healthy people smilingWe all grew up with consistent messages to brush, floss, and get dental checkups regularly. But how does dental hygiene actually affect the bacteria in our mouths? This article takes a look at how the traditional method of managing the oral microbiome- dental hygiene- actually affects the oral microbiome based on the latest evidence. We will cover toothbrushing, floss, interdental brushes, water flossers, tongue scraping, scaling and root planing, and mouthwash. Dentists and hygienists, find out how to strike the perfect balance for your patient’s oral microbiome and what dental hygiene methods protect the good bugs while warding off the bad. Consumers, find out if brushing and flossing significantly changes your mouth bacteria, why mouthwash should be used with caution, and what ingredients to watch out for in your oral care products. There is a lot of science in this article, so skip to the bottom if you want the key takeaways. Hint: Brushing, flossing, water flossing, and gentle tongue scraping are the winners for protecting good bacteria while warding off the bad.

We are grateful to our sponsor, SuperMouth, for making this blog possible.

Supermouth products

SuperMouth has an innovative and comprehensive line of non-toxic, oral care products customized for different ages and stages of life. Their products build the good oral bacteria and provide nutrients for teeth, like D, K, and nano-hydroxyapatite. Every ingredient is non-toxic, with the best rating by the Environmental Working Group. Their electric toothbrush bristles are soft and hug the tooth line. It has a dryer and UV light, which reduces the chances that your toothbrush is causing you more harm than good!

 

 

The Magnificent Oral Microbiome

In recent years, we have come to recognize that the bacteria, fungi, parasites, and viruses living in the mouth (known as the oral microbiome) are not all trouble-makers. In fact, the majority are harmless or beneficial. Only a very small percentage are pathogenic, or harmful. The microbes in the mouth have far-reaching consequences for inflammation, immune defenses, the intestines, heart health, brain function, lung disease, metabolism, and healthy pregnancy. So, it pays to have good ones living in the mouth, not bad ones.

When the oral microbiome is in balance, the mouth is healthy and symptom-free. On the other hand, when the oral microbiome is out of balance, it is called “oral dysbiosis.” This is when unfriendly microbes rise to power and nudge out the good ones. Symptoms include bleeding gums, cavities, root canal infections, bad breath, or gum disease.

“The oral microbiota is stable and in harmony with the host, unless disturbed by medication, disease, low pH, or significant changes in the diet.1

The impact of diet on our mouth bacteria cannot be understated. Refined sugar and ultra-processed foods, common in our modern diets, are absolute murder for our oral microbiome. Our ancient ancestors, who had no dental hygiene practices to speak of, were free of cavities and gum disease because of their hunter-gatherer diet.2 But don’t get me on my soapbox…

What we eat, drink, medications we take, when we brush our teeth, how we breathe, and when we use toothpaste, mouthwashes, or gargles—at all times we are continuously shaping our oral microbiomes.3 Think of it as a constant dance. You can reduce bacterial biofilms with the above methods, but they never go away. You can obliterate them with harsh antimicrobial products. They will go away, but they come back stronger and in different proportions than before. Even applying antibiotics to the mouth lining only reduces bacteria for a matter of hours.4 In a nutshell: Resistance is futile.

 

woman brushing her teeth

Bacteria love to live in biofilm communities.

A biofilm is a group of microorganisms that attach themselves to a surface and cover themselves with a protective shield (or slime). This mechanism helps microbes stay attached to a surface so that they don’t get swept or washed away. The stuff that coats a biofilm is made of polysaccharides, or a long chain of carbohydrates, which provide structure and can grab on to tougher minerals like magnesium and calcium to further strengthen the protective shield of the biofilm. The biofilm has a water supply, and is a place where microbes can gather together in mixed ecological communities, talk to each other, and avoid antibiotics and the immune system.5,6

The first biofilm ever discovered was dental plaque!

 

dentist with model of teeth

The Oral Microbiology of Dental Plaque

I was hoping to skip the microbiology lesson, but it is necessary to understand why we have dental hygiene. It will also help us understand how dental hygiene impacts the oral microbiome. If you are excited about the oral microbiome in all its glory, keep reading. If not, skip ahead.

Dental plaque accumulates in a 1-2-3 predictable manner on any hard surface in the mouth- teeth, braces,7 dentures, and dental implants. “Socransky’s complexes” provide a framework for organizing and understanding bacteria that live and grow on our teeth and gums.8

Step 1. The saliva coating the tooth provides a base for bacteria to cling to. Pioneer colonizers (the early bacteria) attach to the tooth’s surface and start growing. They are generally normal and friendly bacteria species, called commensals. They can live in oxygen and are “aerobic” bacteria or facultative anaerobes (meaning they can survive both with oxygen, or with none). They make up the bottom of the Socransky pyramid (yellow, green, purple, and blue bacteria complexes). These bacteria are still easy to rub or brush off the teeth at this stage. The problem is that they pave the way for other, more worrisome, bacteria to join the biofilm.

