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The Oral Microbiome

The oral microbiome consists of a diverse group of microbes that live in the oral cavity and provide the microbial gateway to the gastrointestinal tract. It includes bacteria, archaea, fungi, protozoa and viruses which interact with each other and with the host. After the gut, it is the second largest microbial community in the body. The oral microbiome plays an important role in the balance between health and disease, not only orally but also systemically throughout the body.

Controlling the environment

The normal temperature of the oral cavity is around 37°C which provides a stable environment for bacteria to thrive. Saliva has a pH of 6.5 to 7, which is a favourable pH for most species of bacteria and helps to keep the bacteria hydrated as well as serving as a medium for the transportation of nutrients to microorganisms.


The oral bacteria exist within a complex structure called the oral biofilm (also known as dental plaque). In healthy individuals, this is dominated by bacteria that maintain stability via interactions with the immune system and other microorganisms.

Drugs, diet, injury and infection can all compromise the oral microbiome. These disruptions provide opportunities for pathogenic bacteria to colonise which can lead to dental cavities or periodontal disease.

Dental Cavities

Increased consumption of carbohydrates such as refined and processed foods results in changes in the biofilm environment causing an acidic environment which can lead to dental cavities over time.

Periodontal Disease

The most common complaint of a disrupted microbiome is periodontal disease. It involves chronic inflammation of the tissue that surrounds and supports the teeth and is characterised by bleeding, swollen gums and pain. Diet, smoking, stress and lifestyle habits can all contribute to the disease.

The Industrial Revolution

Two of the greatest dietary shifts in human evolution resulted from the following:

  1. The adoption of a carbohydrate-rich Neolithic (farming) diet

  2. The advent of industrially processed flour and sugar

The transition from hunter-gatherer to farming shifted the oral microbial community to a disease-associated composition.

The now ubiquitous cariogenic bacteria apparently became dominant during the Industrial Revolution.

Modern oral microbiota are markedly less diverse than historic populations, which might be contributing to chronic oral (and other) disease in post-industrial lifestyles.

The development of the oral microbiome

The oral microbiome is first acquired during birth, and delivery mode has an impact.

Vaginally born infants have bacterial communities similar to the mother’s vaginal bacterial communities whereas Caesarean section infants have bacterial communities similar to those present in the mother’s skin.

Breastfeeding also represents a significant source of oral microorganisms. Environmental influences include contact with siblings, friend in playgroups and pets.

Impacts on the oral microbiomes


Frequent antibiotic use can compromise the composition and function of the oral microbiome.

Dietary Changes

Fibre and polyunsaturated fatty acids are closely associated with diversity in the oral microbiome.

Eating sugary, processed foods provides a favourable environment for disease associated bacteria.


Smoking creates an anaerobic environment and alters the salivary pH thereby adversely affecting the composition of the oral microbiota. The detrimental effect of smoking on the oral microbiota is stable and persists for several years, even after quitting.

Systemic disease

What happens in the mouth, doesn’t stay in the mouth. Poor oral health can lead to systemic disease. The oral microbiome is part of a highly interconnected series of microbiomes across the human body. Through a process of bacterial translocation, disruptions in the oral microbiome can contribute to conditions such as Alzheimer's disease, cardiovascular disease, cystic fibrosis, rheumatoid arthritis and diabetes.

Top tips to support your oral microbiome

  • Brush twice daily with an electric toothbrush

  • Floss daily with dental floss or interdental brushes

  • Visit your dentist and oral hygienist regularly

  • Add prebiotic and probiotic fibre to your diet.

  • Focus on an anti-inflammatory diet rich in leafy green vegetables, protein and wholegrains.

  • Include polyphenol rich foods such as such as berries, apples, almonds, olives, spinach and flax seeds

  • Eat healthy fats such as oily fish, nuts and their butters, seeds, avocados and olive oils.

  • Include fat soluble vitamins such as A, D, E and K

  • Ensure daily intake of important minerals including magnesium and calcium

  • Avoid snacking to allow the oral pH to recover between meals.

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