From disease to health: Making sense of the oral microbiome

Summary

The oral microbiome is a particularly important topic for oral health professionals, or at least it should be. This vast ecosystem of microorganisms in the mouth has the potential to change the way oral health professionals practice and could even lead to a new era of personalised, evidence-based, interdisciplinary medicine. 

The importance of the oral microbiome lies in its explanatory potential: understanding it better would put health and disease in a precise and integrated context. Oral health professionals are at the forefront of this revolution, so it is important they integrate research findings into their daily practice. This article offers a general overview of what you need to know about the oral microbiome.

Table of contents

• Tracing the origins of the oral microbiome
• The players – Bacteria, fungi, and more
• From health to disease: the role of biofilms
• The oral-systemic connection – We are holobionts
• How diet can improve our oral health
• New opportunities of interdisciplinary care for oral health professionals
• The workflow of the future
• 10 essential studies for understanding the oral microbiome

Tracing the origins of the oral microbiome

The first tentative steps towards exploring the oral microbiome date back to the 17th century. Since then, our understanding of the oral microbiome has expanded dramatically, from the rudimentary focal infection theory to today’s advanced genetic sequencing techniques.

The first observations of microorganisms in the oral cavity were made by the pioneering Dutch microbiologist Antonie van Leeuwenhoek, whose homemade microscope enabled him to make the first drawing of dental plaque in 1683.

In a letter to the Royal Society of London in 1683, he described "numerous tiny living creatures moving in a lively manner" within his own dental plaque. His illustrations from that time depict recognisable bacterial forms, such as cocci, fusiform bacteria, and spirochetes. Struck by their sheer abundance, he remarked that the number of these microorganisms in the plaque on human teeth likely exceeded the population of an entire kingdom.

„I then most always saw, with great wonder, that in the said matter there were many very little living animalcules, very prettily a-moving.“ Antonie van Leeuwenhoek about plaque biofilm bacteria he observed in the 17th century.

Two centuries later, American dentist and microbiologist Willoughby D. Miller proposed the focal infection theory. His teacher, Nobel Prize winner Robert Koch, had just discovered the Mycobacterium tuberculosis after developing a solidified culture medium, which allowed for the isolation and identification of pure bacterial cultures. Miller applied this to oral microbiology and cultured and characterised bacteria from necrotic -“gangrenous”- tooth pulps. He soon concluded that “The human mouth may harbor microorganisms which, under favourable conditions, produce diseased conditions in the remote parts of the body."

Building upon Miller's ideas, British physician William Hunter delivered a seminal lecture in 1910 titled Oral Sepsis as a Cause of Disease. Hunter raised concern about the prevalent dental practices of his time, more specifically the use of artificial crowns and bridges, which he believed could trap bacteria and lead to systemic infections. Miller’s focal infection theory gained further traction in the early 20th century, but after a particularly unsettling fad of extracting teeth as a preventive measure against systemic disease, the theory gradually fell out of favour due to a lack of evidence.

Timeline of key findings in oral microbiome

A more nuanced understanding began to emerge in the late 20th century, driven by advances in microbiology and epidemiology. The advent of DNA sequencing revolutionised the study of the oral microbiome, revealing a complex and dynamic ecosystem of bacteria that interact not only with each other but also with the body’s immune and inflammatory responses. 

Today, researchers recognise clear links between oral health and systemic conditions, including cardiovascular disease, diabetes, and Alzheimer’s. Rather than a simple cause-and-effect model, the latest research suggests that an imbalanced oral microbiome may contribute to chronic inflammation, a key driver of numerous diseases. The story of the oral microbiome is far from complete. As scientific techniques continue to advance, our understanding of this hidden world—and its profound impact on human health—is only beginning to unfold.

The players – Bacteria, fungi, and more

The oral microbiome is the second-largest microbiome in the human body after the gut microbiome. From birth, it undergoes significant changes. Factors such as mode of delivery, breastfeeding, diet, environment, hormonal changes, and oral hygiene all impact the composition of the oral microbiome. This composition is vast and dynamic: a diverse community of bacteria, archaea, fungi, viruses, and protozoa that make or break our health. 

Bacteria

The majority of the microorganisms in the oral microbiome are bacteria. The Human Oral Microbiome Database (HOMD) currently lists 774 bacterial species as part of the oral microbiome. The most abundant bacterial genera in the oral cavity, in terms of absolute numbers, include Streptococcus, Actinomyces, Veillonella, Neisseria, Haemophilus, Fusobacterium, and Porphyromonas. 

These bacteria are not evenly distributed throughout the mouth. They form communities in different ecological oral niches, often in the form of biofilm. These niches, which roughly include the tongue, saliva, teeth, and mucosal surfaces create unique microenvironments that support bacterial survival.

Factors such as varying oxygen levels, nutrient availability, and surface attachment sites make for different biofilm composition. As a result, the microbes colonising the tongue differ significantly from those on the teeth or gum line.