  • Streptococcus gordonii
  • Streptococcus intermedius
  • Streptococcus mitis
  • Streptococcus oralis
  • Streptococcus sanguis
  • Capnocytophaga sputigena
  • Capnocytophaga gingivalis
  • Campylobacter concisus
  • Eikenella corrodens
  • Aggregatibacter actinomycetemcomitans (serotype a)
  • Veillonella parvula
  • Actinomyces odontolyticus
  • Actinomyces spp.

Step 2. When pioneer bacteria consume all the oxygen, it carves out a home for less friendly bacteria that need protection from oxygen in the biofilm, too. These are known as secondary colonizers or “bridge species” and these are not always friendly. They may be opportunistic bacteria, meaning that they are harmless for most people, but can cause disease if the conditions are right.  In the Socransky pyramid visual aid, these anaerobic bacteria are known as the “orange complex.” Now we have a party; the plaque will grow and mature and become stronger and harder to remove.9

  • Campylobacter showae
  • Campylobacter gracilis
  • Campylobacter rectus
  • Eubacterium nodatum
  • Fusobacterium nucleatum
  • Peptostreptococcus micros
  • Prevotella intermedia
  • Prevotella nigrescens
  • Streptococcus constellatus

Step 3. If the plaque continues to grow until it uses up all of the oxygen in the area, some really bad hoodlums can move into the biofilm, known as “late colonizers.” These guys also avoid oxygen (anaerobic). They are pathogenic bacteria that burrow in and can promote oral dysbiosis, inflammation, and damage to the gums. They are known as the “red complex.”

  • Tannerella forsythia
  • Porphyromonas gingivalis
  • Treponema denticola

Socransky’s Model of Subgingival Periodontal Pathogens, from AAOSH

Figure 1. Socransky’s Model of Subgingival Periodontal Pathogens, from AAOSH.

When the plaque biofilms are disrupted early in the colonization process, they are less likely to welcome in the harmful bacteria, especially the red complex. THAT is why we brush, floss, and get dental cleanings. The more frequently we disturb the plaque, the more likely it will favor the friendly bugs or the pioneer species. When we fall off brushing for some time, the plaque communities advance and can welcome in harmful pathogens. We are only recently learning how the commensal bacteria, or friendly mouth bacteria, also help prevent plaque from advancing into a disease state, ward off bad bacteria, and reduce inflammation.9

Every time you get a dental cleaning, your hygienist is scraping bacterial biofilms off your teeth. Little villages of bacteria are being physically removed because their hard biofilm exterior makes it nearly impossible to get rid of them by brushing alone.

Dental plaque biofilm cannot be eliminated. However, the pathogenic nature of the dental plaque biofilm can be reduced by reducing the bioburden and maintaining a normal flora with appropriate oral hygiene methods.10

 

dental research

Making Sense of Oral Microbiome Research

Measuring the oral microbiome with DNA analysis only began about 17 years ago, in 2008.11 This is super new science.

Most studies are focused on microbes that are pathogens (red complex) or opportunists (orange complex). As shown in the pyramid figure, the foundation of the pyramid is a beneficial microbial community. However, the middle colonizers are not so great, and the late colonizers pretty much spell certain trouble. Unless you work with oral microbiology a lot, you won’t be familiar with the names of the species. Still, I spell them out for reference above.

When a study says that pathogenic species were removed, that is a good outcome. If middle colonizers replace pathogens, that’s good news. Very few studies look at levels of good bacteria and commensals. However, a dental hygiene measure that preserves commensal species is very promising. If more species from the bottom of the pyramid increase, that’s a good outcome. Ultimately, I am looking for studies that show bad bugs decreased and good bugs stayed the same or even increased.

Factors That I Considered When Reading Oral Microbiome Studies

  • Commensals (including green, yellow, blue, and purple parts of the pyramid)
  • Opportunistic bacteria (orange complex)
  • Pathogens (red complex)
  • Diversity

Lastly, oral microbiome studies are interested in the diversity of the oral microbiome. Alpha-diversity, usually measured by the Shannon Index, tells how many different species are in a sample (known as “richness”) and how evenly they are distributed. While a highly diverse microbiome is considered a crowning glory in the gastrointestinal tract, the jury is still out about microbial diversity in the mouth. Some studies suggest biodiversity of the oral microbiome is a measure of health.2 Yet in the mouth, higher microbial diversity is seen in those with bleeding gums and in periodontal disease.12 Flossing may reduce alpha-diversity. It’s not yet clear if higher diversity is a good thing in the mouth.

Commensal– these normal bacteria harmlessly coexist with us and often provide us with health benefits.

Opportunist– these common microbes may not cause problems. On the other hand, they can overgrow and cause disease when the circumstances are right, such as when you have a weakened immune system or disturbed microbiome.

Pathogen– causes disease.

 

man brushing his teeth

Dental Hygiene and the Oral Microbiome

Dental hygiene physically removes the microorganisms in the mouth. For the dental industry, this is still the mainstay for keeping bad oral bacteria at bay. Physical removal of plaque includes toothbrushing, flossing, and non-surgical therapies like scaling and root planing.

