Dental Health and Diet – The Oral Microbiome

I have never had a cavity in my life! However, I did have inflamed and receding gums for many years which suddenly stopped after a major dietary change. My gums are now healthy and are no longer receding, bleeding, or inflamed. I was certain that this had to do with my oral microbome and diet so I decided to do some extensive research and this article is the result of my obsessive research!

For years we have been told that excess sugar causes tooth decay and to brush em’, brush em’, brush em’ – and Colgate / Crest / Aquafresh, etc. will keep your teeth and gums healthy.

Although there is some truth to this, I hate to tell you but this is not based on science….. not current science anyway. BUT – they will keep marketing toothpastes and mouth washes and your dentist will continue to get rich!

aquafresh sugar acid protection
Sugar Acid Protection?

The oral microbiome plays a critical role in maintaining oral health.

A Balanced Oral Microbiome

Oral Homeostasis is the balance and stable health of your teeth and gums, and has everything to do with the healthy balance of the microbes or ‘microflora’. Oral Dysbiosis is the imbalance of the microflora wherein the unhealthy microflora overpopulates the oral microbiome.

Oral Dysbiosis

The first question you might ask is ‘What causes dysbiosis of the oral microbiome?’ I can tell you for certain that it is not sugar alone, contrary to that popular belief. Various oral microflora thrive in certain environments, and some thrive on various types of foods / nutrients which I will explain in detail herein.

This study looked at 29 periodontally healthy controls and 29 subjects with chronic periodontitis:

Distinct and complex bacterial profiles in human periodontitis and health revealed by 16S pyrosequencing (Micro organism DNA sequencing / detection).

They found that the healthy control group of study participants vs. the unhealthy group had significant differences in their oral microflora.

Technically the paper states: “Spirochaetes, Synergistetes and Bacteroidetes were more abundant in disease, whereas the Proteobacteria were found at higher levels in healthy controls. Within the phylum Firmicutes, the class Bacilli was health-associated, whereas the Clostridia, Negativicutes and Erysipelotrichia were associated with disease. “

In non-techincal terms: the unhealthy bacteria / microflora is over abundant in those with periodontitis (oral disease), and the healthy bacteria was flourishing in those without periodontitis.

The unhealthy bacteria thrives and can survive in an acidic environment. Some of these harmful oral microflora thrive on fat – especially Erysipelotrichia. I will discuss this in more detail below.


Most of us have heard of Gingivitis. It is the inflammation of the gums (gingiva), and is the beginning stages of periodontal disease. Gingivitis destroys the connective tissue (the gums) and ultimately results in further progression and tooth loss.

There is strong evidence that points to Porphyromonas gingivalis, as the keystone species (microflora) in the development of chronic periodontitis.

Porphyromonas gingivalis, a gram-negative anaerobe, is a major etiological agent in the initiation and progression of severe forms of periodontal disease. P. gingivalis is essentially an opportunistic pathogen and can also exist in commensal harmony with the host, with disease episodes ensuing from a shift in the ecological balance within the complex periodontal microenvironment.

WHAT THIS MEANS: P. gingivalis is almost always present in our oral microbiome living in harmony with it’s host (you). As an opportunistic pathogen, it waits until it has the right environment to thrive. That oral environment is acidic, and lacking in the healthy microflora.

Bad Breath / Halitosis / Oral Maladour

Got Bad Breath? Know someone that does? Not only is it an unpleasant odor to the receiver of bad breath, it is embarrassing to the person with bad breath. Some don’t even realize they have bad breath.

It is easy to judge someone that has bad breath and think that they just don’t brush their teeth or have good oral hygiene. You might think: “Geez, get a breath mint or piece of gum”. Most people that have bad breath don’t know how to manage it and most normal remedies like frequent brushing, flossing, and mouth wash aren’t very helpful.