Source: https://www.mdpi.com/2218-1989/14/5/277

While bacteria dominate, other microorganisms groups play crucial roles too. Each type interacts within the biofilm community, influencing microbial balance, immune responses, and overall oral health.

Fungi

In addition to bacteria, the oral mycobiome includes more than 100 fungal genera, with Candida and Malassezia being the most predominant. Candida albicans is associated with dental caries, particularly in children with early childhood caries, due to its ability to interact with Streptococcus mutans and reinforce cariogenic biofilms.

Archaea

Though less abundant in the oral microbiome than bacteria and fungi, archaea play a crucial role in microbial metabolism by influencing bacterial activity. Methanobrevibacter oralis, the most common oral archaeon, acts as a hydrogen scavenger, consuming hydrogen produced by fermentative bacteria such as Prevotella and Veillonella. 

Viruses

The oral virome consists mainly of bacteriophages, which regulate bacterial populations through predation. Recent studies suggest that the diversity and abundance of phages in the oral microbiome are greater than previously thought, indicating their potential role in modulating microbial ecology and influencing oral diseases.

Protozoa

Protozoa are single-celled eukaryotic microorganisms that can either be free-living or parasitic. While they are less studied than bacteria and fungi in the oral microbiome, some protozoa have been associated with periodontal disease. The most common oral protozoa include:

• Entamoeba gingivalis – Found in dental plaque and subgingival biofilms, often in individuals with periodontitis. It can ingest host immune cells, contributing to inflammation.
• Trichomonas tenax – A flagellated protozoan found in dental plaque, particularly in patients with poor oral hygiene and periodontal disease.

Although their exact role in oral health and disease is still being explored, protozoa may contribute to biofilm dynamics, inflammation, and tissue destruction in periodontal infections.

An overview of essential bacteria

Most bacteria in the oral microbiome belong to seven phyla – broad taxonomic groups that categorise bacteria based on shared genetic and physiological characteristics: Actinomycetota (Actinobacteria), Bacteroidota (Bacteroidetes), Bacillota (Firmicutes), Fusobacteriota (Fusobacteria), Pseudomonadota (Proteobacteria), Saccharibacteria (TM7), and Spirochaetota (Spirochaetes). 

Each of these phyla contributes to the delicate balance of the oral microbiome, shifting toward dysbiosis when conditions favour pathogenic species. Here’s a breakdown:

From health to disease: the role of biofilms

The oral microbiome exists in a delicate balance: the microorganisms in our mouth can contribute to either eubiosis (health) or dysbiosis (disease). Mature biofilm lies at the core of the transition from health to disease. Let's delve into the process of how a healthy environment turns pathogenic.

Step 1: The birth of biofilm

Let’s start with the best-case scenario: a healthy oral microbiome. Saliva plays a vital role in maintaining this healthy balance. It helps wash away debris, regulates pH, and provides antimicrobial protection through immune components like immunoglobulin A, lysozyme, and lactoferrin. 

Saliva also enables microorganisms to adhere to oral surfaces, and supplies the nutrients they need to grow. This is how the first thin layer of biofilm forms: as a means of protection and structural integrity, microorganisms embed themselves in a matrix composed of extracellular DNA, polysaccharides and proteins.

Step 2: Cooperation versus competition

Initially, the biofilm is dominated by gram-positive, facultative anaerobic bacteria, such as Streptococcus species. However, through quorum sensing, bacteria coordinate gene expression, enzymatic activity, and structural modifications. As the matrix strengthens over time, it fosters microbial diversity, while also creating favourable conditions for the survival of anaerobic species.

Step 3: A turn for the worse

As the biofilm matures, pathogenic bacteria start to thrive:

• Gram-negative anaerobes begin to dominate, increasing virulence potential.
• Bacterial by-products, such as proteases and endotoxins, trigger host immune responses.
• The protective matrix enhances resistance to brushing, antimicrobial agents and immune system attacks.

This transition to dysbiosis sets the stage for oral diseases, particularly periodontal disease and dental caries.

Step 4: The body fights back, and loses

At this point, dysbiosis is fully established, so an inflammatory response is triggered:

• White blood cells are recruited in an attempt to neutralise bacterial invasion.
• Biofilm-induced immune evasion means the extracellular matrix acts as a shield, making it difficult for white blood cells and antimicrobial agents to effectively eliminate the bacteria. During this battle, tissue-damaging enzymes are released.
• This chronic inflammation and connective tissue breakdown leads to the deepening periodontal pockets.

Rather than eliminating the infection, the immune response contributes to disease progression by exacerbating tissue destruction.

The worst offenders

Unlike dental caries, which result from acidogenic bacteria, periodontitis is driven by polymicrobial synergy rather than a single pathogenic species. Certain bacterial complexes serve as strong indicators of disease:

• Aggregatibacter actinomycetemcomitans – associated with aggressive periodontitis.
• Tannerella forsythia and Prevotella spp. – implicated in chronic inflammation.
• Socransky’s famous Red Complex:
  • Porphyromonas gingivalis – immune modulation and connective tissue degradation.
  • Tannerella forsythia – epithelial invasion and inflammatory response.
  • Treponema denticola – tissue penetration and destruction.

