Mouth bacteria could be a critical clue to figuring out gut infections. The oral microbiome with 20 billion bacteria and 770 species pales in comparison to its cousin, the gut microbiome with 100 trillion microbes. Still, the interconnections of these two sites along the gastrointestinal tract are compelling. Bacteria living on our teeth can take the “waterslide” down the esophagus and dive right into the stomach, small intestine, or large intestine. They can also reach the gut through the bloodstream. Yet some sources think the problem starts with the gut: an unhealthy gut could allow oral bacteria to take hold and cause harm to the GI tract.

We discuss a case of a 37-year-old woman with moderate gingivitis, tooth decay, a failed root canal, gut dysbiosis, and lifelong eczema who was treated with a functional dentistry/functional medicine approach. She showed a remarkable improvement in gum health, inflammation, energy, and her eczema cleared up without the need for topical or oral steroids. If you are suffering with mouth symptoms, gut symptoms, or both, or if you are a practitioner treating these issues, the oral-gut connection may just be your key to a long-lasting solution.

Thank you to our sponsor, Terra & Co., for making this blog possible.

Terra & Co.’s Gentle Green Pulling Oil is deliciously smooth, mildly minty, and a refreshing addition to your morning oral hygiene routine. It moisturizes and cleanses the mouth without stripping, drying, or killing your friendly mouth bacteria.


Takeaway Points

* The gut and oral microbiomes are of major interest because they powerfully affect whole-body health.

* The gut and the mouth have so many similarities and close proximity; they are like “kissing cousins.”

* The mouth is uniquely positioned at the front entrance to the gastrointestinal tract and therefore can influence things downstream.

* For stubborn illnesses of the gastrointestinal tract, oral dysbiosis could be a possible hidden cause.

* Address gut and mucosal health to improve illnesses in the mouth.


The Oral-Gut Connection


It’s common knowledge these days that a healthy gut microbiome can do many good things for you. These friendly gut bacteria help you get nutrition from your diet, tune your metabolism, boost your mood, get rid of toxins, fight off infections, and soothe joint inflammation. Meanwhile, the gut is the major site of your immune system, not to mention neurotransmitters like serotonin. Compared to the gut’s 100 trillion bacteria, its kissing cousin, the mouth, is estimated to have only 20 billion microbes. Still, mouth bacteria pack a punch. Friendly mouth bacteria protect us from infections, lower our blood pressure, and strengthen our immune systems. But when bad bacteria take over in the mouth, they can set off heart disease, Alzheimer’s disease, premature birth, rheumatoid arthritis, lung infections, and more.

How are mouth and gut bacteria connected?


Microbes- The oral microbiome and gut microbiome are the two most diverse microbiomes in the human body containing bacteria, fungi, viruses, parasites, and bacteriophages.

Geography– The mouth and the gut microbiomes are part of the same long tube, the gastrointestinal tract.

Immunity– the immune tissues that embrace the gut and the mouth microbiomes are similar. Secretory IgA, an immune protein, communicates information from the mouth to the gut.

Mucosal lining– Both the gut and mouth microbiomes live on and around a mucosal lining- a barrier- to help protect us (our bloodstream) from the outside world (food, liquids, infections, toxins, etc.).

Diet and sugar– Everything we eat and drink influences the microbial populations in the mouth and gut.


The constant flowing of saliva, chewing of food, and brushing of teeth removes bacteria from the oral cavity and pushes them downstream, toward the GI tract.1 This is great if there is a healthy, rich oral microbial ecology in the mouth. But if there is gum disease or pathogenic bacteria in the mouth, it can provide a continual source of problematic microbes to the gut. This could result in chronic, recurrent dysbiosis in the stomach, small intestine, or colon that are resistant to the usual treatments.

On the big picture level, the oral and gut microbiomes have been said to have an impressive 45 percent overlap.2  However, when we zoom in, the bacteria that live in the mouth are quite different than those that live in the gut. They are each perfectly suited to their unique homes. Bacteria from the mouth can arrive in the gut by swallowing or they can travel through the bloodstream.


Figure 1. Two major ways that mouth bacteria can colonize the gut: by the bloodstream or by swallowing in the gastrointestinal tract.3


The stomach has harsh, acidic conditions that should kill oral bacteria coming downstream from the mouth. If someone has healthy digestion, a healthy gut microbiome, and a strong gut barrier, it is believed that oral bacteria shouldn’t be able to set up shop in the gut. However, certain oral bacteria do live in the gut of healthy people, such as Streptococcus and Veillonella species.3


Multiple medical and dental publications acknowledge that the oral microbiome has significant impacts on the gut microbiome and it can be a reservoir for gastrointestinal infections.