Halitosis is not caused by poor oral hygiene, it is caused by oral dysbiosis (overgrowth of certain bacteria) in hard to reach places. In 2005, scientists were unable to determine the specific oral bacteria that caused halitosis. The study concluded that “halitosis may be the result of complex interactions between several bacterial species”.

In 2008, another study concluded that “tongue surfaces not accessible to routine oral hygiene procedures can significantly contribute to oral malodour.”

Halitosis is caused by the production of ‘Volatile Sulfur Compounds’ by mainly proteolytic anaerobic bacteria. Halitosis-related proteolytic anaerobi bacteria include: Porphyromonas gingivalis (P. gingivalis), Clostridium perfringens (C. perfringens) and Fusobacterium nucleatum (F. nucleatum). In addition, healthy oral fungi play a role in eating the sulfur compounds.

What Destroys The Healthy Oral Microflora?

There are a number of things that destroy the healthy microflora balance in turn creating oral dysbiosis.

  • Mouthwash: Even though mouthwash kills unhealthy bacteria, it also kills some healthy bacteria. The active ingredient in mouthwash is cetylpyridinium chloride which is an ammonium compound. It is an antiseptic that kills bacteria and other microorganisms. Oral rinses containing cetylpyridinium chloride, can alleviate plaque-induced gingival infections, but how oral microbiota respond to these treatments in human population remains poorly understood. If your mouthwash contains alcohol, alcohol will also destroy your oral microbiome. There is little research on how fast the oral cavity repopulates with beneficial bacteria after the use of antibacterial mouth wash.
  • Flouride: For many years we have thought that flouride (which is the main mineral in tooth enamel) was the key to remineralization of tooth enamel. Although there is truth to this, there is currently no scientific consensus that drinking flouride helps prevent tooth decay. In fact, we are now finding in laboratories that flouride, which is an antimicrobial agent (which kills bacteria), also destroys healthy bacteria. Flouride DOES help with tooth remineralization when used in low doses (.5%) in toothpastes and mouth washes, but I don’t think we should be drinking it.
  • Alcohol: Alcohol is also an antimicrobial agent. We use alcohol swabs to sterilize wounds and as a disinfectant because it kills bacteria. It also kills the healthy bacteria in your oral microbiome, and leaves behind the unhealthy bacteria.
  • Antibiotics: Although antibiotics can be necessary at times when we are sick, they also kill the healthy microbes in our bodies, including our oral microbiome. It is said to take a full year to rebuild a healthy gut microbiome after taking antibiotics. The oral microbiome recovers more quickly than the gut microbiome, but is still affected by antibiotics.
  • Antibiotics In Animal Flesh: When you consume meat that comes from a factory farm (99% of the meat supply), you are also consuming the antibiotics that are given to those animals.
  • Antibiotics In Dairy: Most dairy cows are given antibiotics. If you are consuming dairy products, you are consuming the antibiotics given to the dairy cows. Dairy is also acidic. (Bovine Milk’s pH level is below neutral at about 6.7 to 6.9. This is because it contains lactic acid.)
  • Some Artificial Sweeteners: When the bacteria found in the digestive system is exposed to: aspartame, sucralose, saccharine, neotame, advantame, and acesulfame potassium-k, it becomes toxic when exposed to concentrations of only one mg./ml of these artificial sweeteners. It is the same in the oral microbiome!
  • Pesticides: Pesticides are an antimicrobial agent. An antimicrobial is an agent that kills microorganisms or inhibits their growth. The consumption of pesticides does affect the microflora in both the mouth and the gut, but few studies have been done to know exactly how much.
  • Excessively Hot Foods and Beverages: Cooking most foods to an internal temperature of 165 °F kills bacteria. Eating excessively hot food or drinking excessively hot beverages (above 165 °F) will also kill the good bacteria in your mouth. It is always best to heat foods above 165 °F for safety concerns, however you should not eat them at this temperature, you should allow them to cool a bit. Prolonged exposure to excessive hot (or cold) beverages or food can alter your oral microbiome composition. Similarly, when our immune system has a virus, it responds by raising our body temperature (FEVER) in order to kill of the virus. A shift in the temperature of our oral microbiome also alters the microflora’s diversity. (Incidentally, drinking extremely hot beverages like tea and coffee has also show a dramatic increase in the risk of developing esophageal cancer.
  • Smoking: In a large study, the difference in oral microflora was substantial between smokers and non-smokers. Loss of beneficial oral species due to smoking can lead to pathogen colonization and ultimately to disease.
  • Acidic / Low Oral pH Levels: pH is a key environmental factor affecting the physiology, ecology and pathogenicity of the oral biofilms colonizing the hard tissues of the human mouth. I will discuss this in more detail below.
  • IMPORTANT UPDATE: Water pH is neutral but carbonating water lowers the pH to around 4.5 making it acidic and VERY hard on tooth enamel and your oral pH. Say NO to soda and carbonated beverages!
  • Prescription and Illicit Durgs: There are many prescription medications as well as drugs that reduce saliva and create ‘dry mouth’ including antidepressants, diuretics, betablockers, antihistamines, opioids, antacids, amphetamines, etc. Saliva plays a very important role in oral health.