These pathogens thrive within mature biofilms, which reinforces the chronic nature of periodontal disease.

Healthy and unhealthy oral environments: What you need to know

Eubiosis

A stable oral biofilm consists of commensal and symbiotic microorganisms that:

• Prevent the overgrowth of pathogens.
• Maintain immune homeostasis by modulating inflammatory responses.
• Promote mineralisation and oral tissue repair.
• Contribute to salivary and digestive functions.
• Regulate plaque by forming structured biofilms that inhibit the adhesion of harmful bacteria.

Dysbiosis

Dysbiosis occurs when opportunistic pathogens dominate and trigger inflammation. This shift can be caused by:

• Poor oral hygiene: Leads to plaque accumulation, favouring pathogenic bacteria.
• Smoking and diet: Alters oxygen levels and nutrient availability, favouring anaerobic pathogens.
• Reduced salivary flow: Saliva washes away debris, neutralises acids, and transports antimicrobial compounds.
• Stress and systemic disease: Weakening immune regulation, allowing dysbiotic shifts.
• Antibiotics: Eliminate beneficial bacteria, enabling pathogenic overgrowth.

The oral-systemic connection – We are holobionts

When oral disease takes hold, systemic complications are not far behind. The American Dental Association (ADA) reports over 200 connections between oral health and systemic diseases. This is hardly surprising, as the oral microbiome does not exist in isolation. Humans and their microbiomes form a "holobiont", a co-evolved system where microbes play a crucial role in physiology. 

Definition of holobiont

The term “holobiont” was first introduced in 1991 by Lynn Margulis and initially referred to a simple biological entity involving a host and a single inherited symbiont. It was extended to define a host and its associated communities of microorganisms (also referred to as the microbiota which corresponds to the collection of microorganisms in interaction with their host and ranging from mutualistic to parasitic interactions). A host and its microbiota thus constitute a holobiont. This term is now widely used in different contexts and applies to virtually all metazoans, with current research focusing mainly on human, animal, and plant holobionts.

Source: Simon, J.-C., Marchesi, J. R., Mougel, C., & Selosse, M.-A. (2019). Host-microbiota interactions: from holobiont theory to analysis. Microbiome, 7(1), 64. https://doi.org/10.1186/s40168-019-0619-4

Oral diseases – particularly periodontal disease – are not confined to the mouth. Chronic inflammation caused by bacterial infections in the gums can spread throughout the body and cause serious systemic conditions. 

Three mechanisms contribute to the oral-systemic connection:

1. Chronic inflammation
   • Periodontal disease can trigger persistent inflammation that can lead to systemic conditions.
   • Inflammatory mediators like C-reactive protein (CRP), interleukin-6 (IL-6), and tumor necrosis factor-alpha (TNF-α) are released into the bloodstream, increasing risks of cardiovascular disease, insulin resistance in diabetes, and neuroinflammation linked to Alzheimer’s disease.
2. Bacterial translocation
   • Harmful oral bacteria such as Porphyromonas gingivalis and Fusobacterium nucleatum can enter the bloodstream through inflamed gum tissue.
   • These bacteria have been found in atherosclerotic plaques in heart disease patients, amniotic fluid in preterm births, and brain tissue in Alzheimer’s patients, suggesting a direct link between oral infections and systemic diseases.
3. Immune system dysregulation
   • Periodontal disease can alter immune function, making patients more susceptible to infections and autoimmune conditions.
   • Diabetic patients, for example, have a weakened immune response, increasing their risk of severe gum infections. Conversely, untreated periodontal disease can worsen blood sugar control, creating a bidirectional relationship between diabetes and oral health.

The main systemic diseases and their links to oral dysbiosis

1. Diabetes

In 2019, 6% of the global population had diabetes, amounting to 463 million people. This number is expected to rise to 10.2% (578 million) by 2030 and 10.9% (700 million) by 2045. 

Although the number of diabetics is growing, risk factor management does exist, and research has shown that 80% of type 2 diabetes can be prevented with a healthier diet and regular exercise. This suggests that there must be risk factors for diabetes that are being overlooked, such as oral and gut dysbiosis. The link between diabetes and periodontal disease is bidirectional: patients with diabetes have a higher risk of developing periodontitis, and vice versa.

Those with diabetes have a 2-3 times higher risk of chronic periodontitis, and periodontitis is considered the sixth complication of type 2 diabetes. Additionally, periodontal treatment has been shown to reduce HbA1c levels by up to 0.4% in type 2 diabetes patients. Diabetes patients have been found to exhibit a specific oral microbiome signature.