Gastrointestinal illnesses that have been linked to the oral microbiome include:3,4


Image by Sabrina B. from Pixabay

How Does Bacterial Imbalance in the Mouth Cause Dysbiosis in the Gut?

It is hard to determine the chicken or the egg. We don’t know, and it may be a long time before we do, if diseases strike the gut first, the mouth first, or both at the same time.

Here is what we do know. If you swallow pathogenic bacteria that cause gum disease (Porphyromonas gingivalis), it can trigger gut dysbiosis and immune system changes.5 Swallowing these bad bacteria allows them to set up in the gut. But that’s not all. At the same time, inflammatory Th17 cells are swallowed also. Bad bacteria from the mouth together with inflammatory immune cells can set off inflammatory disease in the gut, too.6 When this same pathogen is swallowed, it promotes leaky gut in animals.3

In Crohn’s inflammatory bowel disease up to 80 percent of patients have symptoms of oral disease.7 Inflammation in the mouth may be mild or severe, and it may begin years before any sign of bowel disease begins.8 And the oral microbiome is significantly different in these patients compared to healthy people, supporting the idea that bacteria from the mouth colonize the gut.9

Traffic doesn’t just flow from the mouth to the gut. Some authors propose that gut dysbiosis may come first. They suggest that problems in the gut could make harmful mouth bacteria more dangerous. For example, having gut inflammation, poor digestion, or taking antibiotics can open the door for harmful oral pathogens to take hold in the gut. Taking proton pump inhibitors throws off the body’s natural defenses against infections by reducing stomach acid and can promote bacterial overgrowth in the gut. However, PPIs can also set the stage for bacteria from the mouth to overgrow in the gut. One interesting note: PPIs don’t just harm the gut microbiome; proton pump inhibitors also promote the overgrowth of oral bacteria.10


Oral-Gut Microbiome Case Study

Case contributed by Dr. Sarah Tevis Poteet, DDS, PA

This case study involves a 37-year-old woman who had moderate gingivitis, cavities, gut dysbiosis, severe fatigue, immune dysfunction, and severe eczema. She turned around her oral health and improved her gut and skin health with a functional dentistry and functional medicine approach.

Brooke’s Story

A 37-year-old African American woman, called “Brooke” for the purposes of this case, went to see her functional dentist. She said, “My gums are bleeding and my teeth are sensitive. I want a more holistic approach to dental care. I feel like my mouth is contributing to my health issues.” Brooke had not been to see a dentist in several years. She had dental anxiety and was afraid of being overwhelmed with dental problems. However, she felt she was in a health crisis and finally forced herself to take steps to get help.

Brooke was 5’3” and weighed 135 pounds. She had been eating a vegan diet for four years. Brooke had suffered from severe eczema since she was in elementary school (~25 years) on the backs of her legs, arms, elbows, neck, and back. She had been on long-term topical and systemic steroids for her skin. When her new primary care doctor started to limit her steroid prescriptions, she experienced steroid withdrawals and inflamed, itchy, swollen eczema breakouts all over her body.

Image by Mudassar Iqbal from Pixabay


At home, Brooke used an electric toothbrush twice daily and fluoride-free toothpaste. Brooke took hydroxyzine for anxiety. She had iron deficiency anemia. She was taking vitamins C, D, and a turmeric supplement for inflammation at the time she visited her functional dentist.

Initial Exam and Lab Findings

During her clinical assessment, her functional dentist found several cavities and old amalgam fillings (mercury fillings). Brooke had a failed root canal #3 and partially impacted teeth #17 and #32. Her periodontal assessment June 2021 showed 1-4 mm generalized probe depths. Brooke showed moderate bleeding on probing, light plaque, light tartar, and 15 areas with 4 mm pockets. She was diagnosed with moderate gingivitis. A PerioPath test from OralDNA Labs was ordered.

Oral microbiome test findings showed the presence of three high-risk pathogens: Porphyromonas gingivalis, Tannerella forsythia, and Treponema denticola. The latter was well above the mean bacterial level observed in patients with moderate to severe chronic periodontitis. Three moderate-risk pathogens were measured: Fusobacterium nucleatum, Prevotella intermedia, and Peptostreptococcus micros.

Figure 2. Test results for Brooke, a woman with moderate gingivitis and fifteen areas with 4 mm pockets, before and after treatment.

