacklin P, Salminen S, Isolauri E. A possible link between early probiotic intervention and the risk of neuropsychiatric disorders later in childhood: a randomized trial. Pediatric research. Jun 2015;77(6):823-8. doi:10.1038/pr.2015.51
- Rosenfeld CS. Microbiome Disturbances and Autism Spectrum Disorders. Drug Metab Dispos. Oct 2015;43(10):1557-71. doi:10.1124/dmd.115.063826
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- Pahumunto N, Sophatha B, Piwat S, Teanpaisan R. Increasing salivary IgA and reducing Streptococcus mutans by probiotic Lactobacillus paracasei SD1: A double-blind, randomized, controlled study. J Dent Sci. Jun 2019;14(2):178-184. doi:10.1016/j.jds.2019.01.008
Cass Nelson-Dooley, MS, is a researcher, author, educator, and laboratory consultant. She studied medicinal plants in the rain forests of Panama as a Fulbright Scholar and then launched a career in science and natural medicine. Early on, she studied ethnobotany, ethnopharmacology, and drug discovery at the University of Georgia and AptoTec, Inc. She joined innovators at Metametrix Clinical Laboratory as a medical education consultant helping clinicians use integrative and functional laboratory results in clinical practice. She owns Health First Consulting, LLC, a medical communications company with the mission to improve human health using the written word. Ms. Nelson-Dooley is an oral microbiome expert and author of Heal Your Oral Microbiome. She was a contributing author in Laboratory Evaluations for Integrative and Functional Medicine and Case Studies in Integrative and Functional Medicine. She has published case studies, book chapters, and journal articles about the oral microbiome, natural medicine, nutrition, laboratory testing, obesity, and osteoporosis.