Tell-tale bacterial markers in diabetics include an increase in Aggregatibacter, Neisseria, Gemella, Eikenella, Selenomonas, Actinomyces, Capnocytophaga, Fusobacterium, Veillonella, and Streptococcus. Actinobacteria significantly increased the odds of diabetes by 10% in subjects with gingival bleeding, while Fusobacteria increased this risk by 14%.

2. Cardiovascular Diseases

Cardiovascular diseases are the leading cause of death worldwide. In 2021, they accounted for 20.5 million deaths, approximately one-third of all global deaths. Risk factors include age, smoking, hypertension, insulin resistance, and obesity, but the rising mortality suggests that additional contributors like immune-inflammatory responses and oral microbiota dysbiosis may also play a role. 

Interestingly, one enormous 2018 study tracked nearly one million people for 21 years to explore the link between tooth loss and coronary heart disease. While a modest connection was found, it vanished in lifelong non-smoking men, suggesting smoking was the real culprit. 

For some unclear reason, the link remained in women. In other words: poor oral health might not directly cause heart disease—correlation does not equal causation. Instead, shared risk factors like smoking may explain the relationship. A key takeaway from this study is that, despite the clear links between oral health and cardiovascular disease, it is also important to control for confounding risk factors in health research.

3. Alzheimer’s disease 

Emerging research suggests a connection between periodontitis and cognitive decline, including Alzheimer’s disease and dementia. While some studies indicate that periodontitis may be a risk factor for cognitive decline, others propose that individuals experiencing cognitive deterioration struggle with maintaining oral hygiene due to functional decline, making them more susceptible to periodontitis.

Then again, oral bacteria or their components can trigger inflammatory responses via the TLR-4/NF-κB pathway, increasing CRP, TNF-α, IL-6, and IL-1, which activate microglia and exacerbate neuroinflammation. 

One study found that periodontitis is associated with a significantly faster rate of cognitive decline in individuals with Alzheimer’s disease. Over a six-month period, participants with periodontitis experienced a sixfold increase in cognitive deterioration compared to those without it. The study suggests that this link may be mediated by increased systemic inflammation, reinforcing the idea that oral health plays a role in neurodegenerative disease progression.

Through bacterial translocation, gram-negative oral bacteria and virulence factors can cross the blood-brain barrier and create a bidirectional link between periodontitis and Alzheimer’s disease. Lipopolysaccharides from Treponema denticola, for instance, were found post-mortem in the brains of Alzheimer patients, whereas the gingipains produced by Porphyromonas gingivalis have demonstrated neurotoxic effects both in vivo and in vitro, contributing to the degradation of Tau protein—an essential component for normal neuronal function. In contrast, periodontal treatment had a favorable effect on Alzheimer’s-related brain atrophy as explored by magnetic resonance imaging.

4. Adverse pregnancy outcomes

Pregnant women are more prone to oral infections due to hormonal and immune changes, which increase the chance of gingivitis and periodontitis. During pregnancy, a pathogenic shift typically occurs, which reverts postpartum.

Oral dysbiosis in periodontitis increases the risks of adverse pregnancy outcomes like preterm birth, preeclampsia, gestational diabetes, low birth weight, stillbirth, and perinatal birth. A study examining 2,474 pregnant women found that those with periodontal disease were nearly twice as likely to experience an early preterm birth (before 34 weeks) compared to those without it.

However, when considering all preterm births (before 37 weeks), the link was not as pronounced, suggesting that the impact of gum disease on preterm birth depends on how preterm birth is defined.Proposed mechanisms include bacterial translocation to the placenta, inflammatory mediators (IL-6, IL-8, TNF-α) that induce fetal inflammation, and microbiota shifts through sexual activity.

Pathogens like Porphyromonas gingivalis, and Fusobacterium nucleatum can translocate to the fetal-placental unit and are associated with preeclampsia, neonatal sepsis, and stillbirth.

5. Cancer

Emerging evidence suggests that oral dysbiosis may also contribute to the development of certain cancers, particularly oral and gastrointestinal cancers. Chronic inflammation caused by oral pathogens, such as Fusobacterium nucleatum and Porphyromonas gingivalis, can lead to DNA damage and promote carcinogenesis. 

Fusobacterium nucleatum has been found in colorectal cancer tissues and is associated with tumor progression and poor prognosis. Similarly, Porphyromonas gingivalis has been implicated in the development of oral squamous cell carcinoma (OSCC) due to its ability to induce chronic inflammation and inhibit apoptosis in epithelial cells.

Inflammatory mediators, such as interleukin-6 (IL-6) and tumor necrosis factor-alpha (TNF-α), produced in response to oral pathogens, can also promote tumor growth and metastasis. Alarmingly, individuals with severe periodontal disease have a 24% higher risk of developing cancer compared to those with healthy gums. These findings underscore the importance of maintaining oral health as a preventive measure against cancer.