The goal of dental hygiene is to disturb mature plaques and favor immature plaque species (early colonizers and mixtures of aerobes and facultative species). This can help prevent the overgrowth of pathogens. Toothpastes help this approach to suppress the microbes, hopefully killing pathogens and shifting the oral microbiome toward healthy balance.13

However, it’s important to note that dental hygiene methods do not differentiate good bacteria from bad bacteria. They reduce all bacteria.

Mechanically removing plaque helps reduce harmful microbes, but it also removes good microbes. It’s probably okay in the long run as one author says because “… oral health is typically preserved or restored because of the colonization resistance exerted by commensal species.”13 In layman’s terms: good bacteria help rebuild a healthy oral microbiome after dental hygiene takes all the microbes down a few notches.

 

Brushing teeth and the oral microbiome

In 1890, Willoughby Miller wrote the first book implicating oral bacteria as a cause of tooth decay. Called Micro-organisms of the Human Mouth, it sparked a worldwide movement of toothbrushing and flossing.14

Dental hygiene keeps plaque lower and helps prevent cavities and oral dysbiosis. Brushing teeth helps to minimize the buildup of plaque on teeth, remove stains, and food debris. The World Health Organization recommends toothbrushing to reduce dental plaque. Studies show that well-off teenagers who brushed their teeth daily with a fluoride-containing toothpaste, had dietary and oral hygiene counseling, fluoride treatments, and regular dental visits since early childhood, had a low rate of oral dysbiosis, specifically in the form of cavities.1

However, toothbrushing misses over 40% of plaque, even when done by experts.15

So, what happens if you don’t brush your teeth?

When people stopped all forms of oral hygiene, the bacteria in their mouths skyrocketed after only 4 days. By day 10 without oral hygiene, everyone in the study had developed moderate to severe gingivitis. When they resumed their normal dental care, they were able to lower the overall amounts of bacteria on their teeth. But the composition of the microbiome on their teeth (supragingival, above the gums) did not bounce back to baseline, even after two weeks of renewed oral hygiene. It seemed that the changes to the tooth microbiome stuck, despite getting back on the dental hygiene wagon.16 What we do can dramatically affect our microbial populations; even 10 days without brushing can change your microbiome semi-permanently.

People who report that they brush teeth more frequently have lower amounts of certain bacteria: Gemella, Streptobacillus, Granulicatella, and Porphyromonas. This supports the notion that brushing teeth lowers dental plaque.7 Toothbrushing with toothpaste and tongue cleaning twice daily reduced Fusobacterium, Prevotella, and Porphyromonas in plaque. This effect was also seen with a novel approach to easily disrupt the microbiome throughout the day called “Gum and tooth rubbing with Index Finger Tongue cleaning and water Swishing” (GIFTS), for use by children or adults who cannot brush teeth.15

But sometimes the effects of brushing don’t pack much of a punch when it comes to the oral microbiome.

For example, oral hygiene doesn’t affect the major players in the oral microbiome. It affects the relative proportions of each bug in the community. Even two human populations with totally different brushing and flossing habits both had the same “core microbiome.” The same 24 bacterial species were found in all participants, and the same 78 species were found in 90 percent of the participants. That’s a lot of overlap!

In one study using a fluoride-containing Colgate toothpaste and Reach unflavored waxed floss, people who brushed had very similar total bacteria as those who brushed and flossed. Over 12 weeks, bacterial abundance of commensal species decreased in those who brushed, and it was similar for those who brushed and flossed. Gingivitis- and bad-breath-related bacteria also decreased in those who brushed, and it was no better if they brushed and flossed.17 Adding flossing to the brushing routine didn’t change the diversity or richness of the species, either.17

In a study of geriatric patients with dementia, brushing teeth and cleaning dentures more frequently did not result in a noticeable change in the oral microbiome (bacteria or fungi).18 The treatment group included brushing teeth at least 2 minutes after breakfast and dinner and cleaning dentures daily (for those who had them) for 6 weeks, compared to the control group who brushed less than 2 minutes at least once per day, with less frequent cleaning of dentures (at times only one time her week).

 

Toothbrushes

An unpublished data analysis by Bristle, an oral microbiome lab testing company, showed that of 100 people, those who used electric toothbrushes had higher levels of commensal bacteria compared to those who brushed teeth manually. This was quite surprising! They suggested that effectively disrupting plaque development may open the door for healthier microbes to move in and grow. They also found that people under 30 years old who used electric toothbrushes twice daily had fewer bad-breath-related bacteria.

Toothbrushes are exposed to microbes from the mouth and the environment and can become heavily contaminated. Previous studies have shown that toothbrushes can introduce unhealthy microbes into the mouth on a regular basis, but there is little research as of yet that tells us if the toothbrush could have a lasting impact on the oral microbiota, or if its influence is transient.3 Remember to change your toothbrush head every three months, at least!

