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A Review of the Oral Microbiome: Orli Reports

A warm welcome to our guest blogger today, Orli Kadoch!

Hi everyone, my name is Orli and I am the Science Coordinator at uBiome who put together the dental campaign on

The first (and most important part) of putting together a study is background research.  Every relevant paper leads us to better understand how to improve our own research methods and strategy.  Informed by Dr. Jeremy Horst, a practicing dentist and PhD bioinformatician who is our advisor on this study, I’ve read countless papers on the dental/oral microbiome.

Today I’ll be reviewing one of my favorites, a review paper by Massimo Costalonga and Mark C. Herzberg entitled The oral microbiome and the immunobiology of periodontal disease and caries.

This review paper covers many interesting topics relating to the oral microbiome and would be a useful read to anyone interested in this field of research, or even a curious citizen scientist. Costalonga & Herzberg examine various ecological niches within the oral microbiome, including the surface of the tooth or tooth enamel, the saliva, the gingival sulcus (the sample site of uBiome’s gum kit), oral mucosa, and the dorsal and lateral surfaces of the tongue.

Oral health is associated with less diverse and rich oral microbiota, which, interestingly, is exactly the opposite of what constitutes health in the gastrointestinal tract.  For example, in periodontal disease (aka: gum disease), inflammation in the gum tissue occurs, which alters the nutrient foundation of the tissue.  As the foundation is altered, a greater number of disease-causing organisms (pathobionts) enter the area, compared to organisms associated with dental health (symbionts).  Over time, this leads to connective tissue and bone destruction, hallmarks of periodontal disease.

Diet can also impact the dental microbiome and thusly, impact an individual’s susceptibility to dental caries.  Consumption of refined carbohydrates, prevalent in more recent/modern years (e.g., sucrose) has slightly shifted the human oral microbiome to include higher frequencies of caries-causing bacteria such as S. mutans, Veillonellaceae, Lachnospiraceae, and Actinomycetales.  One might infer that the modern diet has played a large role in the prevalence of dental caries and periodontal disease. However, it is important to note the possibility of inaccurate oral microbiome measurements from ancient, preserved samples compared to viable microbes sampled in modern day.  uBiome hopes to gather more information regarding variations in diet and resultant changes in dental microbial communities through our dental campaign.

As our mouths are an open system to the environment, it is reasonable to conclude that all the organisms found in the oral microbiome can possibly account for all the organisms in the natural environment that surrounds us. So where do these organisms (bacteria) congregate within the microbiome, and what does this tell us about the functionality of various niches?

The oral cavity is home to distinct ecological niches, summarized in this chart below:

Saliva No indigenous bacteria found here. Bacteria present are those shed from the surrounding niches, with the majority coming from the tongue biofilm. Most prevalent bacteria: Prevotella and Streptococcus
Teeth The only non-shedding surface in the oral cavity, allowing for biofilm development. Biofilm contains initial microbial colonizers of the oral cavity, including streptococcal adhesins. As biofilm matures, it protects surface from food and pH fluctuations. Tooth microbiota can differ depending on location of the tooth, amount of saliva present, and the anatomy of the tooth surface itself (more grooves are associated with higher risk of caries). Most prevalent bacteria: Streptococcus ssp. and Veillonella
Gingival Sulcus/Periodontal Pocket A space between the tooth and the gum tissue that surrounds the tooth. Contains immune mediators and white cells. Once activated by surrounding dental biofilm, epithelial and connective tissue can be destroyed by neutral protease, elastases, collagenases, and metalloproteinases contained in the sulcus. Most prevalent bacteria in healthy gingival sulci (defined by a pocket less than 4mm deep): Acinetobacter, Haemophilus, and Moraxella. In periodontal disease, P. gingivalis, Tanerella forsythia, and Treponema denticola, disrupt the microbial community of the sulcus. At later, more advanced stages of the disease, Negativicutes, Seleomonas, and Megasphera appeared in higher frequencies.

As indicated, periodontal disease seems to result from a polymicrobial infection and is consistent with the dysbiosis hypothesis, which states that periodontal disease is marked by the increase in otherwise low-frequency species in the periodontal pocket.  While once many thought P. gingivalis operated alone and was sufficient to initiate periodontal disease, we now know that commensal bacteria must also be present for disease to occur.

While research in this field has allowed us to understand more about periodontal disease, there are still some challenges we face in this area of research.  For one, sampling properly can become problematic as distinct ecological sites are localized very close together.  Additionally, our ability to understand the distinct bacteria related to the progression of periodontal disease can be a challenge as it is difficult to measure unless there is already significant tissue damage (roughly 1-2mm loss).  There is much work to be done to fine-tune these measurements and more clearly define the various stages of tissue and bone destruction, but we hope that by promoting dental research efforts like uBiome’s and the efforts of many scientists, we can make important discoveries in this field.

Lastly, this review paper discusses dental caries (cavities) briefly.  Caries are the most common disease in children, and their treatments can yield a very painful and traumatic experience for all involved.  Streptococcus mutans was thought to be the only caries-causing bacteria, however, recently, researchers have realized the disease to be much more complex.  Caries initiation is predominantly marked by Streptococcus spp., Veillonella spp and Actinomyces spp S mitis, and S. sanguinis. In a few studies Streptocuccus mutans has been found to be only a minor influence in caries active vs. caries-free individuals; however, it still is thought to be a keystone pathogen in the initial stages of caries formation (enamel demineralization). Similar to periodontal disease, microbiota of a caries lesion contain greater bacterial diversity and richness compared to healthy plaque microbiota.

There is clearly much to be done in dental microbiome research, particularly in identifying clear microbial hallmarks of distinct stages of periodontal disease and dental caries.  The more we can find out how these bacteria interact with environmental factors, genetic factors, and other potentially correlated systemic diseases or viruses, the more effectively we can detect and treat these harmful and prevalent dental problems.  Come join us at so we can all learn more!


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