6. Oral–gut microbiome axis 

Most microbiome research focuses on organ-specific microbiomes. However, emerging evidence highlights the role of interorgan microbial networks, particularly the oral–gut microbiome axis. As the body's two largest microbial ecosystems, the oral and gut microbiomes can influence disease pathogenesis through microbial transmission. 

Pathogenic bacteria from the mouth, such as Porphyromonas gingivalis and Fusobacterium nucleatum, can enter the gut through swallowing or via the bloodstream, leading to gut dysbiosis. These bacteria survive stomach acid, colonise the intestines, and disrupt gut microbiota.

This imbalance is linked to inflammatory bowel disease, which affects 7 million people worldwide and includes conditions like Crohn’s disease and ulcerative colitis. Periodontitis prevalence is significantly higher in IBD patients (32%) compared to non-IBD controls (15%). Inflammatory bowel disease is connected to oral lesions: 50% of those suffering from inflammatory bowel disease develop oral lesions. 

In addition, a dysbiotic oral-gut microbiome is connected to cardiovascular disease, neurodegenerative disorders, and gastrointestinal cancers. In patients with periodontitis, stool samples show a decrease in beneficial bacteria and an increase in pathogenic species like Fusobacterium and Tannerella, contributing to intestinal inflammation and the risk of colorectal cancer.

The oral-gut connection to cancer is striking. Periodontitis increases the risk of esophageal adenocarcinoma by 43% and tooth loss raises it to 59%. Fusobacterium nucleatum, rare in healthy guts, is frequently found in colorectal cancer patients. Porphyromonas gingivalis increases the risk of pancreatic cancer by 59%, and postmenopausal women with periodontitis have a 73% higher risk of gallbladder cancer.

These bacteria promote chronic inflammation, immune suppression, and tumor growth.Vice versa, the intestinal microbiome can influence the development of periodontitis. One study in mice examined the two-way immune interaction between the gut and mouth in periodontitis. Porphyromonas gingivalis can migrate to the gut, triggering an immune response that increases pro-inflammatory Th17 cells, which then travel back to the gums and worsen bone loss.

These findings suggest that modifying gut bacteria or blocking Th17 migration could be potential strategies for treating periodontitis and related inflammatory diseases.

7. Respiratory disease

Diseased mouths are also affecting the lungs. A growing body of research reveals how bacteria from the mouth can migrate to the respiratory system, contributing to diseases like pneumonia, chronic obstructive pulmonary disease (COPD), and even severe cases of COVID-19.

Through microaspiration—where small amounts of saliva and bacteria are inhaled into the lungs — oral microbes can settle in the respiratory tract, potentially triggering infections and chronic inflammation. Among the main culprits are Porphyromonas gingivalis and Fusobacterium nucleatum. In patients with COPD, for example, these oral bacteria have been found in lung tissues, suggesting they may contribute to the worsening of symptoms.

The damage is not solely the result of direct infection. The inflammatory response triggered by gum disease can have far-reaching effects throughout the body. Periodontal infections release pro-inflammatory molecules, such as interleukin-6 (IL-6), a cytokine linked to lung damage and severe respiratory distress. In fact, studies of COVID-19 patients have found that those with poor oral health and elevated levels of IL-6 were more likely to experience severe complications.

How diet can improve our oral health

For decades, oral health professionals have aimed to control inflammation and prevent disease almost exclusively through mechanical plaque removal and antimicrobial treatments. However, an emerging perspective is shifting the focus from treatment to prevention, placing diet at the forefront of oral health. 

Scientists and clinicians alike are now recognising the profound impact of nutrition on the delicate ecosystem of the mouth. By incorporating prebiotics, probiotics, synbiotics, and postbiotics into daily nutrition, dental professionals may not only improve oral health but also support systemic well-being.

The risks of the modern diet

The foods we consume do more than nourish us — they shape the microbial communities that live within us, and nowhere is this more apparent than in the oral microbiome. 

For many, the modern diet poses a threat to oral health. Processed foods, refined sugars, and an overabundance of animal-based fats foster the growth of harmful bacteria such as Streptococcus mutans and Porphyromonas gingivalis, both implicated in tooth decay and gum disease. 

Frequent consumption of sugary beverages, white bread, and processed cereals lowers oral pH, creating a breeding ground for pathogenic biofilms. Meanwhile, excessive intake of saturated fats from processed meats, dairy, and fried foods fuels systemic inflammation, which exacerbates periodontal disease.

Beyond diet: the role of biotics

In addition to whole foods, targeted interventions with prebiotic, probiotic, synbiotic, and postbiotic supplements are gaining traction as potential tools for maintaining oral balance.