 

Floss, interdental brushes, and water flossers

All of the microbes we’ve been talking about can accumulate between teeth, which is hard to reach with a toothbrush. Different methods to target the space between teeth include manual floss, water flossing, and interdental brushes. Oral microbiome research on flossing is still sparse and findings are not consistent.

In an in-house data analysis by Bristle Health, the more often people flossed (which may include a variety of flossing methods), the less microbial diversity they had in their mouth bacteria. Further, in people who reported more frequent flossing, pathogens were lower, which would likely reduce gum inflammation.

This was consistent with a published study, where people who frequently flossed and used toothpicks, had lower alpha-diversity.12 The reverse also proved true, in people who rarely used dental floss, mouthwash, and toothpicks, they showed more bacterial diversity.

People who reported flossing more frequently did not show significant changes to the microbiome in one study.7 This may be why the evidence to support regular flossing for removing dental plaque is not very strong.19 Still, it seems that manual flossing is beneficial for gum health, even if it doesn’t significantly change the oral microbiome.

 

Interdental brushes

Interdental brushes, like GUM softpicks, seem to be effective at reducing the overall bacterial load.20 Interdental brushes can shift the microbial community towards fewer pathogens and more health-associated microbial species between teeth. Young people with healthy gums who used interdental brushes decreased their oral pathogens and opportunistic bacteria (red and orange complexes), along with inflammation and bleeding. Friendly bacteria from the yellow and purple complexes increased.20 Interdental brushes may be more effective than floss, and they produce better outcomes when used in combination with brushing.21

 

Water flossers

Oral irrigation directly applies a stream of pulsating water to remove the oral biofilm and they show good clinical effects for teeth and gums. In people with gingivitis, a Waterpik Water Flosser used for four weeks increased commensal early colonizers such as Streptococcus, Veillonella, and Fusobacterium. A shift away from anaerobic late colonizing bacteria was seen.22 However, it did not significantly change biodiversity, even though bleeding on probing was resolved in four weeks. This effect was superior to manual flossing, although inflammation decreased in all subjects whether they used manual floss or water flossers.

In a group of sixty-three people with gingivitis, water flossing for 12 weeks changed dental plaque microbes. Prevotella genus and Prevotella intermedia (orange complex) were reduced. Coryneobacterium genus was higher. Plaque bacteria were more aerobic than with brushing alone, suggesting more beneficial species were thriving. Water may provide more oxygen to the dental biofilm, shifting its composition. In addition, gum inflammation (represented by bleeding and pocket depth), as well as bad breath, were all improved.23

It is possible for water flossers to colonize bacteria and provide a source of unwanted microbes, similar to a toothbrush.24

 

Toothpaste and the oral microbiome

Toothpaste and mouthwashes are part of dental hygiene. They change the oral microbiome with biochemical agents- instead of mechanical removal.

Traditional toothpastes are antibiotics. Antibacterial toothpaste can suppress both beneficial bacteria as well as pathogenic bacteria.3 Crest toothpaste, Proctor & Gamble25 killed “bad” oral bacteria and Candida albicans, but also killed beneficial mouth bacteria, such as Streptococcus salivarius and Lactobacillus salivarius. Colgate Total 12 White, Colgate & Palmolive, Co. killed all tested bacteria (Streptococcus mutans, Streptococcus sanguinis, and Enterococcus faecalis).26

Some ugly ingredients have been used in toothpastes which are not so safe or healthy for the mouth. For example, sodium lauryl sulfate (SLS), cocamidopropyl betaine, and fluoride at commonly used concentrations are toxic to the mouth lining.27

Other toothpastes are out there that have been designed to shift the oral ecology, not completely wipe it out.3 Check out SuperMouth’s toothpaste and mouthwash, which are part of their non-toxic line of oral health products that promote healthy mouth bacteria and strong teeth.

For more information, take a look at my article on best toothpaste ingredients, where I review different toothpaste ingredients and the research behind them.

 

Mouthwash and the oral microbiome

Mouthwash isn’t the golden child it used to be. It is often used to promote white teeth, get rid of bad breath, and just in general to use as part of a “minty-fresh” oral health routine. But some dental experts, like Dr. Mark Burhenne, DDS, think mouthwash is one of the worst things you can possibly do for your mouth. While mouthwash may leave you feeling like you have a fresh and healthy mouth, it’s not so. Mouthwashes often contain essential oils, fluoride, alcohol, or peroxide.

Here are the ways mouthwash can do more harm than good.

