Cosmos ID Reveals What’s Really Inside Your Mouth

Written by: Bonnie Feldman, DDS, MBA, Hailey Motooka, BS, Sarah Hinton

Like the shoemaker with badly repaired shoes, I am a dentist with advanced periodontal disease.  For many years I have struggled with rapidly advanced gum disease despite my consistent brushing, flossing, and rinsing routine. I have tried all sorts of toothbrushes, a myriad of toothpastes and many rinses, all to no avail. I have consulted “dental” experts, “oral pathology” experts and “periodontal disease” experts⁠— nothing helped.  It wasn’t until my research on the oral microbiome that I began to consider the microbes that inhabit my oral cavity as factors that play a part in my poor oral health.

A new understanding of the oral microbiome is shaping how we think about caries, periodontal and oral diseases, as well as diseases far removed from the mouth, such as heart and lung disease, cancer, and some autoimmune diseases. While the traditional view held that oral diseases were caused by a small number of specific pathogens, we now think of the oral microbiome as an ecosystem of finely tuned bacterial, fungal, and viral communities that all contribute to oral microbiome equilibrium.

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Different ‘omics techniques chart

Advances in ‘omics studies (metabolomics, transcriptomics, genomics, etc.) have provided researchers and scientists with the technologies to better characterize microbiome profiles. Having previously done this type of gut microbiome profiling for my “leaky” gut, I was curious if there were any companies out there that could do the same for my oral microbiome or “leaky” mouth.

An Introduction to CosmosID

I had previously tried an oral DNA sampling test; however, the PCR technology used by that company is now outdated in comparison with newer technologies such as the Next Generation Sequencing (NGS) that is offered by CosmosID. I decided to try CosmosID after it was recommended to me by a good friend and respected periodontist, Dr. Alvin Danenberg.

The instructions were straightforward and only required me to swab the inside of my cheek and mix the swab into the blue vial containing a clear liquid. The whole process altogether took  ~3 minutes. In comparison to gut microbiome testing, which requires a fecal sample for testing (yuck), the oral microbiome test was quick and painless. The only reservations I had was my skepticism that a simple cheek swab would be able to provide any insightful information about my oral microbiome. Regardless, I sent the vials back to the lab and waited patiently to receive my results.

Getting to know my oral microbiome

To my pleasant surprise, the results from the CosmosID test were much more comprehensive than my previous testing with PCR technology.  The test was able to identify 261 strains of bacteria, 6 species of fungi, and 23 viruses within my oral microbiome. I was impressed to see that the test had also taken into account the often disregarded, yet extremely abundant, fungal and viral components in my oral cavity.

Example of fungal and bacteria species in oral cavity

In the ‘Bacteria’ drop down menu, you can decide if you wish to view information on fungi, viruses, protists, and even bacteria with antibacterial resistance. The curation of Cosmos ID databases are organized phylogenetically and contain hundreds of millions of marker gene sequences.

The markers represent both coding and non-coding sequences uniquely identified by taxon and/or distinct nodes of phylogenetic trees. This means that the tree structure was created based on genomic relatedness of organisms rather than predetermined taxonomy based on phenotype. This allows CosmosID to have a high degree of accuracy in identifying microorganisms based on their DNA in metagenomic samples. It also helps identify the closest match to genomes that do not have strain level references in the database (if, for example, they have never been sequenced before).

While the information provided based on the categories above can be confusing, CosmosID also offers visual diagrams. This aspect of CosmosID  is what amazed me the mostthe ability to organize the abundance of bacteria, fungi, and viruses into colorful, visually appealing, and comprehensive diagrams.

Such as the diagrams shown below:

Example of COSMOS ID Test Results

In order to get actionable information simply listing what is in my oral microbiome is not sufficient.  I need to be able to compare my sample to a healthy cohort. Although, the platform is capable of making comparisons within and between large cohorts, the size of the healthy cohort we used to compare datasets derived from my oral sample is limited, so that we must take the results with some caution.

With the help of CosmosID’s chief science officer, Dr. Nur A Hasan, I was able to compare my oral microbiome data to the oral microbiome datasets (n=34) derived from buccal mucosa, saliva, tongue, throat, supra- and subgingival plaque of healthy individuals. We noticed that I have a higher abundance of Streptococcus mutans a bacterial strain that is associated with oral diseases such as dental caries and gum disease. I also contained high abundances of Actinomyces timonensis, viral Streptococcus phages, and fungal Nosema bombycis. Additionally, Shannon species alpha diversity index of my sample looks similar to that of buccal mucosa, lower than saliva and higher than supragingival plaque (see the figure below). Shannon index measures the number of species in a sample but scales them based on the evenness of the community.  

Alpha Diversity from COSMOS ID

Principal Coordinate analysis based on beta diversity (i.e., diversity dissimilarities based on microbial composition and abundance) of my samples (red circles below) revealed that my oral microbiome didn’t clustered with any of the buccal mucosa, saliva, tongue, throat, supra- and subgingival plaque samples as they did within each sample type. This also makes sense since the sample I sent in was merely a swab of the inside of my cheek.

Principle Coordinate Analysis from COSMOS ID

Due to the myriad of genetic, immune regulatory, and environmental factors, the oral microbiome composition alters on a daily, even hourly, basis. So it is hard to say whether or not the differences in my oral microbiome contribute to my susceptibility to periodontal disease. However, the oral microbial profiling specificity has the potential to be harnessed for future salivary diagnostics and biomarker testing for systemic diseases.

With Cosmos ID’s new way of testing our oral microbiomes, we can usher in a new era of oral well-being where possibly resolving leaky mouth is key to cultivating better overall systemic health!

Curious to learn more about the mouth? Want to learn more ways to maintain microbial balance in the mouth?

Check out our ebook on the oral microbiome!

Have you ever tried a microbiome testing company? Let us know in the comments below!

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