• Prebiotics are non-digestible fibers that fuel beneficial microbes and can help promote a healthier oral ecosystem. Arginine, found in nuts, seeds, and whole grains, neutralises acidity in the mouth and fosters the growth of beneficial bacteria. Nitrates from leafy greens like spinach and beets enhance nitric oxide production, which has antimicrobial and anti-inflammatory properties. While not technically a prebiotic, xylitol has a prebiotic effect in the mouth by acting as a sugar substitute. Easily found in sugar-free gum, xylitol selectively inhibits Streptococcus mutans, reducing the risk of cavities while supporting beneficial microbes.
• Probiotics are living microorganisms that can colonise the oral cavity. They have been studied for their ability to reduce inflammation, prevent plaque buildup, and suppress harmful bacteria. Strains such as Lactobacillus reuteri, Bifidobacterium lactis, and Streptococcus salivarius have demonstrated benefits, ranging from competing with pathogenic microbes for space and nutrients to producing antimicrobial compounds that actively suppress harmful species. Probiotics are found in fermented foods like yogurt, kefir, kimchi, and sauerkraut, making them an easy addition to a health-conscious diet.
• Synbiotics, which combine probiotics with their preferred food sources, offer an even more effective strategy. A smoothie blending kefir with prebiotic-rich bananas, or a salad dressed with probiotic miso and paired with nitrate-rich leafy greens, creates an ideal environment for beneficial bacteria to thrive.
• Postbiotics, the metabolic byproducts of probiotics, provide additional antimicrobial and anti-inflammatory benefits. Short-chain fatty acids such as butyrate and acetate help regulate immune responses, while bacteriocins—natural peptides with antimicrobial properties—actively suppress disease-causing bacteria in the mouth.
  

Food beneficial for oral & overall health

What this means for oral health professionals

The role of diet in our oral health is becoming impossible to ignore. Educating patients about how food influences their microbiota may be just as critical as advising them to brush and floss. Encouraging a diet rich in fiber, polyphenols, and fermented foods could help prevent disease at its root, rather than just managing symptoms. 

For high-risk patients — such as those with periodontitis, dry mouth, or recurrent cavities —supplementing with probiotics and postbiotic-based mouthwashes may provide additional support. Perhaps most importantly, tracking oral health changes alongside dietary shifts can empower patients take an active role in their well-being.

New opportunities of interdisciplinary care for oral health professionals

Our understanding of the oral microbiome and its impact on the rest of our body presents new opportunities for oral health professionals. By integrating oral microbiome research into clinical practice, oral health professionals can contribute to early disease detection, highly personalised treatment, and interdisciplinary, preventative care. The oral microbiome bridges the gap between oral and systemic health care. So, specific tools and strategies will play an increasingly important role in oral care:

Oral microbiome analysis and salivary diagnostics

Oral health professionals should adopt advanced diagnostic tools to analyse the oral microbiome and identify patients at risk for systemic diseases. Salivary microbiome profiling offers a non-invasive method for detecting high-risk pathogens and inflammatory markers. 

Oral health professionals can incorporate these tests into routine examinations, enabling early intervention. For instance, a patient with periodontitis and elevated C-reactive protein levels may be at risk for cardiovascular disease. Early detection allows for collaborative care with cardiologists to manage both oral and systemic health.

Personalised treatment plans

Microbiome analysis and salivary diagnostics allow for highly personalised treatment plans tailored to each patient’s unique microbial profile. Patients with high levels of P. gingivalis may benefit from targeted antimicrobial therapies, while those with dysbiosis linked to diabetes may require probiotics and dietary interventions. 

In an oral care practice that considers the oral microbiome, a diabetic patient with periodontal disease could receive a combination of scaling and root planing, along with probiotic supplements and glucose monitoring, to improve both oral and systemic outcomes.

Emerging therapies

Oral health professionals should stay at the forefront of emerging therapies. There are several modern strategies for modulating the oral microbiome for the better, which also serve as a welcome strategy in the fight against antibiotic resistance. Here's a closer look at these approaches:

• RNA therapy: Unlike antibiotics, which kill bacteria indiscriminately, RNA-based treatments can specifically target bacterial gene expression to reduce virulence, without disrupting beneficial microbes.
• Quorum quenching: Rather than killing bacteria, these compounds inhibit bacterial quorum sensing and biofilm formation, reducing pathogenicity while preserving microbial diversity.
• Phage therapy: Bacteriophages selectively target and kill harmful bacteria without affecting beneficial microbes, reducing the risk of antibiotic resistance and avoiding broad-spectrum microbial disruption.
• Diet and prebiotic, probiotic, and synbiotic supplements: While mechanical biofilm removal through professional cleanings and at-home oral hygiene remains the foundation of care, nutritional modifications can serve as a powerful adjunct therapy. In addition, prebiotic, probiotic, and synbiotic supplements can restore microbial balance naturally by supporting beneficial bacteria and improving resilience against dysbiosis.
• Xylitol: Xylitol inhibits the metabolism of cariogenic bacteria, reducing acid production and preventing biofilm adhesion.

In contrast to these methods, traditional treatments such as antibiotics and antiseptics often disrupt the entire microbiome, leading to microbial resistance, recolonisation by pathogens, and systemic side effects. These new strategies are targeted and microbiome-friendly with fewer long-term consequences.

