Inside the Oral Microbiome (And Why It Matters Beyond Your Teeth)

You've probably heard of the gut microbiome. Fewer people know that the mouth has one too, and it's just as complex.

More than 700 species of bacteria, fungi, and other microbes live in your mouth right now [1,2]. That makes it the second most diverse microbial community in the human body after the gut [1]. 

Some of these microbes protect you. Some, left unchecked, cause the problems you already know: cavities, bleeding gums, bad breath. The balance between the two is what dentists call oral homeostasis, and it’s what your daily routine should be managing, whether you realise it or not.

This is one of the fastest-growing areas of dental research, and it's starting to reshape how scientists think about gum disease, tooth decay, and even conditions that seemingly have nothing to do with your teeth at all.

Here's what the research actually shows.

What's living in your mouth, and where

You can think of your oral microbiome as an ecosystem of different ‘neighbourhoods’, each one hosting a slightly different community [3]:

• The tooth surface, where hard, fixed enamel allows dense, long-term bacterial biofilms (what we know as plaque) to build up over time.

• The gumline and gum pocket, a low-oxygen area that favours different (often more harmful) bacterial species as it becomes inflamed.

• The tongue, which harbours much of the bacteria responsible for bad breath.

• Saliva, which constantly replenishes and washes across every surface we just mentioned.

The main types of bacteria found across these zones include Streptococcus, Actinomyces, Veillonella, Prevotella, and Fusobacterium, alongside fungi like Candida and even resident viruses [3,4].

[IMAGE: simple diagram showing the different "zones" of the mouth microbiome — teeth, gums, tongue, saliva]

In a healthy mouth, these species coexist in a balanced way: beneficial bacteria compete with harmful ones for space and nutrients, help regulate pH, and produce compounds used in other places of your body. Problems start when this balance is disrupted, creating what researchers call dysbiosis. Common triggers include:

• A sugar-heavy diet, which feeds acid-producing bacteria disproportionately

• Inconsistent brushing and flossing, which lets biofilm mature undisturbed

• Smoking, which depletes oxygen, increases acidity, and reduces saliva

• Certain medications that decrease or stop saliva flow

• Various traditional oral care products, particularly harsh, broad-spectrum antiseptics [1]

Why your gums are the real battleground

Gum disease doesn't happen overnight. It typically follows a clear progression:

1. Gingivitis — plaque builds along the gumline, causing redness, puffiness, and bleeding.

2. Early periodontitis — left untreated, the infection begins moving below the gumline.

3. Advanced periodontitis — the infection breaks down the tissue and bone holding teeth in place, which can make teeth wobbly or even cause tooth loss.

The bacteria most strongly associated with the progression from early gingivitis to advanced periodontitis, often called the "red complex" species, specifically love an oxygen-poor, inflamed environment. In other words, gum disease creates the very conditions that allow it to get worse. That's why catching an imbalance early, and keeping the whole ecosystem in good shape, is much more effective than fighting individual bacteria when gum disease is already present.

The link to the rest of your body

Your mouth is connected to your bloodstream, your airways, and your digestive tract, and researchers have spent the last two decades mapping how much oral health influences the rest of the body. Chronic gum inflammation has been associated with:

• Cardiovascular disease. Large reviews have found a consistent association between periodontal disease and increased cardiovascular risk, likely driven by shared inflammatory pathways [5].

• Diabetes. The relationship runs both ways: diabetes raises the risk of gum disease, and gum disease makes blood sugar harder to control [6,7].

• Cognitive health. Several reviews have linked periodontitis with a higher risk of Alzheimer's disease and cognitive decline, with proposed mechanisms including chronic inflammation and specific oral pathogens [8,9,10].

• Pregnancy outcomes. Gum disease has been associated with adverse pregnancy outcomes, including pre-term birth [11].

Although these are associations, not proof of direct causation, the pattern is consistent enough that oral health can no longer be treated as separate from the rest of the body.

[IMAGE: simple infographic showing the mouth connected to heart, brain, and body via bloodstream, illustrating the systemic link]

The microbiome-blood pressure connection

One of the clearest examples of how bacterial balance in the mouth impacts the wider health system involves nitric oxide, a molecule your body needs to keep blood vessels relaxed and blood pressure in a healthy range.

• Certain oral bacteria convert dietary nitrate (found in leafy greens and beetroot) into nitrite [12,13].

• Your body then converts that nitrite into nitric oxide.

• Clinical research shows that mouthwashes containing chlorhexidine, a powerful broad-spectrum antiseptic, significantly reduce the abundance of these nitrate-reducing bacteria within as little as seven days of daily use [12,13,14].

• This measurably lowers nitric oxide availability in the body, and in hypertensive patients, has been directly linked to a rise in blood pressure [15].

It's just one of many clear signs that wiping out oral bacteria indiscriminately - good and bad alike - can have direct consequences well beyond the mouth.

Supporting the balance instead of destroying it

This is where prebiotics, probiotics, and paraprobiotics in oral care like Eēsēcome in. Instead of an all-out antibacterial attack by harsh antiseptics, the goal is to support the microbes that support you:

• Probiotics are live beneficial bacteria strains, like Streptococcus salivarius M18 and K12, shown in clinical trials to reduce gum bleeding and inflammation and to compete directly against harmful, cavity-causing bacteria [16,17].

