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Oral Microbiome


Exploring the Oral Microbiome: The Hidden World in Your Mouth

With over 700 species of bacteria, your oral microbiome is the second-largest microbial community after your gut. Here’s how it affects your health and how to support it.

8 minutes

34 Citations

Bad breath? Before you reach for that mouthwash, take a moment to consider the complex ecosystem of microbes (mostly bacteria) thriving in your mouth. Contrary to decades of popular misconceptions about oral care, not all bacteria are harmful. And much like your gut, your mouth is home to at least 6 billion beneficial microbes.1 From aiding in digestion to protecting you from gum disease, these bacteria play a critical role in maintaining oral and overall health. So how you care (or don’t care) for your oral microbiome can have serious consequences for your health. 

“Certain habits and lifestyle choices can throw off the delicate balance of good and bad bacteria in your mouth,” says Nini Tran, DDS, Ph.D., assistant professor at the UCLA School of Dentistry and a member of Seed’s Scientific Board. “It’s like a constant tug of war.” 

Fortunately, a few routine habits can nurture and support this delicate ecosystem. Ahead, learn about the microbial world inside your mouth and some of the simple but powerful ways you can nurture it.

Oral Microbiome 101

More than 700 species of bacteria colonize the oral cavity, making it the second-largest microbial community in humans after the gut.2 (Your mouth, interestingly, is one of the most studied microbiota, since saliva and surfaces like the teeth and tongue can be easily sampled —unlike the gut microbiota, which are much harder to access.3)

The mouth is home to a collection of microbial communities in different sites, including your saliva, dental plaque, tongue, cheeks, throat, and tonsils.4,5 Think of each area like its own, unique ecosystem composed of different microbes. 

Your oral microbiome is shaped throughout life, starting the moment you’re born (though your biological mother’s microbiome may influence your development even before birth). At birth, some of the first microbes you are exposed to are from your mother’s birth canal. Delivery mode appears to influence the diversity of the oral microbiome later on in an infant’s life, with vaginally born children showing a higher number of species three months after birth compared with children born by cesarean section.6 (Diversity is one marker of microbiome health.) 

Feeding also impacts an infant’s oral microbiome. Three-month-old breastfed infants have shown a higher colonization of health-associated oral flora—primarily Lactobacilli—than formula-fed infants, suggesting breastfed infants may have more beneficial flora.7 This makes sense because breastfeeding infants get bacteria from the breastmilk and the mouth-to-skin contact. As children grow, the bacterial composition of their mouth changes, too. Oral microbiome diversity can be affected by factors like diet, living conditions, and environment—think: exposure to family members, pets, and nature.4,8

The oral microbiome continues to mature and evolve throughout childhood. Baby teeth provide new surfaces for microbial colonization, and with the emergence of adult teeth, the oral microbial habitat changes again.9 Teeth are a particularly interesting home for bacteria. Unlike most surfaces on and within the human body, teeth don’t routinely shed. So the bacteria that colonize your teeth aren’t subjected to the same turnaround as those that colonize other human cell surfaces (like those in your gut). Once bacteria colonize your teeth, they’re able to multiply and stick around relatively easily. 

As a child grows, it’s typical for their bacterial diversity to decrease.9 But while diversity is often considered preferable when we talk about the microbiome (specifically, the gut microbiome), many adults can have a healthy oral microbiome despite it being less diverse than that of a child. It’s not necessarily a one-to-one relationship—it’s just one of many clues when assessing the state of an oral microbiome. 

After childhood, scientific analysis has shown most people’s oral microbiomes are relatively stable over time.8,10 But external factors (like that antimicrobial mouthwash we mentioned earlier) and major lifestyle or physiological changes (like hormonal shifts in puberty and pregnancy) can significantly influence it.11 An interesting study highlights the way external factors can throw off the oral microbiome. Researchers found a significant decrease in sailors’ oral microbial diversity and in microbial metabolism after they went on sea voyages that lasted more than three months in which they were subject to highly intense work, a different diet, shifted circadian biorhythms, and a humid, salty environment.12 

The bottom line? You may not be heading to sea anytime soon, but as with many health outcomes, your lifestyle can play a crucial role in the health of your oral bacteria. While the various species in your mouth have adapted to be resilient to threats like constant oxygen exposure, moisture, brushing, and chewing, they’re also vulnerable to imbalance. Understanding the role they play, and what happens when things get out of whack, can help these essential microorganisms do their job in your mouth and beyond.

How Oral Bacteria Affect Your Health

The entire bacterial community in a healthy mouth works together to support the human host (that’s you). Some bacteria (such as Streptococcus salivarius) have the ability to inhibit inflammation.13 Specific bacteria also regulate acid activity to protect against tooth decay, enamel erosion, cavity formation, and chronic bad breath. People without cavities have species (for example, certain Streptococcus species) that are able to convert amino acids or compounds in the diet to pH-balancing compounds, which lessens their risk of developing cavities.14 

In the long term, an imbalance of “good” and “bad” oral bacteria poses harm to the mouth and body. It is now generally accepted that oral disease occurs due to a state called dysbiosis, which happens when the balance of the oral ecosystem is disrupted and disease-promoting bacteria take over.15 A balanced microbiome, therefore, is important to maintain or restore oral health. For periodontal disease, the problem begins when pathogens travel from the surfaces in your mouth and colonize beneath the gum line. Periodontal disease progression happens when periodontal pathogens start to thrive in oxygen-depleted areas in the mouth below the gum line and cause inflammation.