The Oral Microbiome As An Ecosystem

Similar to other ecosystems, there is a constant battle going on inside your mouth. Microflora, oral biofilms, pH balance, saliva, temperature, humidity, and nutrients all play a role in a symbiotic relationship to create a healthy environment within your oral cavity and to prevent tooth decay, oral diseases, and other diseases within your body.

“There is a dynamic interaction between the oral environment and the composition and metabolism of the resident oral micro flora. A substantial change in a key environmental parameter that affects microbial growth can disrupt the natural balance of the micro flora and select for organisms that are potentially pathogenic. The host environment dictates the composition and gene expression of the resident microbiota. Changes in oral environmental conditions can disrupt the normal symbiotic relationship between the host and its resident microbes, and increase the risk of disease.”

Oral Biofilms

A quick lesson for understanding oral biofilms: A biofilm is a thin, slimy film of bacteria that adheres to a surface. The slimy film that you see on the surface of a stagnant pond is a biofilm. A biofilm is basically a grouping of microorganisms that bind together in a community on a surface. An oral biofilm is one that adheres to the surface of your teeth and/or gums.

In order for a biofilm to form, the microbiological populations must dominate other microbes / bacteria / flora when the environment favors them. When an ecologic shift away from balanced populations happens, the bacteria are able to bind together.

When harmful oral bacteria bind together and then form a biofilm on your teeth, that biofilm first creates dental plaque or tartar. If that plaque becomes calcified, it often needs to be removed by a dentist from All On 4. Progression and build-up of dental plaque causes carries (cavities or tooth decay), and gum disease may proliferate.

Brushing your teeth and using harsh mouthwashes may disrupt the formation of unhealthy oral biofilms. However, using harsh chemicals may also disrupt and kill healthy bacteria in your mouth. A better goal is to create the right oral environment so that unhealthy bacteria cannot thrive and have a negative impact on your oral health.

Saliva’s Role In Oral Health

Saliva plays an essential role in shaping and maintaining the ecological equilibrium of the resident oral microbiota. Low salivary pH levels and altered salivary composition, often lead to dysbiosis and associated risks of gingivitis, caries and fungal infection.

In addition to balancing the oral pH levels, saliva will block the adherence of certain microorganisms to oral surfaces, so having good saliva flow is important. Saliva is antimicrobial and also supplies healthy bacteria with nutrients through enzymatic breakdown of dietary starch and proteins and salivary glycoproteins.

Reductions in saliva flow results in extended periods of low pH in the biofilm disrupts the symbiotic microflora relationship. I will discuss in more detail how to balance the saliva pH and nutrient content below.