Brooke had recently begun care with a functional medicine practitioner for her eczema, severe fatigue, and constipation. Functional lab tests had been ordered and revealed gut dysbiosis. Brooke was positive for SIBO (breath test), gut bacteria overgrowth (stool test), a fecal parasite, and poor digestion. Her test showed low levels of beneficial bacteria. Other testing showed nutritional insufficiencies, intestinal permeability (leaky gut), and possible mold exposure (urinary mycotoxins). Small intestinal bacterial overgrowth (SIBO) is a condition of excess bacteria in the small intestine where they don’t belong. Symptoms include loss of appetite, abdominal pain, bloating, constipation, diarrhea, weight loss, and an uncomfortable feeling of fullness after eating.

Brooke’s medical lab results showed a very high c-reactive protein (CRP) of 8.2 (reference range <1.0 mg/dL), a very low vitamin D of 15.9 (reference range 20-40 ng/mL), and a low DHEA-S of 16 (range for women 30 to 39 years: 45-270 ug/dL). Her ferritin was extremely low. Her hemoglobin A1c was normal at 5.3% (range is <5.7%) and her homocysteine was normal (9.0 umol/L; reference range 5-15 umol/L).


Functional Dental Treatment of Moderate Gingivitis

The functional dentist began treating Brooke’s gingivitis and oral pathogens with EMS Guided Biofilm Therapy and ultrasonic with ozone water. She applied ozone gases subgingivally to disrupt bacteria and reduce inflammation. Systemic antibiotics were given (500 mg metronidazole 1 tab, twice daily for 8 days).

At home, Brooke was asked to use a Sonicare electric toothbrush two times each day. She also was prescribed Dentalcidin liposomal oral rinse, Closys oral rinse, SPM Active fish oil (Metagenics), vitamin D, a dental probiotic (ProbioraPro®), and oral probiotics for gut-systemic health.

With her functional medicine practitioner, Brooke took treatments for gut dysbiosis, digestive enzymes, and stomach acid support. Her house was tested for mold and she was treated for possible mold colonization of the gut with binders. Nutritional treatment was initiated, especially for iron. She transitioned to a Paleo diet without grains or sugar. For a short time, she did a low-FODMAP diet to help control skin itchiness. Bloodwork showed that she was reactive to gluten and she removed it from her diet completely, including trace levels.

Follow-up Dental Exam and Lab Testing

Brooke’s follow-up oral microbiome lab test showed a 44% reduction in her bacterial load. It was collected in January 2022, seven months after initiating treatment. The high-risk pathogens, Porphyromonas gingivalis and Treponema denticola, were undetectable after treatment. Other moderate-risk pathogens and low-risk pathogens were decreased.

At that time, further dental work was done to extract the failed root canal and impacted lower wisdom teeth. Active tooth decay was treated and Brooke’s amalgams were removed using The Safe Mercury Amalgam Removal Technique (SMART).

A subsequent dental exam showed that Brooke’s mouth had undergone a remarkable recovery. Pocket depths and bleeding were greatly reduced. Before treatment, Brooke had 15 areas of 4 mm pockets with bleeding and after treatment, she only had one 4 mm pocket with bleeding. The functional dentist commented that Brooke had, “remarkable improvement in inflammation, appearance of the tissue, and plaque.”

Brooke was instructed to continue with her Sonicare toothbrush, CloSYS oral rinse (stabilized chlorine dioxide), and her dental probiotic. The dentist recommended she continue with maintenance dental hygiene appointments, which would include EMS Guided Biofilm Therapy, ultrasonic, and ozone therapy.

Brooke went on to work with her functional medicine practitioner. Follow-up functional medical testing showed improvement in all of her bloodwork. Her practitioner said that her metabolic markers were healthier. Her follow-up stool test improved, but another dysbiotic organism appeared, which was treated with herbal therapy. SIBO testing was not repeated because Brooke’s gut symptoms improved and the test was inconvenient.

Photo by Anna Shvets

Brooke’s Health Outcomes

At the time of her most recent dental cleaning in February 2023, Brooke had discontinued CloSYS oral rinse but continued to use her Sonicare toothbrush and a Waterpik. She was taking the ProbioraPro® dental probiotic, an adrenal support supplement, topical progesterone, and iron, in addition to vitamins C and D3. She was drinking eight glasses of water daily. Brooke was sleeping 6-7 hours a night and complained of snoring. Her dentist identified a Mallampati score of III (obstructed airway) and recommended a sleep study.