Perhaps most importantly, it’s crucial to know that your oral microbiome doesn’t exist in a vacuum—its functions can have ripple effects throughout your body. That means that it’s not just your mouth that reaps the benefits of a thriving oral microbiome (or the consequences of dysbiosis). Bacteria tend to travel to other parts of the body, so oral health and overall health often go hand in hand. The oral cavity and gut are linked physically (through the GI tract), as well as chemically (through the enzymes in your saliva that helps you digest food). Experts know that oral bacteria commonly relocate to the gut, where they can change the composition of gut microbiota and potentially affect the immune system.16 

While more research is needed to understand the impact of oral bacteria on systemic health, studies have found associations between the oral microbiome and a number of systemic diseases and conditions:15,17 

  • Diabetes: Severe gum disease can impact your body’s ability to regulate blood sugar, increasing the risk of Type 2 diabetes.18
  • Heart disease: Gum disease has also been associated with an increased risk for cardiovascular disease, which increases the risk for heart attack.19
  • Cancer: Researchers have found that oral dysbiosis that manifests as periodontitis has been linked with oral, esophageal, gastric, lung, pancreatic, prostate, hematologic, and breast cancers.17
  • Inflammatory bowel disease (IBD): Research has shown that certain harmful organisms and cells from the mouth were able to translocate and colonize in the intestines, causing ulcerative colitis and Crohn’s disease in mice with gum disease.20 A 2020 meta-analysis demonstrated that periodontitis was positively associated with IBD, however the mechanisms aren’t totally understood yet.21
  • Respiratory conditions: Certain oral microbiota (like those within the Haemophilus and Moraxella species) have been associated with chronic respiratory diseases, such as asthma and chronic obstructive pulmonary disease (COPD), potentially through aspiration of oral bacteria into the lung, leading to lung microbiota dysbiosis and inflammation.22

9 Ways To Support a Thriving Oral Microbiome 

Some factors, such as your genetics and early life experiences, are beyond your control. But the choices you make now can also profoundly affect the health of your oral microbiome. While research has yet to determine the exact protocol for maintaining a thriving community of oral microbes, we do know that there are some key best practices for supporting your oral microbiome, as well as certain factors that underlie or contribute to oral diseases. These include: 

  • Brush and floss regularly. As periodontal infection likely plays a role in enabling the systemic spread of oral bacteria, good oral hygiene is important to control the total bacteria load and prevent dissemination to other body sites. To support a healthy mouth and body, Dr. Tran recommends following your dentist’s advice to regularly brush and floss.23
  • Avoid antiseptic mouthwashes. Over-the-counter antiseptic mouthwashes can wipe out beneficial oral microbes due to an active ingredient called chlorhexidine. A 2020 study showed that healthy people who used chlorhexidine mouthwash experienced a major shift in their salivary microbiomes. Alcohol-based mouthwashes, Dr. Tran says, can also lead to dysbiosis.11
  • Reduce your sugar intake. Diet can result in shifts of the oral microbiome.24 For example, certain types of bacteria convert sugar and starch into acids that can erode enamel, increasing calcium in the oral cavity and creating a hostile environment to healthy microbes. “People with a sugary diet will have a higher proportion of unhealthy bacteria than healthy ones,” Dr. Tran says. (Added sugars, primarily, are to blame—Dr. Tran says it’s still important to eat lots of fruits and veggies, which unlike many processed foods, have other health benefits.)
  • Make sure you’re eating enough fiber. Fiber intake has been shown to increase bacteria diversity levels and decrease “bad” bacteria.25
  • Quit smoking and/or vaping. Not only have cigarettes been shown to be rich in pathogenic bacteria (which can be inhaled and colonize the oral cavity), but smoking them also alters oral microbial ecology, increasing the acidity of saliva, depleting oxygen, causing bacteria to adhere to mucosal surfaces, and impairing host immunity.26,27,28
  • Reduce your alcohol intake. Heavy alcohol consumption may alter oral microbial composition and potentially affect how bacteria function.29,30
  • Work with your doctor to use antibiotics sparingly. Many studies have shown that antibiotics can affect the number and diversity of oral microbes, and that the functions of the oral microbiome may be drastically changed as a result of antibiotic treatment.31
  • Reduce your stress. This is potentially easier said than done, but there is a scientific basis for this recommendation. The stress hormone, cortisol, can enter the blood and negatively impact the organs. Similar to other steroid hormones, cortisol has been found in saliva, suggesting it may impact the mouth directly.32
  • Take a high-quality probiotic. More recent studies also suggest that certain probiotics could help prevent cavities, in addition to other periodontal diseases, by enriching the population and diversity of your oral microbiome. Keep in mind that not all probiotics are created equal. Look for a probiotic with clinically studied strains.33,34

So, as you seek to support your well-being, and as research on the oral microbiome continues to evolve, keep your mouth in mind—and all the ways the oral microbiome is working to support your health.


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