Tooth Remineralization:

Low dose fluoride applied to the tooth enamel surface does help remineralize teeth and protect them. Dr. Ellie Phillips’ Complete Mouth Care System suggests that Crest Cavity Protection (Regular) with .5% sodium fluoride is the best bet for toothpaste, and I tend to agree with Dr. Phillips. However, and even though it is an expensive toothpaste, hydroxyapatite toothpaste has decent research for efficacy and is as effective as fluoride toothpastes, without the potential ill effect on the oral microbiome. Research articles are here .


Xylitol works to reduce the harmful cariogenic bacteria species streptococcus mutans. Chewing a couple of xylitol mints after meals can help your oral microbiome.

Creating An Environment For A Healthy Oral Microbiome

As you can see, the oral microbiome is a complex system. Obviously, good oral hygiene and avoiding the things that destroy healthy flora is helpful. pH balance is the key to dental health.

Oral pH: When the natural pH balance in the mouth shifts significantly, bacteria with harmful effects can begin to dominate. pH and nutrient status are believed to be two of the main drivers of oral disease. People who have a diet high in simple carbohydrates (which includes sugar), and/or a diet high in fats or acidic food, the pH level of the mouth will drop more frequently to lower levels than in people with a more healthful diet. This in turn leads to a significant increase in acid-tolerating bacteria such as S. mutans and Erysipelotrichia, and the displacement of oral-health-associated, neutral-pH-loving bacteria.

Acidic Foods, Simple Carbohydrates and pH levels: When the natural balance in the mouth shifts significantly, bacteria with harmful effects can begin to dominate. pH and nutrient status are believed to be two of the main drivers of the oral dysbiosis and periodontal disease. People who have a diet high in simple carbohydrates (which includes sugars), the pH of the mouth will drop more frequently and to lower pH levels than in people with a more healthful diet. This in turn leads to a significant increase in acid-tolerating, disease causing bacteria such as S. mutans and Erysipelotrichia and the displacement of oral-health-associated, neutral-pH-loving bacteria.

Healthy oral bacteria thrive on fiber and polyphenols. Polyphenols are the most abundant antioxidants in our diets. Polyphenols protect the body’s tissues against oxidative stress and associated pathologies including dental carries, cancers, coronary heart disease and inflammation.

In summary, fruits, vegetables, beans, and nuts are very high in polyphenols and fiber.

Arginine: Arginine is an important amino acid found in saliva as well as many foods. Arginine is what produces nitric oxide which is important to your heart and blood vessel health, keeps our cells healthy, and supports healthy pH levels in our oral microbiome as well as directly on the surfaces of our teeth. Nuts, Seeds, Soybeans, Peanuts, Sea Vegetables, Chickpeas, and Lentils are all high in Arginine.

Dietary Fats: Bacteroides and Enterobacteriaceae are substantially associated with a high-fat diet.

Bacteroides like P.gingivalis, and the Enterobacteriaceae Erysipelotrichia are causative in periodontal disease. Erysipelotrichia is also prevalent in those with cancer and obesity (more below).

A high fat diet will lower the pH levels in your mouth, feed acid loving bacteria, and create oral dysbiosis, in turn creating cavities and oral disease.

The Western diet is high in fat and high in refined carbohydrates. If you don’t want to be effected by Western diseases, don’t eat a Western diet high in fat and refined carbohydrates. As you can see throughout this article, a low fat diet rich in unrefined whole plant foods is best for oral health as well as overall health.

Read My Article: ‘Can We Say What Diet Is Best For Health?

Diet BEst For Health

Fermented Foods: Fermented foods play a very important role in our overall health. The healthy bacteria Lactobacillus reuteri is found in fermented foods.

Lactobacillus reuteri is antifungal and has antifungal effects on oral Candida species and mutans streptococcis (s.mutans). Oral candidiasis (or oral thrush) is caused by Candida. Cavities are caused by s.mutans.

