The oral microbiome is fast becoming my favourite biome to interpret.
For one thing, there is a wealth of research in this area that has not had much practical application until very recently, when DNA-based oral microbiome tests became available to the public.
Mounting evidence has linked oral health with just about every body system you can think of. And yet it’s probably the most neglected. Outside of brushing twice daily, those drying, good bacteria-killing, mouthwashes filled with alcohol, and some trips to the dentist, most of us don’t know what’s going on in our mouths.
We get small clues like bad breath, ulcers, white tongue, cavities, or dryness, but the causes and solutions are a question mark.
We are a long way from there now. Thanks to smart human beings who do the hard scientific research, we know most of the primary and secondary pathogens involved in many oral conditions, and can accurately map them in your oral microbiota.
Here are a few:
Periodontitis
Primary Pathogens:
- Porphyromonas gingivalis
- Tannerella forsythia
- Treponema denticola
- Campylobacter rectus
Secondary Pathogens:
- Fusobacterium nucleatum
- Prevotella intermedia
- Aggregatibacter actinomycetemcomitans
- Haemophilus parainfluenzae
Gingivitis
Primary Pathogens:
- Streptococcus sanguinis
- Actinomyces naeslundii
Secondary Pathogens:
- Fusobacterium nucleatum
- Prevotella intermedia
- Treponema spp.
- Haemophilus spp.
Caries
Primary Pathogens:
- Streptococcus mutans
- Streptococcus sobrinus
- Candida albicans (in cases of early childhood caries)
Secondary Pathogens:
- Lactobacillus casei
- Lactobacillus rhamnosus
- Campylobacter spp. (occasionally found)
Plaque
Primary Pathogens:
- Streptococcus mutans
- Streptococcus sanguinis
Secondary Pathogens:
- Actinomyces spp.
- Fusobacterium nucleatum
- Haemophilus spp.
Halitosis
Primary Pathogens:
- Volatile sulfur compound-producing bacteria (e.g., Porphyromonas gingivalis)
- Candida albicans (in some cases)
Secondary Pathogens:
- Fusobacterium nucleatum
- Treponema spp.
- Campylobacter spp. (occasionally involved)
- Various anaerobic bacteria producing foul-smelling compounds.
The secondary pathogens are interesting because, while they are not strictly the initiators of disease processes, in high enough amounts they can often trigger enough inflammation to produce symptoms.
In oral diseases like periodontitis, gingivitis, and caries, the interaction between primary and secondary pathogens is crucial. These pathogens form a complex biofilm matrix, which contributes to the pathogenicity of oral diseases.
Biofilm Matrix
Structure: The biofilm matrix consists of bacteria embedded in a self-produced extracellular polymeric substance (EPS), which includes polysaccharides, proteins, and DNA. This structure allows for the protection of the bacteria from host immune responses and antimicrobial treatments.
Primary Pathogens: Primary pathogens, such as Porphyromonas gingivalis and Streptococcus mutans, are typically the initial colonizers that establish the biofilm. They create an environment conducive to the growth of other bacteria.
Secondary Pathogens: Secondary pathogens, such as Fusobacterium nucleatum and Candida albicans, tend to join later, often because of the changes in the oral environment created by the primary pathogens. These secondary organisms can enhance the pathogenic potential of the biofilm by contributing to inflammation and tissue destruction.
Damage Caused by Secondary Pathogens
Threshold Levels: While primary pathogens are often the main drivers of disease, secondary pathogens can also cause damage if they reach sufficiently high levels. For instance, Fusobacterium nucleatum and Campylobacter rectus can exacerbate inflammation and tissue breakdown when present in significant quantities.
Synergistic Effects: The interaction between primary and secondary pathogens can have synergistic effects. Secondary pathogens may enhance the virulence of primary pathogens, leading to more severe tissue damage. For example, Candida albicans can influence the pathogenicity of bacteria in the biofilm, especially in individuals with compromised immune systems or those with conditions like diabetes.
Inflammation: High levels of secondary pathogens can trigger a robust inflammatory response, further contributing to tissue damage. The immune response aimed at controlling these pathogens can result in collateral damage to the surrounding tissues.
With all that in mind, like every other microbiome in the human body, the balance of good bacteria is a protective factor. Important species like Streptocuccus salivarius and Lactobacillus species reduce our risk of infection, change the composition of plaque (which is just bacterial biofilm) to be more favourable, and protect against gum inflammation.
Yet to tell you the truth, I rarely observe an oral microbiome with healthy levels of good bacteria. It could be our societal overuse of antibiotics or agricultural sprays, or our diets that are favouring the growth of bad bacteria.
This person reported experiencing bad breath, which can be explained by the overgrowth of commensal yeast Candida albicans which produces gases called volatile sulfur compounds (VSC), in particular one called methyl mercaptan. VSCs are known to cause the malodour we call bad breath or halitosis. Likewise, the depleted Lactobacillus and Streptococcus salivarius are not providing enough protection against infection, or enough lactic acid to regulate the salivary pH.
Another bacteria involved with bad breath as a secondary pathogen is Fusobacterium nucleatum. Yes, that’s the same species found in the gut microbiome that has recently been correlated with colon cancer. In this sample, it is within acceptable limits, however very close to the upper range. This may be contributing to bad breath through VSC production too.
So the goal was to reduce these species – why not just use antibiotics and blow it all up then start from scratch? Well for starters, antibiotic resistance is a real and serious problem. Secondly, anyone who works with the human microbiome will tell you that once good bacteria is gone, it’s a time consuming process to restore them. Probiotics are transient (they don’t stay there forever) and prebiotics may target select species, but it’s hard to get back diversity.
Put simply it’s quite a long process that requires patience, so the ideal scenario is not obliterating your good bacteria to start with, if you can avoid it. Note: antibiotics save lives, that’s not being discounted.
And lastly, we have the tools available to correct this state of dysbiosis WITHOUT harming the good bacteria – so let’s use them!
The tools: Targeted probiotics (they are antibacterial too and compete with bad bacteria for resources), antimicrobial herbs, and prebiotics (help support the good bacteria to flourish).
After only 2 months of an oral microbiome restoration protocol involving these tools, let’s look at the results.
The pathogen Staphylococcus aureus has almost completely reduced while the oral thrush yeast, Candida albicans, is now within a healthy range. To get these results typically good bacteria would be damaged, but Lactobacillus species have more than doubled in population which is fantastic. With the causes of bad breath shifting, this client decided to continue the treatment to enhance these great results.
So you can see why dealing with chronic bad breath is difficult. It is not resolved by popping some breath mints or doing further damage with harsh mouthwash.
Curious about your oral health? Check out our Oral Microbiome Test and get started on your tailored treatment.