Her dental exam showed 1-3 mm probing depths and no bleeding. The dentist noted that Brooke had, “great periodontal improvement and healthy gums,” 20 months after her initial visit.

Brooke reported that she felt much better. Her skin was completely improved from what it had been like her whole life. The eczema was gone on her legs, arms, elbows, and back. She no longer used steroids at all and managed her skin with diet and lifestyle. She noticed that stress and dietary gluten triggered her eczema breakouts. She ate the rainbow of vegetables and still included meat in her diet. Her energy was back and she had regular bowel function.

While her skin was not perfectly clear, she was very happy with her health as of this writing. In the past, when her skin would flare up, she would go to the doctor to get more steroids. After almost two years of treatment, when Brooke got occasional flare-ups of eczema on her hands and neck, she had the tools to address it and felt less anxious about her skin. She believed that the inflammation in her mouth had affected her whole body and she said the improvements to her mouth and gut health were critical for her skin to heal.

The functional dentist encouraged continued care with her functional medicine doctor and her oral health measures. Brooke was grateful and joyful about the progress she made with her oral health and was motivated to continue with her dental care habits.


Improve Eczema, Energy, Gingivitis, and Bowel Function by Treating the Mouth-Gut Axis

Brooke suffered from severe eczema, immune dysfunction, constipation, extreme fatigue, bleeding gums, and cavities. A combined functional dentistry and functional medicine workup pointed to oral dysbiosis, gut dysbiosis, intestinal permeability, poor digestion, nutritional insufficiencies, mold exposure, and gluten intolerance as underlying causes. It took nearly two years of diet changes, lifestyle, supplements, and antimicrobial treatments before Brooke felt like a new woman. Her skin was improved and she didn’t use steroids anymore. Her gums were healthy. Inflammation decreased and she was energized. Now when she gets skin flare-ups, they are mild and she notes that they are triggered by stress and gluten intake.

Brooke had a combination of imbalanced bacteria in the mouth and in the gut. Bleeding gums with periodontal pockets greater than 4 mm in fifteen areas suggested that her mouth lining was permeable (“leaky gums”). Her very high c-reactive protein suggested that Brooke was experiencing whole-body inflammation.11 Infected root canals can increase inflammatory markers such as CRP.12

Gingivitis is an inflammatory immune reaction to bacterial imbalance in the mouth. Brooke’s oral microbiome test showed a number of high-risk pathogens, including Porphyromonas gingivalis. This pathogen is common in gum disease and when swallowed, can cause gut dysbiosis, leaky gut, and inflammation in the gut. P. gingivalis and Treponema denticola are associated with high CRP and inflammation.13

Brooke’s gingivitis improved dramatically with a functional dentistry approach of biofilm removal, antimicrobials, and nutritional support. Mercury amalgams were removed safely. Her gums, plaque levels, and inflammation turned around completely. Follow-up oral microbiome testing showed a 44% reduction in bacterial overgrowth. Two high-risk pathogens disappeared and other oral pathogens decreased. Her improvement continued and was maintained even 20 months after her initial visit. It is likely that the functional medicine interventions to avoid gluten, treat her gut, and boost her nutrition significantly aided the success of her dental treatment.

Brooke’s oral dysbiosis could have contributed to her SIBO gut dysbiosis. The microbial communities in the mouth closely resemble those in the first part of the small intestine, or the jejunum. Classical oral pathogens have been detected in the small intestine, where they don’t belong. For these reasons, researchers say, “the oral cavity presents a potential reservoir for a wide range of opportunistic pathogens that have been linked to GI disorders.”14 In patients with functional dyspepsia, a disorder of poor digestion and slow gastrointestinal movement, SIBO was present in over 70% of this group and oral microbiota were also out of balance.15

Brooke’s stool test showed that she had poor levels of protective, friendly gut bacteria. Eczema is more common in people who are depleted in beneficial commensal gut bacteria.16 The gut microbiome calms the immune system so that it doesn’t overreact. Immune reactions to normally harmless substances, such as food reactions common in eczema/atopic dermatitis, point to an immune system that is not being properly trained by the microbiome.

In this case, the mouth and the gut were treated simultaneously. Treating dysbiosis in her mouth helped to reduce inflammation in the mouth and the gut. With functional dental treatment, her oral microbiome improved, which may have promoted a healthier gut microbiome. Likewise, treatment of the gut may have improved her oral health. The antibiotics and antimicrobials would have decreased bacterial overgrowth in the mouth and the gut. The functional dentist used probiotics (both dental probiotics and oral/systemic probiotics) to address both parts of the gastrointestinal tract at the same time. Brooke’s oral inflammation visibly improved with treatment. Her symptoms resolved.