In one study, they found that supplementing with oral L. reuteri reduced the amount of periodontal pathogens in the subgingival microbiota.

See: Probiotic effects of orally administered Lactobacillus reuteri-containing tablets on the subgingival and salivary microbiota in patients with gingivitis. A randomized clinical trial.

MORE READING on Lactobacillus reuteri in Human Health and Diseases:

Probiotic & Prebiotic Supplements: Do they work and will they help in preventing oral disease? The short answer is NO. If they do, it is relatively short term.

This study of various probiotic lactobacilli strains were tested for growth inhibition of oral mutans streptococci and candida, and showed a significant but somewhat varying ability to inhibit growth of oral mutans streptococci and Candida albicans. It also showed that the effects only lasted about 4 weeks.

See: Growth inhibition of oral mutans streptococci and candida by commercial probiotic lactobacilli–an in vitro study.

In addition to probiotic supplements having a short term effect, the supplement industry is mostly unregulated, and countless sicknesses and even deaths have a been reported from taking various probiotic supplements. They may help in rebuilding your microbiome after antibiotics, but again the effects are short term. Your health is better served by eating a healthy diet rich in fiber and fermented foods.

Read My Article ‘Top 12 Longevity Foods

Top Longevity Foods

Why Oral Health Is Important

You oral microbiome is your first line of defense for all diseases. Oral infection, mainly periodontitis, where a wide array of causal organisms have been implied to systemic infections such as cardio vascular disease, diabetes mellitus, rheumatoid arthritis, and Alzheimer’s disease.

“The oral microbiome is particularly imperative to health because it can cause both oral and systemic disease. The oral microbiome rests within biofilms throughout the oral cavity, forming an ecosystem that maintains health when in equilibrium. However, certain ecological shifts in the microbiome allow pathogens to manifest and cause disease. Severe forms of oral disease may result in systemic disease at different body sites.

See: The oral microbiome in health and disease and the potential impact on personalized dental medicine.

Obesity: The salivary microbiome in those with obesity is distinctly different than that of normal weight people. This study shows that the proportions of Erysipelotrichia and Bacteroidia were increased in the saliva samples of obese group.

See: Characterization of the salivary microbiome in people with obesity.

An overgrowth of Bacteroidia is from simple carbohydrates and is also seen in those with inflammatory bowel disease.

See: The dynamics of gut-associated microbial communities during inflammation.

Stroke: Mouth bacteria found in stroke patients’ brains. Streptococcal bacteria, mostly of oral origin, may contribute to the progression and thrombotic events of cerebrovascular diseases.

See: Oral Bacterial Signatures in Cerebral Thrombi of Patients With Acute Ischemic Stroke Treated With Thrombectomy.

Coronary Artery Disease: The oral microbiome is increasingly considered a very significant player in human health and disease. This study shows that there are 23 atherosclerotic plaque-associated oral commensal bacteria in coronary artery disease pathology.

See: Linkages between oral commensal bacteria and atherosclerotic plaques in coronary artery disease patients.

Cancer: Specific bacteria can cause various types of cancer. Erysipelotrichia mentioned above is implicated in esophageal cancer as well as colorectal cancer.

See: Oral microbiome composition reflects prospective risk for esophageal cancers

See: Comparison of Oral and Intestinal Human Microbiota in Patients with Colorectal Cancer


Creating the right environment for oral health as well as your overall health comes from eating a plant rich diet that is low in fat and low in refined carbohydrates. A healthy oral microbiome comes from having a balanced pH level from the foods you consume in your diet. Eat antioxidant and fiber rich foods that feed healthy oral flora, and avoid the things that destroy your oral microbiome. Adding fermented foods to your diet will help feed the healthy bacteria and is antimicrobial against the unhealthy bacteria.

As always, if you have any questions about this article or any of my content, please feel free to reach out to me directly ctiexec @ gmail . com