  • Kills good mouth bacteria
  • Dries out the mouth
  • Depletes the mouth of nutrients found in saliva
  • Damages mouth tissue and teeth
  • Contributes to bad breath and cavities

Chlorhexidine-containing mouthwash (an antibiotic mouthwash used widely in conventional dental offices) reduces commensal bacteria and alters microbial diversity. It also can promote- caries-associated bacteria. Even more concerning, chlorhexidine mouthwash can encourage drug resistant microbes and make it easier for them to spread.13

Chlorhexidine is commonly prescribed to address inflammation and infection around the site of a dental implant. However, in a study using it to treat this condition, there was no change to the pathogenic bacteria observed over 15 days, even at the higher 0.12% concentration. Diversity wasn’t affected either, suggesting that it had little to no effect. The researchers therefore recommend using caution when prescribing chlorhexidine mouthwashes for the treatment of peri-implantitis, since it may not work at all.28

Rinsing with Listerine® Cool Mint®, along with brushing with Colgate, reduced total bacteria and commensal bacteria at week four and week 12 of treatment, more than brushing alone. It also reduced gingivitis- and bad-breath-related bacteria more than brushing. It decreased diversity and species richness compared to brushing only, which was considered a positive effect.17

Rinsing with Listerine Cool Mint everyday increased opportunistic bacteria such as Fusobacterium nucleatum and Streptococcus anginosis, compared to placebo. These bacteria have been implicated in oral diseases, making the researchers question if this was a beneficial daily practice.29

Multiple studies show that mouthwash can actually increase a person’s blood pressure. That’s because friendly tongue bacteria can lower your blood pressure by helping your body make a substance called nitric oxide.30 When people used antiseptic mouthwash to kill off some of their oral microbiota, the bacteria could no longer help with nitric oxide production, and blood pressure increased! Mouthwash isn’t just bad for the microbiome, it’s bad for heart health, too.

Check out my in-depth article on mouthwashes and gargling solutions and how they affect the oral microbiome.

 

Tongue scraping and the oral microbiome

The tongue is home to a community of microbes all of its own. Microorganisms, human cells, food, and saliva components cover the tongue surface and form what is called the tongue coating. The tongue may share microbes with dental plaque and gum disease bacterial communities. When people fall off of their oral hygiene practices, more gum-disease-causing bacteria show up on the tongue.31

The American Dental Association recommends regular tongue cleaning because of its role in bad breath. Eastern medicine analyzes the coating of the tongue to determine systemic health.31 Because the link between tongue bacteria and teeth bacteria is not strong, regular tongue cleaning still isn’t a widespread dental recommendation in the United States.31

Preliminary studies suggest that you can certainly change your tongue microbiome for the better with tongue cleaning. Tongue scraping decreases tongue coating, as well as aerobic and anaerobic bacteria on the tongue.32 Cleaning the tongue as part of an oral hygiene program helped to reduce bacteria involved in plaque development. It reduced early colonizers and secondary colonizers involved in plaque buildup.15

Regular tongue scraping helps produce nitric oxide naturally and reduce blood pressure.33 When you clean your tongue regularly, you increase friendly nitrate- and nitrite-metabolizing bacteria like Neisseria and Haemophilus parainfluenza. Daily tongue cleaning increases the amount and metabolic activity of these bacteria, which helps to turn nitrates from the diet into nitric oxide—a natural compound that helps lower blood pressure. When participants did not regularly clean the tongue, their oral microbiomes were not able to produce nitric oxide naturally.33 Using antiseptic mouthwash can also disrupt this essential system by killing bacteria on the tongue, which was discussed earlier.

Read more about nitrate-reducing bacteria and the wonderful things they do for our health.

 

Scaling and root planing shift the oral microbiome

Scaling and root planning (SRP) is a non-surgical, deep-cleaning dental procedure used to treat gum disease. It mechanically removes plaque and calculus from teeth, both above and below the gumline. Root planing smooths the root surfaces of the teeth. By removing residual bacteria and toxins, it is thought that gum tissue can reattach more closely to the tooth.

One study showed that in 12 people with gum disease, SRP reduced pathogens like Porphyromonas and Treponema. It increased beneficial genera like Actinomyces, Streptococcus, and Haemophilus. However, while SRP reduces disease-associated bacteria, the patient’s oral microbiome was not simply “healthy” immediately — the ecosystem was still shifting. In fact, at six weeks out, the pathogen-related microbes increased, while good bacteria went down.34 That’s not usually what we are hoping for.

In patients with periodontitis, SRP restructured the oral microbiome. They saw Porphyromonas gingivialis decrease, while Fusobacterium nucleatum increased.35 How unhealthy the microbiome is in an area of the mouth may dictate how susceptible it is to change. Areas of the mouth where clinical attachment level was more stable (“healthier”) showed less restructuring of the microbiome after SRP.

The oral microbiome may be resistant to these treatments. Even 24 hours after deep cleaning in a periodontitis patient, there is a dysbiotic signature remaining within the oral microbiome.13

Systemic effects of dental hygiene

Dental hygiene generally seems to reduce the bacteria in the mouth- both bad and good species. The studies are not all consistent. For example, water flossing improves the oral microbiome, but manual flossing shows little changes. We may not yet understand all of the ways dental hygiene benefits the body, but we do know it has far-reaching effects beyond the mouth. This is known as the oral-systemic link. Brushing and flossing reduces heart disease, systemic inflammation, and reduces unhealthy microbes in the mouth and gut.36 Brushing teeth promotes healthier bacteria in the gut microbiome.37 Brushing and flossing are a physical therapy to keep the oral mucosa and gums healthy. They stimulate and strengthen your gum tissue and help the gums stay tight around the teeth, like a suction cup. This fortifies the barrier in your mouth and supports a strong immune system.