• Paraprobiotics (aka postbiotics) go a step further. These are inactivated probiotic cells: gently heat-treated so they're no longer alive, but still carrying the beneficial compounds that interact positively with your oral environment [18]. Because they're not living organisms, paraprobiotics are shelf-stable in products (like our [Balancing Toothpaste]) without refrigeration, while still delivering a genuine biological benefit.

• Clinical research on paraprobiotic-based toothpaste and mouthwash has shown meaningful reductions in gum bleeding, plaque, and harmful bacterial counts, in some studies outperforming conventional chlorhexidine rinses over a 6-month period [18,19].

[IMAGE: product shot of Eēsē toothpaste, mouthwash, and floss laid out together as a "routine"]

Why the full routine matters

No single product manages your oral microbiome on its own. Each part of a routine does a different job:

• Brushing removes surface plaque, but misses roughly 40% of tooth surface area between your teeth [20].

• Flossing reaches those spaces, cleaning away biofilm (plaque) before it hardens into calculus, which only a dentist can remove.

• Rinsing distributes beneficial compounds around the whole mouth, including areas a brush and floss can't fully reach, and supports saliva, your mouth's own natural defence system.

Used together and consistently, these steps do more than freshen your breath. They shape which bacterial communities thrive in your mouth and protect your health, day after day.

See how the Eēsē routine puts this research into practice →

References

1. Zhang Y, et al. Oral Microbiome: A Review of Its Impact on Oral and Systemic Health. Microorganisms. 2024;12(9):1797.

2. Sedghi L, et al. The oral microbiome: Role of key organisms and complex networks in oral health and disease. Periodontology 2000. 2021.

3. Baker JL, et al. Ecology of the Oral Microbiome: Beyond Bacteria. Trends in Microbiology. 2017.

4. Deo PN, Deshmukh R. Oral microbiome: Unveiling the fundamentals. J Oral Maxillofac Pathol. 2019;23(1):122-128.

5. Arbildo-Vega HI, et al. Periodontal disease and cardiovascular disease: umbrella review. BMC Oral Health. 2024.

6. Arbildo-Vega HI, et al. An Umbrella Review of the Association Between Periodontal Disease and Diabetes Mellitus. Healthcare. 2024;12(22):2311.

7. Preshaw PM, Bissett SM. Periodontitis and diabetes. British Dental Journal. 2019.

8. Zhang X, Huang X, Chang M. Association between periodontal disease and Alzheimer's disease: a scoping review. Front Aging Neurosci. 2025.

9. Arbildo-Vega HI, et al. Association between periodontal disease and Alzheimer's disease: umbrella review. Front Dent Med. 2025.

10. Wu Z, Ni J, Cui M. Periodontitis and Alzheimer's Disease: Is There a Connection? Dent J (Basel). 2024;12(1):6.

11. Bourgeois D, et al. Periodontal pathogens as risk factors of cardiovascular diseases, diabetes, rheumatoid arthritis, cancer, and chronic obstructive pulmonary disease. Microorganisms. 2019;7(10):424.

12. Bryan NS, Tribble G, Angelov N. Oral Microbiome and Nitric Oxide: the Missing Link in the Management of Blood Pressure. Curr Hypertens Rep. 2017;19(4):33.

13. Bescos R, et al. Effects of Chlorhexidine Mouthwash on the Oral Microbiome. Scientific Reports. 2020;10:5254.

14. Joshipura K, et al. Over-the-counter mouthwash use and risk of pre-diabetes/diabetes. Nitric Oxide. 2017;71:14-20.

15. Bondonno CP, et al. Antibacterial Mouthwash Blunts Oral Nitrate Reduction and Increases Blood Pressure in Treated Hypertensive Men and Women. Am J Hypertens. 2015;28:572-575.

16. Babina K, et al. A Three-Month Probiotic (the Streptococcus salivarius M18 Strain) Supplementation Decreases Gingival Bleeding and Plaque Accumulation: A Randomized Clinical Trial. Dent J (Basel). 2024;12(7):222.

17. Ng E, Lim LP. An Overview of Different Interdental Cleaning Aids and Their Effectiveness. Dent J (Basel). 2019;7(2):56.

18. Butera A, et al. Paraprobiotics in Non-Surgical Periodontal Therapy: Clinical and Microbiological Aspects in a 6-Month Follow-Up Domiciliary Protocol for Oral Hygiene. Applied Sciences (via PMC). 2022.

19. Sadeghi-Nejad, et al. A comprehensive review of the application of probiotics and postbiotics in oral health. Front Cell Infect Microbiol. 2023.

20. American Dental Association. Interdental Cleaning guidance summary.

21. Dawes C. Salivary flow patterns and the health of hard and soft oral tissues. J Am Dent Assoc. 2008;139:18S-24S.

This article is intended for general educational purposes and is not a substitute for advice from your dentist or doctor. If you have symptoms of gum disease, please see a dental professional.