Brooke reported that all of her follow-up tests improved. It is expected that Brooke’s CRP would decrease on follow-up testing. While she reported that her bloodwork improved across the board, she could not confirm an improvement in CRP at the time of this writing. Improving the oral barrier and gut barrier, as well as microbiota balance, likely contributed to her eczema resolution.17 This has been termed the gut-skin axis.

When asked if she thought it was her mouth or her gut that proved critical to her recovery, Brooke said, “I don’t know which one helped me get better, but I don’t think I would have gotten better had I not treated both.” After dysbiosis, barrier permeability, allergens, and nutrition were improved, Brooke learned to manage her overarching triggers for skin breakouts: stress and dietary gluten.

Steps to Address Both Oral and Gut Health


  • Patients, look for functional dentists and functional medicine practitioners to be on your healthcare team
  • Clinicians, find functional dental/biological dental providers that you can collaborate with and refer out to
  • Assess both the oral cavity and gut symptoms in clinical visits
  • Test the oral microbiome and gut microbiome
  • Dental hygiene measures used in this blog:
    • EMS Guided Biofilm Therapy
    • Ultrasonic and ozone therapy
    • Sonicare electric toothbrush
    • Waterpik
  • Antimicrobials:
    • Antibiotics, as prescribed
    • CloSYS oral rinse
    • Dentalcidin oral rinse
  • Probiotics and prebiotics (for the oral cavity and the GI tract)
  • Nutrients such as vitamin D and fish oil pro-resolving mediators
  • Heal and hydrate the oral mucosa with Terra & Co.’s Gentle Green Oil Pulling with hydroxyapatite
  • Heal the gut mucosa with glutamine, aloe, and deglycyrrhizinated licorice (DGL)
  • Optimize digestion using digestive enzymes, betaine hydrochloride, and good mealtime habits of relaxing and chewing.
  • Choose an anti-inflammatory, low-allergen, whole-food diet, rich in fiber and plants, and extremely low in sugar and refined carbohydrates
  • Avoid proton pump inhibitors
  • Avoid antibiotics when possible

Remember the Mouth-Gut Connection

The mouth is at the headwaters of the gastrointestinal tract. The microbial communities living in the mouth flow downstream by way of saliva to the tune of 140 billion bacteria per day!2,18,19 The mouth is therefore “seeding” the rest of the gastrointestinal tract with microbes on a daily basis. Harmful mouth bacteria that show up in the gut can contribute to irritable bowel syndrome, inflammatory bowel disease, or colorectal cancer.3 Dental and medical researchers have reported that the oral microbiome may have a great effect on the health of the gut.20 If you have gut symptoms or mouth symptoms, remember that both the gut and oral microbiomes may be involved. Restoring health in both places may be required for long-term solutions.


This blog is dedicated to my husband’s mother, Deborah Clark Prescott, whom we miss.

April 14, 1952 – February 5, 2023

Beloved mother, sister, and grandmother.

She was a ray of sunshine to all who met her.


Inspired by ancient healing practices of Ayurveda, Terra & Co. developed a premium line of oral care to live in harmony with nature and your oral microbiome. Thoughtfully formulated with non-toxic ingredients to strengthen enamel, whiten teeth, and promote a healthy pH balance and fresh breath. All while consciously packaged with Mother Earth in mind.


Dr. Sarah Tevis Poteet is a native Texan from Waco. She graduated from Texas Tech University and then went to dental school where she earned a Doctor of Dental Surgery degree from The University of Texas Health Science Center at San Antonio. She was one of a select few to also complete an Advanced Education in General Dentistry residency, where she acquired training in complex restorative cases, implants, sedation, and surgery.

Dr. Sarah Poteet is a member of many prestigious dental organizations including the American Dental Association (ADA), Texas Dental Association (TDA), Dallas County Dental Society (DCDS), American Academy for Oral Systemic Health (AAOSH), Academy of General Dentistry (AGD), American College of Dentists (ACD), International College of Dentists (ICD), International Academy of Oral Medicine and Toxicology (IAOMT), and American Academy of Dental Sleep Medicine (AADSM).

In addition to her busy practice, Dr. Poteet volunteers her time with the Women’s Junior League of Dallas. She is also a member of Munger Place Church. She is married to Bryan Poteet, and they have a daughter named Adelle “Elle”.



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Cass Nelson-Dooley, M.S.

Cass Nelson-Dooley, M.S.

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.