 

PCR testing in laboratory

Disclaimer

My statements about oral microbiology are only as good as the information we have today. For two main reasons, I have to hedge my statements: (1) discoveries about oral microbes using culture methods (commonly used in the past) are highly prone to error. DNA analysis methods are far superior and more trustworthy. Whether a study used metagenomic sequencing or quantitative PCR to measure the mouth bacteria can significantly affect the findings. You can read more about the best methods for measuring the oral microbiome here. (2) Historically, there is a huge bias to focus only on pathogens (harmful bacteria). The remaining 98% of the oral microbiome, which are commensals or friendly microbes, have been ignored (or couldn’t even be measured) in scientific studies. We therefore know very little about them or how they respond to dental hygiene. More well-designed research is needed and it may one day prove certain statements in this article to be false.

 

family brushing their teeth together

Brush, Water Floss, and Tongue Scrape Your Way to a Healthier Oral Microbiome

When we talk about dental hygiene, we’re really talking about managing one of the body’s most complex ecosystems. All dental hygiene methods work by disrupting biofilm structure and preventing a shift from early (aerobic, commensals) to late (anaerobic, pathogenic) colonizers. We don’t want to sterilize the mouth; we want to disorganize the biofilm before it matures into something more dangerous. This has historically been done with physical and chemical interventions. Unfortunately, many conventional methods reduce all bacteria, not just bad ones. For people who already have a healthy oral microbiome, avoid killing agents and instead build good bacteria with safe and healthy dental hygiene ingredients and practices, diet, and lifestyle. If you have a dysbiotic microbiome, killing oral microbes with harsher toothpaste, mouthwash, and SRP may be needed under the supervision of your biological or holistic dentist. However, try to recruit help from commensal bacteria, too. Build them up with a hunter-gatherer diet, prebiotics, and probiotics. Brushing, flossing, water flossing, and gentle tongue scraping, seem to be the best dental hygiene methods for protecting good bacteria while warding off the bad. Time is of the essence; more frequent disruption of the microbial colonies promotes healthier good bacteria (early colonizers). The human oral microbiome, as measured by DNA analysis, is still in its infancy. Well-designed studies on dental hygiene- and the good bacteria- in the coming decades will enlighten us, and may even prove that we were wrong all along.

 

colorful vegetables

Balance the Oral Microbiome with Diet, Dental Hygiene, and Safe Ingredients

  • Choose an anti-inflammatory, whole-food diet with plenty of colorful vegetables and fruits, greens, lean protein, nuts and seeds, and fiber. The fiber and prebiotics from this diet will feed good bacteria. Avoid sugar, refined carbohydrates, and packaged foods, which promote unhealthy oral bacteria.
  • Keep up with dental hygiene and dental checkups, especially:
    • Toothbrushing
    • Flossing
    • Interdental brushes
    • Tongue scraping
    • Water flossing
  • Beware of killing off beneficial species with “clearcut” strategies such as antibiotic mouthwashes or antibiotic toothpastes.
  • Carefully select toothpaste and mouthwash that are non-toxic, support the oral microbiome, and nourish teeth and the mouth lining, such as SuperMouth’s customized oral care solutions.
  • Customize dental hygiene programs for different stages of health or disease. People with healthy mouths need fewer antimicrobial agents; people with oral dysbiosis need more aggressive intervention.
  • Find a biological or holistic dental team.
  • Test the oral microbiome, using Bristle or another company, to measure commensals, opportunistic, and pathogenic species, and work with a dentist who knows how to shift the balance.
  • Take dental probiotics to promote the microbiome.

 

Supermouth logo

SuperMouth® is redefining oral care through microbiome science and innovation. Developed by leading dentists and scientists, every SuperMouth product is formulated to support the mouth’s natural ecosystem rather than disrupt it. Our pH-balanced toothpastes, mouthwashes, and sprays feature safe, biocompatible ingredients—like nano-hydroxyapatite, prebiotics, and our patented Liquid Enamel Technology—to strengthen enamel, balance oral pH, and nurture beneficial bacteria. With over 200 products and nearly 300 patents, SuperMouth offers customized systems for every age and stage, transforming daily hygiene into total mouth health. Experience the science-driven evolution of oral care at SuperMouth.com.