Behavioural change and lifestyle advice

Oral health professionals play a key role in educating patients about how oral hygiene, diet, and lifestyle choices impact both oral and systemic health.

Educating patients — especially those with conditions like cardiovascular disease or diabetes — about the risks of oral infections can help reduce systemic inflammation and improve overall well-being. Simple changes, such as reducing sugar intake, adopting a fiber-rich diet, quitting smoking, and managing stress, can support a balanced oral microbiome and lower the risk of systemic diseases. 

The workflow of the future

Despite the well-documented connections between oral and systemic health, healthcare remains largely fragmented. Our growing understanding of the oral microbiome requires collaboration between all healthcare providers, which in turn requires a workflow shift to an interdisciplinary model. Below is an example of what each role could look like, with each healthcare professional playing a distinct yet interconnected part.

1. General dentists - The frontline defenders

Dentists are the first point of contact for patients, identifying early signs of systemic diseases through oral examinations. During checkups, they perform routine oral microbiome analysis and inflammatory marker testing.

This allows them to diagnose periodontal disease or systemic inflammation early, and refer patients to specialists when systemic conditions are suspected. All results are shared with an interdisciplinary team.

2. Dental Hygienists – Guarding oral health

Hygienists play a crucial role in periodontal therapy, biofilm disruption, and patient education. They provide preventive care, including scaling and root planing, and educate patients on maintaining a balanced oral microbiome. Their ability to recognize changes in the oral environment allows for early intervention.

3. Laboratory technicians - The diagnostic experts

Laboratory technicians analyse saliva, plaque, and blood samples to detect high-risk pathogens and inflammatory markers. Their insights support clinical diagnoses and guide personalised treatment plans.

4. Nursing technicians - The patient advocates

Nursing technicians coordinate with both oral health professionals and physicians. They understand the importance of oral health for patients with systemic conditions. They coordinate patient education on the link between oral and systemic health, provide post-procedural care, and ensure adherence to treatment plans. They also assist in infection control, particularly in hospital settings.

5. Phlebotomists - Tracking systemic health

Phlebotomists work closely with lab technicians, collect blood samples to measure systemic inflammation and detect bacteremia caused by oral pathogens. Their work helps correlate oral infections with systemic diseases.

What needs to be done for integrated healthcare

Unfortunately, a lot needs to change if we want an integrated healthcare: more interdisciplinary collaboration, shared patient records, and coordinated management of chronic diseases. 

Education and training should be improved by incorporating oral-systemic health into medical, dental, and hygiene school curricula while requiring ongoing education for practitioners and increasing patient awareness. 

Insurance policies need reform to cover essential oral health services, such as periodontal treatment and salivary diagnostics, supported by research-driven policy changes. 

The adoption of advanced diagnostics, including salivary testing and comprehensive health assessments in dental offices, can facilitate early disease detection. 

Lastly, public health messaging must emphasise the systemic impact of oral health, integrating oral screenings into routine medical exams and launching awareness campaigns to promote preventive care.

10 essential studies for understanding the oral microbiome

The oral microbiome is at the forefront of modern dentistry and systemic health research. Below, we introduce ten essential studies that provide invaluable insights into the role of the oral microbiome in health, disease, and clinical practice.

1. The composition of the oral microbiome

Li et al. (2022) offer a great general overview of the composition of the oral microbiota, the factors that influence its balance, and its role in oral and systemic diseases.

This review article offers insights into how microbial dysbiosis contributes to conditions like periodontitis and caries. It also highlights emerging interventions such as probiotics, prebiotics, and microbiome-targeted therapies.

Li X, Liu Y, Yang X, Li C, Song Z. The Oral Microbiota: Community Composition, Influencing Factors, Pathogenesis, and Interventions. Front Microbiol. 2022 Apr 29;13:895537. doi: 10.3389/fmicb.2022.895537. PMID: 35572634; PMCID: PMC9100676.

2. The gut-oral axis and periodontitis 

Nagao et al. (2022) demonstrated that Porphyromonas gingivalis can translocate to the gut, prompting an immune response that worsens periodontitis. This study highlights the gut-oral axis, suggesting that interventions targeting gut health could play a role in oral disease management.

Nagao, J. I., Kishikawa, S., Tanaka, H., Toyonaga, K., Narita, Y., Negoro-Yasumatsu, K., Tasaki, S., Arita-Morioka, K. I., Nakayama, J., & Tanaka, Y. (2022). Pathobiont-responsive Th17 cells in gut-mouth axis provoke inflammatory oral disease and are modulated by intestinal microbiome. Cell reports, 40(10), 111314. https://doi.org/10.1016/j.celrep.2022.111314 

3. Periodontitis and Alzheimer’s disease

Liccardo et al. (2020) explored the bidirectional relationship between periodontal disease and Alzheimer’s, revealing that chronic gum inflammation may accelerate cognitive decline. Their findings reinforce the importance of oral health in neurodegenerative disease prevention.

