The Oral microbiome

your mouth is a window to your overall health.

So, what’s the connection between oral health and general, overall health? Many people are unaware that regardless of how well or often you brush your teeth, your mouth still teems with bacteria — fortunately, mostly harmless. Your mouth acts as the entry point to your digestive and respiratory tracts, and it turns out we sometimes have a few surprising and unwanted guests residing there, with the ability to move into other niches of the body, and cause disease.

Your mouth hosts around 700 species of microbiota, with the ability to translocate to the gut, the lungs, the sinuses, and even get absorbed into the systemic circulation, impacting a host of other organs, and the cardiovascular system, even the brain.

Normally our natural immune defences and good oral health care, keep bacteria under control. However, use of certain medications can upset the balance of this ecosystem, (decongestants, antihistamines, painkillers, diuretics and antidepressants). One of those ways is reducing saliva flow. Saliva neutralises the acids produced by bacteria in the mouth, and helps to flush away microbes that might otherwise multiply and lead to disease. Another imbalance can be caused by metabolic diseases, such as diabetes, which can lower the body’s resistance to infection, making oral health problems more severe.

So, your oral health is probably more important than you realise, your mouth is literally a window to your overall health.

Saliva testing the oral microbiome

Recent advances in qPCR techniques have made it possible to identify and quantify the composition of the human microbiota, in its various niche habitats. ‘Oral EcologiX‘ by Invivo Healthcare is an easy, do at home saliva test, to assess your oral microbiome, see link below. The mouth alone comprises several distinct bacterial habitats: the tongue, the tonsils, the hard and soft palette, the cheeks and the gums, particularly the gum/teeth margins.

So why might you want to know more detail?

Of the myriad species residing in the mouth, some are useful, bestowing health, whereas other more pathogenic ones have been strongly associated with common, chronic inflammatory diseases. Periodontal disease in the mouth many people are familiar with, but stroke; cardiovascular and arterial disease; endocarditis (an infection of the inner lining of the heart chambers or valves); certain oral, oesophageal & colon cancers; diabetes; Rheumatoid arthritis; pneumonia; Alzheimer’s; liver disease; even pre-term delivery and low birth weight, are all now connected to oral bacteria.

Recent studies have shown that certain pathogenic strains of oral bacteria that colonise the tissue just beyond the throat, increase risk of oesophageal cancer. Such pathogenic strains that translocate even further – to the gut – can lead to IBS, activation of the intestinal immune system and produce chronic inflammation.  P.gingivalis is an oral bacterium that causes periodontal disease and if chronically elevated in the gut can increase risk of colon cancer, inflammatory bowel disease and diabetes.

The bi-directional relationship between diabetes and periodontitis is well established. Oral investigations in diabetic patients have shown they also have significantly increased levels of Capnocytophaga and Tannerellla forsythia, in addition to P.gingivalis. (All three bacteria are tested for in Oral EcologiX – see below). The answer to re-establishing a healthy oral microbiome is most definitely not commercial, antibacterial mouthwash.  These in fact disrupt the balance of a healthy microbiota indiscriminately killing off the favourable, commensal species, whilst allowing hardier pathogens to flourish, with less competition around them.

There is a relationship between the routine use of mouthwash and risk of type 2 diabetes.

The now well established relationship between periodontal disease and diabetes has prompted scientists to take a closer look at oral bacteria and cardiovascular disease, because Stroke and heart disease are the main causes of death in diabetic patients. Evidence of translocation into systemic circulation has been confirmed with oral bacteria being identified in the blood clots of stroke victims.  It should be emphasised at this juncture that the presence of these bacteria flags up ‘increased risk of’ these conditions, not necessarily the presence of overt pathology.

However, identifying said risk, enables the holder of the information to embark on preventative protocols.

Twelve relevant species can be identified using a simple PCR saliva test from INVIVO Healthcare (cost: £126.00) 

I decided to write this piece following a client’s experience, who generously shared their ‘Oral EcologiX‘ results, and did so in part because their oral hygiene practices – deemed exemplary by their dentist – had none-the-less failed to prevent significant colonisation of four pathogenic species (and four more slightly elevated), which after researching both the literature and Invivo’s interpretative guide, in summary suggested an elevated risk for: aggressive periodontal disease; potential infections beyond the oral cavity (endocarditis, urinary tract, spondylodiscitis); atherosclerotic plaques; oesophageal cancer; with a milder risk for pre-term labour; and pelvic inflammatory disease.

Again, it’s worth reiterating that these findings point to an elevated risk for, not necessarily overt pathology, however my client was relieved that ‘P. gingivalis’ was not one of the strains identified in their result, as a growing body of evidence now links this bacteria, found in Amyloid plaques, to Alzheimer’s, which runs in their family.

Armed with this information it motivates one to consider in more detail how one might improve oral hygiene, and how one might embark on a restorative program to nudge the mouth’s ecology back towards a more healthy, balanced one, where commensal species flourish and keep opportunistic pathogens at bay.

Step ONE: remove from your bathroom those commercial, antibacterial mouthwashes. We need to protect and encourage the presence of the good microbes to out-compete the bad ones.

Step TWO: Book in to my clinic to organise your own Oral Ecologix saliva test, with the goal of using the results to kick-start a restorative protocol, to nudge your oral microbiome towards a healthier homeostasis.

Take responsibility, with

 Preventative Functional Medicine 


Olli Patrakka et al., (2019) Oral Bacterial Signatures in Cerebral Thrombi of Patients With Acute Ischemic Stroke Treated With Thrombectomy. J of the American Heart Assoc., 8:e012330

Muszynski D et al., (2022) REVIEW article: Esophageal cancer and bacterial part of gut microbiota – A multidisciplinary point of view. Front. Cell. Infect. Microbiol., Vol 12

Maoyang Lu st al., (2018) Oral microbiota: A new view of body health. Food Science & Human Wellness Vol 8(1): 8-15

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