 

References

  1. Johansson I, Witkowska E, Kaveh B, Lif Holgerson P, Tanner AC. The Microbiome in Populations with a Low and High Prevalence of Caries. Journal of dental research. Jan 2016;95(1):80-6. doi:10.1177/0022034515609554
  2. Adler CJ, Dobney K, Weyrich LS, et al. Sequencing ancient calcified dental plaque shows changes in oral microbiota with dietary shifts of the Neolithic and Industrial revolutions. Nat Genet. Apr 2013;45(4):450-5, 455e1. doi:10.1038/ng.2536
  3. Sedghi L, DiMassa V, Harrington A, Lynch SV, Kapila YL. The oral microbiome: Role of key organisms and complex networks in oral health and disease. Periodontology 2000. Oct 2021;87(1):107-131. doi:10.1111/prd.12393
  4. Tsuda S, Soutome S, Hayashida S, Funahara M, Yanamoto S, Umeda M. Topical povidone iodine inhibits bacterial growth in the oral cavity of patients on mechanical ventilation: a randomized controlled study. BMC Oral Health. Feb 24 2020;20(1):62. doi:10.1186/s12903-020-1043-7
  5. Donlan RM. Biofilms: microbial life on surfaces. Emerg Infect Dis. Sep 2002;8(9):881-90. doi:10.3201/eid0809.020063
  6. Dewhirst FE, Chen T, Izard J, et al. The human oral microbiome. J Bacteriol. Oct 2010;192(19):5002-17. doi:10.1128/JB.00542-10
  7. Willis JR, González-Torres P, Pittis AA, et al. Citizen science charts two major “stomatotypes” in the oral microbiome of adolescents and reveals links with habits and drinking water composition. Microbiome. Dec 6 2018;6(1):218. doi:10.1186/s40168-018-0592-3
  8. Fernandes GVO, Mosley GA, Ross W, Dagher A, Martins B, Fernandes JCH. Revisiting Socransky’s Complexes: A Review Suggesting Updated New Bacterial Clusters (GF-MoR Complexes) for Periodontal and Peri-Implant Diseases and Conditions. Microorganisms. Oct 31 2024;12(11)doi:10.3390/microorganisms12112214
  9. Hernandez P, Sanchez MC, Llama-Palacios A, Ciudad MJ, Collado L. Strategies to Combat Caries by Maintaining the Integrity of Biofilm and Homeostasis during the Rapid Phase of Supragingival Plaque Formation. Antibiotics (Basel). Jun 30 2022;11(7)doi:10.3390/antibiotics11070880
  10. Mani A, Mani S, Anarthe R. A clinical pilot study to evaluate the efficacy of sea salt based oral rinse in gingivitis patients. Int J Experiment Dent Sci. 2015;4(2):116-118.
  11. Zaura E, Pappalardo VY, Buijs MJ, Volgenant CMC, Brandt BW. Optimizing the quality of clinical studies on oral microbiome: A practical guide for planning, performing, and reporting. Periodontology 2000. Feb 2021;85(1):210-236. doi:10.1111/prd.12359
  12. Bertelsen RJ, Barrionuevo AMP, Shigdel R, et al. Association of oral bacteria with oral hygiene habits and self-reported gingival bleeding. Journal of clinical periodontology. Aug 2022;49(8):768-781. doi:10.1111/jcpe.13644
  13. Brown JL, Johnston W, Butcher MC, Burleigh M, Ramage G. The butterfly effect: collateral damage and impacts of antimicrobial strategies on the oral microbiome. NPJ Antimicrob Resist. Oct 1 2025;3(1):84. doi:10.1038/s44259-025-00156-6
  14. History of Dentistry Timeline. American Dental Association. Accessed Nov 28, 2018. https://www.ada.org/en/about-the-ada/ada-history-and-presidents-of-the-ada/ada-history-of-dentistry-timeline
  15. Chhaliyil P, Fischer KF, Schoel B, Chhalliyil P. A Novel, Simple, Frequent Oral Cleaning Method Reduces Damaging Bacteria in the Dental Microbiota. Journal of International Society of Preventive & Community Dentistry. Jul-Aug 2020;10(4):511-519. doi:10.4103/jispcd.JISPCD_31_20
  16. Belstrom D, Sembler-Moller ML, Grande MA, et al. Impact of Oral Hygiene Discontinuation on Supragingival and Salivary Microbiomes. JDR Clin Trans Res. Jan 2018;3(1):57-64. doi:10.1177/2380084417723625
  17. Min K, Bosma ML, John G, et al. Quantitative analysis of the effects of brushing, flossing, and mouthrinsing on supragingival and subgingival plaque microbiota: 12-week clinical trial. BMC Oral Health. May 17 2024;24(1):575. doi:10.1186/s12903-024-04362-y
  18. Khadka S, Bowman JP, Gautam S, et al. The Effect of 6-Week Advanced Oral Care on Oral Microbiome and Mycobiome Composition in People With Dementia Living in Residential Aged Care. Clin Exp Dent Res. Oct 2025;11(5):e70212. doi:10.1002/cre2.70212
  19. Sambunjak D, Nickerson JW, Poklepovic T, et al. Flossing for the management of periodontal diseases and dental caries in adults. Cochrane Database Syst Rev. Dec 7 2011;(12):CD008829. doi:10.1002/14651858.CD008829.pub2