Liccardo, D., Marzano, F., Carraturo, F., Guida, M., Femminella, G. D., Bencivenga, L., Agrimi, J., Addonizio, A., Melino, I., Valletta, A., Rengo, C., Ferrara, N., Rengo, G., & Cannavo, A. (2020). Potential Bidirectional Relationship Between Periodontitis and Alzheimer's Disease. Frontiers in physiology, 11, 683. https://doi.org/10.3389/fphys.2020.00683 

4. Periodontal disease and cancer risk

Nwizu et al. (2020) reviewed epidemiological data linking periodontitis to an increased risk of gastrointestinal and pancreatic cancers. Their study suggests that chronic inflammation and pathogenic bacteria may contribute to carcinogenesis.

Nwizu, N., Wactawski-Wende, J., & Genco, R. J. (2020). Periodontal disease and cancer: Epidemiologic studies and possible mechanisms. Periodontology 2000, 83(1), 213–233. https://doi.org/10.1111/prd.12329

5. Oral Microbiome Signatures in Diabetes Mellitus and Periodontal Disease

Matsha et al. (2020) investigated distinct oral microbiome signatures in patients with diabetes mellitus and periodontal disease. Their findings suggest that oral microbiota analysis could serve as a biomarker for the early detection and management of metabolic disorders.

Matsha, T. E., Prince, Y., Davids, S., Chikte, U., Erasmus, R. T., Kengne, A. P., & Davison, G. M. (2020). Oral Microbiome Signatures in Diabetes Mellitus and Periodontal Disease. Journal of dental research, 99(6), 658–665. https://doi.org/10.1177/0022034520913818 

6. The role of Fusobacterium nucleatum in systemic health

Yang et al. (2023) explored innovative RNA-based therapies targeting pathogenic bacteria in periodontal disease, offering a potential alternative to antibiotics.

Yang, M., Dong, P. T., Cen, L., Shi, W., He, X., & Li, J. (2023). Targeting Fusobacterium nucleatum through chemical modifications of host-derived transfer RNA fragments. The ISME journal, 17(6), 880–890. https://doi.org/10.1038/s41396-023-01398-w

7. Dietary influence on the oral microbiome

Santonocito et al. (2022) highlighted the role of diet in shaping the oral microbiome, emphasizing the benefits of fiber, polyphenols, and probiotics for maintaining oral health.

Santonocito, S., Giudice, A., Polizzi, A., Troiano, G., Merlo, E. M., Sclafani, R., Grosso, G., & Isola, G. (2022). A Cross-Talk between Diet and the Oral Microbiome: Balance of Nutrition on Inflammation and Immune System's Response during Periodontitis. Nutrients, 14(12), 2426. https://doi.org/10.3390/nu14122426

8. Periodontitis and adverse pregnancy outcomes

This study is important because it examines the link between periodontal disease and preterm birth, enhancing our understanding of how maternal oral health affects pregnancy outcomes. Its findings could inform preventive strategies and healthcare policies to reduce the risk of preterm birth through improved periodontal care.

de Oliveira, L. J. C., Cademartori, M. G., Schuch, H. S., Barros, F. C., Silveira, M. F., Correa, M. B., & Demarco, F. F. (2021). Periodontal disease and preterm birth: Findings from the 2015 Pelotas birth cohort study. Oral diseases, 27(6), 1519–1527. https://doi.org/10.1111/odi.13670 

9. Periopathogens in atheromatous plaques

This study examines the presence of periodontal pathogens in atheromatous plaques from carotid and coronary arteries, aiming to explore a potential link between periodontal disease and cardiovascular conditions. By identifying specific periopathogens in these plaques, the research supports the hypothesis that oral infections may contribute to atherosclerosis and cardiovascular disease.

Pavlic, V., Peric, D., Kalezic, I. S., Madi, M., Bhat, S. G., Brkic, Z., & Staletovic, D. (2021). Identification of Periopathogens in Atheromatous Plaques Obtained from Carotid and Coronary Arteries. BioMed research international, 2021, 9986375. https://doi.org/10.1155/2021/9986375

10. Oral microbiota and diagnosing systemic disease

Thomas et al. (2021) explore the role of the oral microbiota in diagnosing systemic diseases, highlighting its potential as a biomarker for conditions such as diabetes and cardiovascular disorders. Their study emphasizes the connection between oral health and overall systemic health, suggesting that changes in the oral microbiome may serve as early indicators of broader health issues.

Thomas C, Minty M, Vinel A, Canceill T, Loubières P, Burcelin R, Kaddech M, Blasco-Baque V, Laurencin-Dalicieux S. Oral Microbiota: A Major Player in the Diagnosis of Systemic Diseases. Diagnostics (Basel). 2021 Jul 30;11(8):1376. doi: 10.3390/diagnostics11081376. PMID: 34441309; PMCID: PMC8391932.