  20. Bourgeois D, Bravo M, Llodra JC, et al. Calibrated interdental brushing for the prevention of periodontal pathogens infection in young adults – a randomized controlled clinical trial. Scientific reports. Oct 22 2019;9(1):15127. doi:10.1038/s41598-019-51938-8
  21. Worthington HV, MacDonald L, Poklepovic Pericic T, et al. Home use of interdental cleaning devices, in addition to toothbrushing, for preventing and controlling periodontal diseases and dental caries. Cochrane Database Syst Rev. Apr 10 2019;4(4):Cd012018. doi:10.1002/14651858.CD012018.pub2
  22. Ge Y, Bamashmous S, Mancinelli-Lyle D, Zadeh M, Mohamadzadeh M, Kotsakis GA. Interdental oral hygiene interventions elicit varying compositional microbiome changes in naturally occurring gingivitis: Secondary data analysis from a clinical trial. Journal of clinical periodontology. Mar 2024;51(3):309-318. doi:10.1111/jcpe.13899
  23. Xu X, Zhou Y, Liu C, et al. Effects of water flossing on gingival inflammation and supragingival plaque microbiota: a 12-week randomized controlled trial. Clinical oral investigations. Aug 2023;27(8):4567-4577. doi:10.1007/s00784-023-05081-4
  24. Bertl K, Edlund Johansson P, Bruckmann C, Leonhard M, Davies JR, Stavropoulos A. Bacterial colonization of a power-driven water flosser during regular use. A proof-of-principle study. Clin Exp Dent Res. Oct 2021;7(5):656-663. doi:10.1002/cre2.393
  25. Shang Q, Gao Y, Qin T, Wang S, Shi Y, Chen T. Interaction of Oral and Toothbrush Microbiota Affects Oral Cavity Health. Frontiers in cellular and infection microbiology. 2020;10:17. doi:10.3389/fcimb.2020.00017
  26. Demir S, Keskin G, Akal N, Zer Y. Antimicrobial effect of natural kinds of toothpaste on oral pathogenic bacteria. J Infect Dev Ctries. Oct 31 2021;15(10):1436-1442. doi:10.3855/jidc.14966
  27. Tabatabaei MH, Mahounak FS, Asgari N, Moradi Z. Cytotoxicity of the Ingredients of Commonly Used Toothpastes and Mouthwashes on Human Gingival Fibroblasts. Front Dent. Nov-Dec 2019;16(6):450-457. doi:10.18502/fid.v16i6.3444
  28. Pose-Otero F, Arredondo A, Parga A. The Effect of Chlorhexidine Mouthwashes on the Microbiota Associated with Peri-Implantitis Lesions: A Pilot Study. Antibiotics 2025;14(10)
  29. Laumen JGE, Van Dijck C, Manoharan-Basil SS, et al. The effect of daily usage of Listerine Cool Mint mouthwash on the oropharyngeal microbiome: a substudy of the PReGo trial. Journal of medical microbiology. Jun 2024;73(6)doi:10.1099/jmm.0.001830
  30. Hyde ER, Andrade F, Vaksman Z, et al. Metagenomic analysis of nitrate-reducing bacteria in the oral cavity: implications for nitric oxide homeostasis. PLoS ONE. 2014;9(3):e88645. doi:10.1371/journal.pone.0088645
  31. Matsui M, Chosa N, Shimoyama Y, Minami K, Kimura S, Kishi M. Effects of tongue cleaning on bacterial flora in tongue coating and dental plaque: a crossover study. BMC Oral Health. Jan 14 2014;14:4. doi:10.1186/1472-6831-14-4
  32. Dwivedi V, Torwane NA, Tyagi S, Maran S. Effectiveness of Various Tongue Cleaning Aids in the Reduction of Tongue Coating and Bacterial Load: A Comparative Clinical Study. The journal of contemporary dental practice. Apr 1 2019;20(4):444-448.
  33. Tribble GD, Angelov N, Weltman R, et al. Frequency of Tongue Cleaning Impacts the Human Tongue Microbiome Composition and Enterosalivary Circulation of Nitrate. Frontiers in cellular and infection microbiology. 2019;9:39. doi:10.3389/fcimb.2019.00039
  34. Liu G, Luan Q, Chen F, Chen Z, Zhang Q, Yu X. Shift in the subgingival microbiome following scaling and root planing in generalized aggressive periodontitis. Journal of clinical periodontology. Apr 2018;45(4):440-452. doi:10.1111/jcpe.12862
  35. Duran-Pinedo AE, Solbiati J, Teles F, Frias-Lopez J. Subgingival host-microbiome metatranscriptomic changes following scaling and root planing in grade II/III periodontitis. Journal of clinical periodontology. Mar 2023;50(3):316-330. doi:10.1111/jcpe.13737
  36. Reichert S, Schlitt A, Beschow V, et al. Use of floss/interdental brushes is associated with lower risk for new cardiovascular events among patients with coronary heart disease. Journal of periodontal research. Apr 2015;50(2):180-8. doi:10.1111/jre.12191
  37. Auchtung TA, Fofanova TY, Stewart CJ, et al. Investigating Colonization of the Healthy Adult Gastrointestinal Tract by Fungi. mSphere. Mar-Apr 2018;3(2)doi:10.1128/mSphere.00092-18
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.